JUNE 10-12, 2018, PURDUE UNIVERSITY, WEST ......6 10:55 AM Peter Jones, Ph.D. (invited speaker) Van Andel Research Institute 11:15 AM Lama Alabdi (selected speaker) Purdue University

JUNE 10-12, 2018, PURDUE UNIVERSITY, WEST LAFAYETTE, IN

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Welcome

Dear Colleagues,

We welcome you to the 2018 Midwest Chromatin and Epigenetics Meeting at Purdue University in West Lafayette, Indiana. The MCEM was first organized in 2006 at the University of Iowa as a means to bring together scientists from the Midwest states working on transcription, chromatin biology, and epigenetics. The primary goal of the MCEM is to foster the exchange of new ideas, develop collaborations, and support the training of future scientists through talks, poster presentations and networking opportunities. Since our last meeting at the Van Andel Institute in 2016, you have made significant technological, clinical and basic discoveries, which we are excited to learn about and discuss at this scientific event. We are honored to have Dr. Karolin Luger, the Jenny Smoly Caruthers Endowed Chair of Chemistry & Biochemistry and

Howard Hughes Medical Institute Investigator, U. Colorado, Boulder, as our keynote speaker. The MCEM committee has

organized a scientific program that includes 8 themed sessions on Epigenetics in Development and Disease, Nucleic Acid

Modifications and Chromatin, Transcription and Gene Expression, RNA-Dependent Epigenetic Regulation, Chromatin and

Genomic Integrity, Plant Chromatin Biology, Chromatin Remodeling and Structure, and Histone modifications and Binding

Proteins. We have invited 16 experts to speak on these topics and have 16 additional talks selected from submitted

abstracts. A poster session will also provide the opportunity for conference attendees present their work, receive critical

feedback, and network. Finally, we would like to thank all the sponsors (see page 47) for their generous financial support.

Invited Speakers: Andrew Belmont, Professor, Cell and Developmental Biology, University of Illinois, Urbana-Champaign Jason Brickner, Professor of Molecular Biosciences, Northwestern University Emily Dhyzuiken, Assistant Professor, Medicinal Chemistry and Molecular Pharmacology, Purdue University Richard Fishel, Professor, Department of Cancer Biology and Genetics Sue Hammoud, Assistant Professor, Human Genetics, University of Michigan Emily Hodges, Assistant Professor, School of Medicine, Biochemistry, Vanderbilt University Peter Jones, Chief Scientific Officer, Van Andel Research Institute Andrea Kazinski, William and Patty Miller Assistant Professor of Biological Sciences, Biology, Purdue University Heng-Chi Lee, Assistant Professor, Molecular Genetics and Cell Biology, University of Chicago Peter Lewis, Assistant Professor, Biomolecular Chemistry, University of Wisconsin-Madison Damon Lisch, Associate Professor, Botany and Plant Pathology, Purdue University Amber Mosley, Associate Professor, Biochemistry & Molecular Biology, Indiana University School of Medicine Catherine Musselman, Assistant Professor of Biochemistry, University of Iowa Carver College of Medicine Scott Rothbart, Assistant Professor, Center for Epigenetics, Van Andel Research Institute Jeff Thompson, Associate Professor of Biology, Denison University Xuehua Zhong, Assistant Professor, Genetics, University of Wisconsin-Madison Best regards,

2018 MCEM Organizing Committee Scott Briggs (Chair) Purdue University Ann Kirchmaier Purdue University Jason Knott Michigan State University Catherine Musselman University of Iowa

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MEETING WEBPAGE www.conf.purdue.edu/MCEM2018

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PARKING Union Club Hotel: Grant Street Parking Garage

First Street Towers: Guests may park in spaces designated as “University Residences” by white signed

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CAMPUS MAPS Printable Map: http://www.purdue.edu/campus_map/graphics/campusmap.pdf

Satellite Aerial Map: http://www.purdue.edu/campus_map/

QUESTIONS For any questions during the meeting please see Ethan Kingery ([email protected]) at the registration table.

FST: First Street Towers PMU: Purdue Memorial Union and Union Club Hotel

PGG: Parking Garage, Grant Street

http://www.conf.purdue.edu/MCEM2018

https://www.housing.purdue.edu/CampusGuests/ConferenceServices/Parking.html

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http://www.purdue.edu/campus_map/

mailto:[email protected]

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KEYNOTE ADDRESS

Building chromatin: assembly and evolution of nucleosomes

6:00 PM June 10, 2018

PMU North Ballroom

Karolin Luger The Jenny Smoly Caruthers Endowed Chair of Chemistry & Biochemistry and Howard Hughes Medical Institute Investigator, U. Colorado, Boulder

Karolin Luger received a B.S. in Microbiology and an M.S. in Biochemistry from the University of Innsbruck in Austria. She obtained her Ph.D. in Biochemistry and Biophysics from the University of Basel in Switzerland, and completed her training as a

postdoctoral fellow and research assistant professor at the Swiss Federal Institute of Technology in Zurich. She is currently Professor of Chemistry and Biochemistry, and holds the Jennie-Smoly-Caruthers Endowed Chair of Chemistry and Biochemistry, at the University of Colorado. She is also an Investigator for the Howard Hughes Medical Institute. Luger started her career at Colorado State University, where she was named a University Distinguished Professor. She was the 2013 National Lecturer at the annual Biophysical Society meeting, and is a member of the National Academy of Arts and Sciences. Luger has served as a member of several NIH study sections and in the National Advisory General Medical Sciences Council. Dr. Luger was a key player in efforts to elucidate the three-dimensional structure of the nucleosome, the basic repeating unit in chromatin. Her more recent work has focused on how nucleosomes are recognized and assembled, and how nucleosome dynamics affect gene expression. A recent study on archaeal chromatin structure suggests potential evolutionary origins of the eukaryotic nucleosome. The lab uses a wide range of techniques, such as X-ray crystallography, cryo-electron microscopy, fluorescence spectroscopy, atomic force microscopy, analytical ultracentrifugation, molecular biology, and life-cell imaging. She is engaged in numerous national and international collaborations.

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PROGRAM AGENDA PROGRAM AGENDA CAN BE FOUND AT www.conf.purdue.edu/MCEM2018

All talks will take place in the Purdue Memorial Union (PMU) North Ballroom

Sunday, June 10, 2018 4:00 PM Registration – PMU South Ballroom Hallway 4:30 PM Wine and cheese opening reception 6:00 PM Welcome and opening remarks – Scott Briggs, Ph.D.

6:10 PM Keynote Address: Karolin Luger, Ph.D. - PMU North Ballroom Jennie Smoly Caruthers Endowed Chair of Chemistry and Biochemistry Howard Hughes Medical Institute Investigator University of Colorado – Boulder

7:10 PM Closing remarks – Scott Briggs, Ph.D.

Monday, June 11, 2018 8:00 AM Continental breakfast – PMU South Ballroom

8:30 AM Opening remarks – Jason Knott, Ph.D.

8:40 AM Session 1: Epigenetics in Development and Disease Session Chair: Jason Knott, Ph.D. 8:45 AM Peter Lewis, Ph.D. (invited speaker) University of Wisconsin-Madison 9:05 AM Sue Hammoud, Ph.D. (invited speaker) University of Michigan Medical School 9:25 AM Marissa Cloutier (selected speaker) University of Michigan 9:45 AM Meghan Fealey (selected speaker) Marquette University, Milwaukee 10:05 AM Break (25 min)

10:30 AM Session 2: Nucleic Acid Modifications and Chromatin Biology Session Chair: Humaira Gowher, Ph.D. 10:35 AM Emily Hodges, Ph.D. (invited speaker)

Vanderbilt University School of Medicine

http://www.conf.purdue.edu/MCEM2018

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10:55 AM Peter Jones, Ph.D. (invited speaker)

Van Andel Research Institute

11:15 AM Lama Alabdi (selected speaker)

Purdue University

11:35 AM Emily Putnam (selected speaker)

Zymo Research Corp.

12:00 PM Lunch – PMU South Ballroom (1 hr 25 min)

1:25 PM Session 3: Transcription and Gene Expression Session Chair: Vikki Weake, Ph.D.

1:30 PM Jason Brickner, Ph.D. (invited speaker) Northwestern University 1:50 PM Amber Mosley, Ph.D. (invited speaker) Indiana University School of Medicine 2:10 PM Sudin Bhattacharya, Ph.D (selected speaker) Michigan State University 2:30 PM Christopher Ball (selected speaker) University of Iowa 2:50 PM Fei Gao, Ph.D. (selected speaker) Mayo Clinic, Rochester 3:10 PM Break (20 min)

3:30 PM Session 4: RNA-Dependent Epigenetic Regulation Session Chair: Beth Tran, Ph.D.

3:35 PM Andrea Kazinski, Ph.D. (invited speaker)

Purdue University 3:55 PM Heng-Chi Lee, Ph.D. (invited speaker)

University of Chicago 4:15 PM Aaron Williams (selected speaker) University of Michigan

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4:35 PM Poster Session 4:35 PM Odd number poster presentations (PMU South Ballroom) 5:50 PM Even number poster presentations (PMU South Ballroom) 7:05 PM End of poster session 7:15 PM Dinner – PMU South Ballroom 9:00 PM Depart – Dinner concludes

Tuesday, June 12, 2018

8:00 AM Continental breakfast – PMU South Ballroom

8:30 AM Opening remarks: Ann Kirchmaier, Ph.D.

8:40 AM Session 5: Chromatin and Genomic Integrity Session Chair: Ann Kirchmaier, Ph.D.

8:45 AM Richard Fishel, Ph.D. (invited speaker) Ohio State University Medical Center 9:05 AM Jeff Thompson, Ph.D. (invited speaker) Denison University, Granville 9:25 AM Stevephen Hung (selected speaker) Case Western Reserve University 9:45 AM Rosaline Hsu (selected speaker) University of Illinois, Urbana-Champaign

10:05 AM Break (25 min)

10:30 AM Session 6: Plant Chromatin Biology Session Chair: Joe Ogas, Ph.D.

10:35 AM Damon Lisch, Ph.D. (invited speaker) Purdue University 10:55 AM Xuehua Zhong, Ph.D. (invited speaker) University of Wisconsin, Madison 11:15 AM Xiangying (Candy) Mao (selected speaker) Purdue University

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11:35 AM Jasleen Singh (selected speaker) Indiana University, Bloomington 12:00 PM Lunch – PMU South Ballroom (1 hr 30 min)

Alternative Careers in Science Discussion/Panel for students and postdocs – PMU North Ballroom

Business Meeting – PMU South Ballroom

1:30 PM Session 7: Chromatin Remodeling and Structure Session Chair: Catherine Musselman, Ph.D.

1:35 PM Emily Dhyzuiken, Ph.D. (invited speaker) Purdue University 1:55 PM Andrew Belmont, Ph.D. (invited speaker) University of Illinois, Urbana-Champaign 2:15 PM Alison Bates (selected speaker) Indiana University School of Medicine, Indianapolis 2:35 PM Francisco Rodriquez-Ropero, Ph.D. (selected speaker) Illinois Institute of Technology 2:55 PM Break (20 min)

3:15 PM Session 8: Histone Modifications and Binding Proteins Session Chair: Scott Briggs, Ph.D.

3:20 PM Scott Rothbart, Ph.D. (invited speaker) Van Andel Research Institute 3:40 PM Catherine Musselman, Ph.D. (invited speaker) University of Iowa College of Medicine 4:00 PM Shruthi Sriramkumar (selected speaker) Indiana University School of Medicine, Bloomington 4:20 PM Kelsey Kalous (selected speaker) Medical College of Wisconsin, Milwaukee 4:40 PM Closing remarks: Scott Briggs, Ph.D.

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KEYNOTE SPEAKER ABSTRACT

‘Building chromatin: assembly and evolution of nucleosomes’

Karolin Luger

Department of Chemistry and Biochemistry, University of Colorado, Boulder

Nucleosome assembly in the wake of DNA replication and transcription are key processes that regulates cell identity and survival. Chromatin assembly factor 1 (CAF-1) is a H3-H4 histone chaperone that associates with the replisome and orchestrates chromatin assembly following DNA synthesis. Little is known about the mechanism and structure of this key complex. We investigate CAF-1 – histone binding modes and describe an intriguing ‘snap-on’ mechanism by which CAF-1 assembles nucleosomes. Unlike CAF-1, the ubiquitous histone chaperone FACT (Facilitates all chromatin transactions) has limited ability to assemble nucleosomes from histones, but rather stabilizes partially disassembled nucleosomes. In contrast to eukaryotes, many archaea have histone-based chromatin that does not require any assembly factors. I will present the structure of archaeal chromatin, and discuss possible implications for the origins of the eukaryotic nucleosome.

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INVITED SPEAKER ABSTRACT

Dysregulation of Polycomb silencing by oncohistones

Peter Lewis

Wisconsin Institute for Discovery and Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison

Covalent modifications to both the DNA and the histone proteins allow chromatin to act as a dynamic information hub that integrates diverse biochemical stimuli to regulate genomic DNA access to the transcription machinery and ultimately establish and maintain cellular phenotypes. Moreover, there is increasing appreciation that chromatin alterations per se, including DNA and histone modifications, are involved in the pathogenesis of cancer. Nowhere is this better supported than with the groundbreaking discoveries of high-frequency, somatic mutations in histones that are drivers of oncogenesis. These mutations (collectively called "oncohistones") cause amino acid substitutions that localize to conserved residues in the N-terminal tail of histone H3 and all seem to be linked, either directly or indirectly, to disruption of normal levels and distribution of histone H3 methylation and thus genomic regulation. Specifically, oncohistones directly or indirectly promote aberrant genome-wide distribution of lysine 27 methylation on histone H3. H3K27 methylation, catalyzed by the Polycomb Repressive Complex 2 (PRC2), is mechanistically linked to establishment and maintenance of gene repression. We are currently using a combination of biochemical and genomic approaches to investigate how oncohistone-driven changes in histone H3 K27 methylation lead to altered chromatin states that profoundly influence gene expression patterns. I will discuss some of our recent mechanistic and functional work on various oncohistone mutations.

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The power of one: Novel perspectives from Single Cell Sequencing of the testis

Sue Hammoud

Department of Human Genetics, University of Michigan

The process of spermatogenesis requires intricate interactions between the germline and soma. Within a given cross-section of a seminiferous tubule, multiple germ and somatic cell types co-occur. This cellular heterogeneity has made it challenging to profile distinct cell-types at different stages of development. To address this challenge, we collected single-cell RNA sequencing data from ~35K cells, and identified all known germ and somatic cells, as well as two novel somatic cell types. Furthermore, our analysis revealed 1) the complete developmental trajectory of germ cells from spermatogonia to spermatids and identifies rare and key developmental transitions, 2) novel candidate transcriptional regulators at several critical transition points during differentiation, 3) the presence of four subtypes of spermatogonial cells and nine subtypes of Sertoli cells, which can be linked to histologically defined developmental stages over the seminiferous epithelial cycle. Overall, our high-resolution cellular atlas provides an unprecedent analysis of the gametogenesis process.

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SELECTED SPEAKER ABSTRACT

A Transgenerational Role for Polycomb Group Protein EED in Imprinted X-chromosome Inactivation

Marissa Cloutier

Marissa Cloutier, Michael Hinten, Clair Harris, Megan Trotter, Aaron Williams, Milan

Samanta, Srimonta Gayen, Emily Maclary, Peter Larson, and Sundeep Kalantry

Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA Embryonic development requires the modulation of gene expression states via cellular epigenetic machinery. Polycomb repressive complex 2 (PRC2) is a key epigenetic regulator that methylates lysine at amino acid position 27 on histone H3 (H3K27me3). PRC2 and H3K27me3 are required to maintain imprinted X-chromosome inactivation. X- inactivation equalizes X-linked gene expression between XX female and XY male mammals via transcriptional silencing of one of the two X chromosomes in early female embryos. Imprinted X-inactivation results in the preferential inactivation of the paternal X-chromosome and initiates in all cells of the preimplantation mouse embryo. The parent-of-origin-specific pattern of inactivation of the paternal-X makes imprinted X-inactivation a paradigm of transgenerational epigenetic inheritance in mammals. PRC2 and H3K27me3 are enriched on the prospective inactive-X during the initiation of imprinted X-inactivation. We previously postulated that the inactive X-enriched PRC2 proteins are transmitted by the oocyte to the early embryo. Here, we test the hypothesis that oocyte-derived maternal PRC2 protein EED acts as a transgenerational epigenetic regulator that potentiates imprinted X-inactivation in

the embryo. We generated mouse embryos devoid of maternal and zygotic EED (Eedmz-/-).

Eedmz-/- embryos failed to initiate imprinted X-inactivation. Paternal X-linked genes that are

normally silenced were expressed in Eedmz-/- preimplantation embryos. Moreover, the maternal X-chromosome ectopically induced Xist lncRNA, a master regulator of X- inactivation

in Eedmz-/- early embryos. In agreement, H3K27me3 is enriched at the maternal Xist locus in wild-type oocytes and embryos. Our results therefore suggest a dual role of maternal EED protein in imprinted X-inactivation initiation. The first is to deposit H3K27me3 at the maternal Xist locus, and thus keep maternal Xist silenced and the maternal X- chromosome active. The second is to silence genes on the paternal X-chromosome. Thus, EED functions transgenerationally to cause inactivation of the paternal X-chromosome while ensuring that the maternal X-chromosome remains transcriptionally active.

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Developmental regulation of chromatin compaction by C. elegans synMuv B proteins

Meghan E Fealey

Meghan E Fealey and Lisa N Petrella

Department of Biological Sciences, Marquette University, Milwaukee, WI 53233

A central question in development is how chromatin is organized to ensure proper gene expression and cell fate. During early embryo development, before gene expression is globally upregulated, chromatin is found in an open state. As development proceeds and cells differentiate, chromatin undergoes both a general whole genome compaction and also becomes organized into open and closed domains based on if a gene will be expressed in a particular lineage. Although this process is highly regulated, many of the proteins involved in this progression are unknown. Here we show that loss of C. elegans synMuv B proteins causes changes in the developmental regulation of chromatin compaction both globally and at target loci. Previous work demonstrated that synMuv B mutants have ectopic expression of germline genes in somatic cells and demonstrate a high temperature larval arrest (HTA) phenotype. The HTA phenotype is rescued by knockdown of chromatin modifiers, suggesting that synMuv B proteins regulate gene expression programs at the chromatin level. We investigated if synMuv B proteins regulate developmental chromatin compaction utilizing extrachromosomal arrays and fluorescent in-situ hybridization. synMuv B mutants display a developmental delay in both general genome-wide chromatin compaction and compaction of tissue specific loci. The timing of compaction is sensitive to temperature in both wild type and mutant embryos but is delayed longer into mid-embryonic development in mutants. Open chromatin during this period may allow germline genes to be poised for ectopic expression in somatic tissues of synMuv B mutants. Interestingly, we found that the most anterior cells of the intestine are the last cells to adopt compact chromatin, suggesting an anterior to posterior pattern of chromatin compaction that has not been previously described. Understanding this pattern and synMuv B regulation of chromatin compaction will help elucidate pathways used to achieve proper gene expression and correct development.

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Spatiotemporal dynamics of DNA methylation across the chromatin accessible genome during monocyte to macrophage transitions

Emily Hodges

Kelly R. Barnett1, Ben Decato2, Timothy Scott1, Bob Chen1, Tyler Hansen1, Jonathan Attalla1, Andrew D. Smith2, Emily Hodges1*

1Department of Biochemistry and Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA. 2Molecular and Computational Biology Section, Division of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA. Different classes of enhancers are characterized by diverse combinations of epigenetic marks representing stages of a stepwise process of gene regulation ultimately dictated by transcription factor (TF) interactions with the cell’s DNA sequence. These “time signatures” ensure proper orchestration of TF activity and are critical for normal specification of cellular function and phenotype. To date, our knowledge of enhancer regulation during cellular differentiation is based on independent genome-wide datasets derived from steady state, asynchronous cell populations or time point associated datasets too far removed from one another to capture transient cellular states. We have previously shown that combined signatures of DNA methylation (DNAme) and DNA accessibility (DNAac) may reflect stages of TF binding activity at enhancer loci. From multiple independent datasets, a surprising number of pre-established DNase hypersensitive sites (DHS) appear to be methylated in stem cells, suggesting that enhancer activation is sequential and DNA demethylation, whether active or passive, is secondary to nucleosome repositioning; yet current models of enhancer dynamics only weakly describe a role for DNAme within this ordered process. To characterize the spatio-temporal relationship between these two distinct biochemical events (DNAac and DNAme), we developed an approach (ATAC-Me) that enables simultaneous measurement of DNAme and DNAac from the same population of DNA molecules by combining transposase-assisted enrichment of DNAac fragments with bisulfite sequencing. We performed ATAC-Me on a densely sampled time course of PMA induced THP1 monocytes differentiated to macrophages. Our approach reveals DNAac and DNAme may be quantitatively decoupled at myeloid enhancers as they become poised, active or repressed during early monocyte to macrophage transitions. We also show that deferred gain and loss of DNAme is a feature of nascent enhancer activity and that transcriptional activity tracks very closely with these enhancer states. Ultimately these studies are critical to disentangle the role of DNAme dynamics in normal cellular differentiation.

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Epigenetic Therapies

Peter A. Jones

Chief Scientific Officer, Van Andel Research Institute, Grand Rapids, Michigan

The 5-azanucleoside DNA methylation inhibitors (DNMTis) have established a presence in the

clinic for the treatment of myelodysplastic syndrome and acute myelogenous leukemia. These

agents act as S-phase specific inhibitors of the DNA methyltransferase enzymes and cause global

decreases in DNA methylation. Hematological patients respond to monotherapies, but the reasons

for doing so are not entirely clear. It will be important to determine the mechanism of action in order

to increase the efficacy of the treatments. Additionally, the use of the DNMTis in solid tumors is

almost certainly going to require the use of combination therapies to increase patient responses. I

will discuss some of the potential mechanisms by which the DNMTis function to cause responses.

For example, they upregulate the expression of silenced tumor suppressor genes, thus resulting in

the restoration of growth control to treated cells. Recently we have become interested in the roles

of sequences constitutively methylated in both normal and cancer cells as targets for DNMTis. The

removal of DNA methylation from gene bodies can result in substantial down regulation of genes,

particularly those in the MYC pathway. DNA methylation inhibitors are also powerful inducers of

human endogenous retroviruses and the function of these in eliciting a state of “viral mimicry” will

be discussed. I will also discuss combinations of various agents which might increase the efficacy

of DNMTi treatment directly such as the inclusion of vitamin C in the treatment regimen and the

use of checkpoint inhibitors in solid tumors to capitalize on the viral defense pathways induced by

drug treatment.

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Regulation of pluripotency by DNA methylation in F9 Embryonal carcinoma

Lama AlAbdi

Lama AlAbdi1, Stephen MacCune

1, Brice, H. Spears

1, Mohd Saleem Dar

1,

Smriti Hoda1, a n d Humaira Gowher

1,2

1Department of Biochemistry,

2Purdue University Center for Cancer Research, Purdue

University, West Lafayette, Indiana 47907

During embryonic stem cell (ESC) differentiation, pluripotency genes must be silenced. Our previous studies delineated the mechanism leading to pluripotency gene repression through the targeted methylation of their enhancers in differentiating ESCs. Several reports detected the expression of pluripotency genes in the undifferentiated cancer stem cell populations in tumors to which tumor initiation, metastasis, and resistance to cancer therapies have been attributed. Due to their small population size and difficulty in isolation, the mechanism by which they escape the repression of their pluripotency program is not fully addressed. We use F9 Embryonal carcinoma cells (ECs) as a model to study cancer stem cells, because of their embryonic origin and potential to generate tumors. Similar to ESCs, F9 ECs can differentiate into germ layers and express all repression factors contributing to early mouse embryogenesis. However, unlike ESCs, when F9 ECs are induced to differentiate they fail to gain DNA methylation at pluripotency gene enhancers leading to incomplete repression of their pluripotency program. Our work investigating the mechanisms leading to incomplete repression of pluripotency genes during F9 ECs differentiation is paramount for our understanding of how cancer stem cells rise and persist as well as the development of differentiation-mediated cancer therapies.

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High-Throughput Locus-Specific DNA Methylation Validation Platforms in Aging Quantification Research

Emily Putnam

Emily Putnam, Yap Ching Chew, Wei Guo, Xiaojing Yang, Mingda Jin,

Keith Booher and Xi Yu Jia

Zymo Research Corp., 17062 Murphy Ave, Irvine, CA, 92614

DNA methylation plays an important role in normal organismal development and in cellular differentiation in higher organisms. Changes in DNA methylation have been shown to correlate with disease risk, response to therapy and survival in a wide range of clinical conditions such as cancer and autoinflammatory diseases. Recent advances in next-generation sequencing and microarray technology have made it possible to map DNA methylation genome-wide, at a high resolution. However, these genomic assays tend to be costly, labor-intensive and impractical in the clinic. Thus, high-throughput DNA methylation assays that measure a small number of genomic regions in large cohorts are needed for validating biomarker candidates discovered from genomic studies. For this reason, Zymo Research has developed two targeted bisulfite sequencing platforms for measuring DNA methylation at multiple loci with multiple samples: Methyl-Check™ and SWARM™ (Simplified Whole-panel Amplification Reaction Method). The presentation will introduce these methods and demonstrate their utility in the development of a DNA methylation panel for aging and other research applications.

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Chromatin-dependent epigenetic transcriptional memory

Jason Brickner

Agustina D’Urso, Bethany Sump and Jason Brickner

Department of Molecular Biosciences, Northwestern University

Transcriptional regulation is the primary means by which cells respond to changes in their environment. We have discovered that the activation of many genes is influenced by the previous experience of the cells. This phenomenon, called epigenetic transcriptional memory, poises previously expressed genes for faster/stronger expression for several generations after these genes are repressed. Using the INO1 gene from budding yeast, we find that memory requires a specific chromatin state, which is permissive for binding of both a memory-specific transcription factor, targeting to the nuclear pore complex and binding of a poised preinitiation form of RNA polymerase II (RNAPII). Most aspects of this model are generalizable both to other yeast genes and to memory of interferon gamma treatment in HeLa cells. I will describe our current understanding of the fitness contributions of memory, the molecular mechanism by which the memory-specific chromatin state is established and the molecular mechanism by which RNAPII can be recruited and maintained in a pre-initiation state.

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Control of RNA Polymerase II elongation via phosphorylation

Amber Mosley

Department of Biochemistry and Molecular Biology, Indiana University School of Medicine

During transcription elongation RNA Polymerase II (RNAPII) must cope with various blocks to elongation including chromatin, GC-rich DNA sequence, and R-loop formation. Our laboratory has focused on the role of phosphorylation in the regulation of RNAPII transcription elongation through chromatin and during transcription termination in eukaryotes. We have found that two phosphatases that regulate the phosphorylation status of the C-terminal domain of RNAPII, Rtr1 and Ssu72, have opposite impacts on transcription elongation. Our data suggest that CTD dephosphorylation is a key regulatory event that mediates the choice between RNAPII elongation and termination.

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Gene Coregulation and Coexpression in the Aryl Hydrocarbon Receptor- mediated Transcriptional Regulatory Network in the Mouse Liver

Sudin Bhattacharya

Navya Josyula1, Melvin E. Andersen

2, Norbert E. Kaminski

3,4, Edward Dere

5,§, Timothy R.

Zacharewski5,4

and Sudin Bhattacharya6,3,7,8,4*

1Biomedical and Translational Informatics Program, Geisinger Health System, Rockville, MD

20850, USA 2Scitovation LLC, Research Triangle Park, NC 27709, USA

3Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI,

48824, USA 4Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, 48824, USA

5Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI,

48824, USA 6Department of Biomedical Engineering, Michigan State University, East Lansing, MI 48824,

USA 7Center for Research on Ingredient Safety, Michigan State University, East Lansing, MI 48824

8Institute for Quantitative Health Science and Engineering, Michigan State University, East

Lansing, MI 48824, USA §Currently at Genentech, South San Francisco, CA 94080

Four decades after its discovery, the aryl hydrocarbon receptor (AHR), a ligand- inducible transcription factor (TF) activated by the persistent environmental contaminant 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), remains an enigmatic molecule with a controversial endogenous role. Here we assemble a global map of the AHR gene regulatory network in TCDD-treated mouse liver from a combination of gene expression and genome-wide TF binding data sets. Using Kohonen self- organizing maps and subspace clustering, we show that genes co-regulated by common upstream TFs in the AHR network exhibit a pattern of co-expression. Directly- bound, indirectly-bound and non-genomic AHR target genes exhibit distinct expression patterns, with the directly bound targets associated with highest median expression. Interestingly, among the directly bound AHR target genes, the expression level increases with the number of AHR binding sites in the proximal promoter regions. Finally, we show that co-regulated genes in the AHR network activate distinct groups of downstream biological processes. This work describes an approach to the reconstruction and analysis of transcriptional regulatory cascades underlying cellular stress response, revealing network hierarchy and the nature of information flow from initial signaling events to phenotypic outcomes.

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Nucleotide resolution analysis of RNA polymerase II initiation and pausing in human cytomegalovirus

Christopher B. Ball

Christopher B. Balla, Kyle A. Nilson

a, Christine K. Lawson

a, Ming Li

a,b, Harrison Fuchs

a, Donal S.

Lusec, Jeffery L. Meier

b, and David H. Price

a

aDepartment of Biochemistry, University of Iowa, Iowa City, IA 52242, USA

bDepartment of Internal Medicine, University of Iowa and Veterans Affairs Health Care System,

Iowa City, IA 52242, USA cDepartment of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic,

Cleveland, OH, 44195, USA.

Human cytomegalovirus (HCMV) is the leading infectious cause of birth defects in the United States and presents a significant threat to the health of immunocompromised individuals. HCMV utilizes the host cell RNA polymerase II (Pol II) transcriptional apparatus for its gene expression. However, the extent to which HCMV follows the host transcriptional paradigm remains unclear. We performed PRO-Seq and PRO-Cap in uninfected and HCMV-infected primary human foreskin fibroblasts to identify sites of initiation, pausing and productive elongation by Pol II with extreme depth at single-nucleotide resolution. Using these methods, we determined that transcription of HCMV is similar to host transcription in that both utilize Pol II elongation control. 91,332 host and 14,006 HCMV transcription start regions (TSRs) were identified and some differences between host and viral core promoter elements were found. Late gene transcription in HCMV utilizes a set of viral factors. One of these factors recognizes TATT instead of TATA as an upstream element and we found that only TATT on the viral genome impacted initiation. We also observed that late in the lytic HCMV infection cycle, Pol II transcription of the HCMV genome is pervasive. A TSR was detected approximately every 17 bp in the HCMV genome, which far exceeds the density observed on the host genome. Chromatinization of the HCMV genome contributes to viral latency, but whether or how chromatin impacts HCMV during the lytic infection cycle is less well defined. We propose a model explaining our results in the context of what is already known, in which transcription of the HCMV genome takes place on a template that is only partially chromatinized.

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Hypoxia-inducible factor 1 alpha (HIF1A) stimulates neuronal nitric oxide synthase (Nos1) transcription by modifying spatial chromatin organization

Fei Gao

Fei Gao, Siva Arumugam Saravanaperumal, Brooke D. Paradise, Sabriya A. Syed, Liang

Cheng, Jeong-Heon Lee, Jian Zhong, Jagneet Kaur, Gabriella B. Gajdos, Brandon W. Simone, Sergii M. Kvasha, Aditya V. Bhagwate, Zhifu Sun, Pritha Chanana, Gavin R. Oliver, Krutika S.

Gaonkar, Huihuang Yan, Jin Jen, Yujiro Hayashi, and Tamas Ordog

Mayo Clinic, Rochester, MN, USA NOS1 is the source of nitric oxide, a neurotransmitter and regulator, in neurons, skeletal and cardiac muscle. NOS1-related diseases include impotence, gastrointestinal motor disorders, muscular dystrophies, neurodegenerative diseases and stroke. The mechanisms regulating Nos1 transcription are incompletely understood. Most tissues experience relative hypoxia (1-5% O2 vs.

21% in air). Nos2 and Nos3 are transactivated by HIF1A and aryl hydrocarbon receptor nuclear translocator (ARNT). Here, investigated whether Nos1 is also subject to hypoxic control, and

whether pharmacological manipulation of HIF1A could stimulate Nos1 expression. In NOS1+

N1E115 mouse neuroblastoma cells and IM-FEN enteric neuron precursors, physiological hypoxia (4% O2) for 3 days increased HIF1A protein, Nos1 mRNA and NOS1 protein levels.

Pharmacological upregulation of HIF1A also increased NOS1. Nuclear HIF1A was detected in

NOS1+

human gastric neurons. In N1E115 cells, by chromatin immunoprecipitation-sequencing (ChIP-seq) we found hypoxia-induced Nos1 transcription to be associated with increased HIF1A and ARNT binding to 3 enhancer-promoter pairs located 86 kb (E1-P1), 76 kb (E2-P2) and 28 kb (E3-P3) upstream of the translation initiation site in Nos1 mRNA. Furthermore, hypoxia dramatically enhanced P1 and moderately increased P3 promoter activity, stimulated the activity of all enhancers, and upregulated transcriptional elongation throughout the Nos1 locus. Chromosome conformation capture by 3C and Hi-C revealed long- range interactions between E1-P1 and E3-P3. Hypoxia weakened these interactions while strengthening enhancer-promoter connectivity within both regions. Genomic deletion of E1 reduced the expression of Nos1 by 82%. ChIP-seq in freshly purified nitrergic neurons identified E1-P1 as the only active cis-regulatory region. We conclude that physiological hypoxia stimulates Nos1 expression by dramatically enhancing the activity of a distal enhancer-promoter pair and simultaneously modifying spatial chromatin organization. Our findings also suggest the activation of hypoxic pathways under physiological conditions. Pharmacologically increasing HIF1A protein stability may be useful for restoring impaired Nos1 expression in a variety of diseases.

23


Ligand-mediated, vehicle-free delivery of small RNAs

Andrea Kasinski

Esteban Orellana1,2, Philip Low3, Loganathan Rangasamy3 and Srinivasarao Mudduri4,

and Andrea Kasinski1,2

1Purdue University, Department of Biological Sciences; 2Purdue University, Center for Cancer

Research; 3Purdue University, Department of Chemistry; 4Ohio State University MicroRNAs (miRNAs) are exceptional candidates for combating many diseases such as cancer; however, their therapeutic power is dwarfed by the lack of safe, robust, specific, and efficient delivery methods. MiRNAs have exclusively been delivered inside of various protective vehicles (dendrimer, copolymer, or liposome) to protect the miRNA from serum nucleases. Unfortunately, the benefit of protecting the miRNA cargo comes with unwanted toxicity. One way to avoid vehicle-associated toxicity is to remove the vehicle entirely. Indeed, our data support rapid and specific uptake of a therapeutically-relevant miRNAs that is conjugated directly to a ligand. We show that ligand-mediated miRNA delivery is a first-in-class method that can be used to delivery miRNAs completely unprotected specifically to tumor cells in culture and in multiple in vivo models, including the murine Kras:p53 double mutant of non-small cell lung cancer (NSCLC). Importantly, efficacy of ligand-delivered miR-34a happens in the absence of unwanted toxicity. Additional evidence indicates that a small molecule ionophore can enhance endosomal mediated escape of the miRNA increasing cytosolic concentrations and targeting. Overall the data generated from these studies showcases a major advance in tumor specific uptake of naked miRNAs, resulting in reducing dosage, toxicity, and tissue off targeting.

24


RNA-mediated epigenetic silencing of foreign nucleic acids

Heng-Chi Lee

Donglei Zhang1, Shikui Tu2, Zhiping Weng2, and Heng-Chi Lee1 1. Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL USA 2. Program in Bioinformatics and Integrative Biology, University of Mass. Medical School, Worcester, MA USA Our genomes face constant threats from invasions of foreign nucleic acids, such as transposons or retroviruses. A defense mechanism is therefore essential to combat these invaders and to maintain genome stability. Remarkably, cells produce short RNA molecules that act as molecular sensors to detect and silence foreign nucleic acids. In particular, small RNAs named PIWI-interacting RNAs (piRNAs) have been found as guardians of the genome by repressing transposons and viruses. Our recently study suggest diverse piRNAs provide cells provide germ cells a gigantic database to recognize diverse foreign nucleic acids, reminiscent of diverse antibodies produced by our immune system to recognize various foreign antigens.

Mechanism of transgenerational inheritance remains poorly understood in animals. We have observed that piRNA triggers remarkable stable silencing of its target that can last for many generations, in some cases indefinitely. Such transgenerational epigenetic memories of non-self allows embryos to mount effective defense responses against those foreign nucleic acids that the germ cells have encountered before, similar to our adaptive immune response that produces antibodies recognizing non-self antigens for years. Interestingly, while chromatin modifications play a role in establishing silencing of piRNA targets, our studies have suggested that the another type of small RNAs are the molecular carrier of silencing memory over generations. Our research highlight a RNAbased mechanism of epigenetic inheritance in animals.

25


Investigating X-chromosome Inactivation in Human Embryonic Stem Cells

Aaron Williams

Aaron Williams1, Marissa Cloutier

1, Surinder Kumar

1, Emily Buttigieg

1, Brandon Lee

1,

Sandra Mojica-Perez2, Andre Monteiro Da Rocha

2, Laura Keller

2, Gary Smith

2,

and Sundeep Kalantry1

1Department of Human Genetics and

2Department of Molecular & Integrative

Physiology University of Michigan Medical School, Ann Arbor, MI 48109

X-inactivation equalizes X-linked gene expression between XX females and XY males via transcriptional gene silencing of one of the two X-chromosomes in early female embryos. During initiation of X-inactivation, XIST, a long-noncoding RNA, is expressed from and coats the inactive X-chromosome, which results in stable transcriptional silencing by recruitment of epigenetic factors in cis. For this reason, XIST RNA coating, detected by RNA fluorescence in situ hybridization (FISH), is an excellent proxy for presence of X-inactivation. Mouse embryonic stem cells (mESCs) have yielded a wealth of data on mouse X-inactivation dynamics. However, to what extent these findings apply to humans is unclear. In collaboration with Gary Smith’s group, we have begun to profile X-inactivation in human embryonic stem cells (hESCs). Unexpectedly, we found hESCs grown in mTeSR media showed loss of XIST RNA expression over successive passaging, while hESCs grown in xenofree (XF) media did not show loss of XIST RNA coating. We hypothesized that differences between the mTeSR and XF media led to the loss of XIST RNA coating in hESCs. MTeSR media contains Lithium (Li) while XF does not. To determine if Li was the causative agent in the loss of XIST RNA coating, we added Li to XF media. When grown in XF media with Li, hESCs displayed loss of X-inactivation, similar to that seen in mTeSR media. Li is a potent inhibitor of the GSK-3 protein, among other kinases. This observation led us to hypothesize that GSK-3 inhibition by pharmacologic agents may also cause loss of X-inactivation. We are currently using three GSK-3 inhibitors to determine if inhibition of GSK-3 causes loss of XIST RNA coating: BIO, LY209, and Alsterpaullone. Our results suggest that pharmacologic inhibition or activation of cell signaling pathways may have unknown effects on the epigenome broadly and on X-inactivation specifically. Our findings are surprising because X-inactivation is believed to be a cell autonomous phenomenon that is immune to extracellular influences. Moreover, our findings suggest that certain media formulations should be avoided in the future if hESCs are to be used for therapeutic purposes.

26


Understanding Nucleosome Remodeling One Molecule at a Time

Richard Fishel

Gayan Senevirathne1, Jeungphill Hanne1, Ralf Budschuh2 and Richard Fishel1, 1 Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH 43210. 2 Department of Physics, The Ohio State University, Columbus, OH 43210 Wrapping genomic DNA into nucleosomes provides the first steps in packing the ~1 m of human DNA into a ~10 mm diameter (~500 μm3 volume) nucleus. Nucleosomes contain dimers of the histone families H2A, H2B, H3, and H4, which form multiple contacts with 146/147 bp of DNA that is wrapped 1.7x around the octamer. These nucleosomes as well as higher order condensed nucleosome structures must be rapidly remodeled/removed during DNA transcription, replication and repair. Single molecule force measures suggest that 20-60 pN may be required to unwrap the DNA from a histone octamer. Fortunately, chromatin remodelers such as the ATP-driven RSC complex appear capable of translocating along the DNA against induced forces of ~30 pN, suggesting that they are capable of remodeling the histone-DNA of most nucleosomes with high efficiency. But are these specialized motors the only mechanism to remodel nucleosomes? We present single molecule studies of two different mechanics that can dissociate a histone octamer from the DNA. The first is exhibited by the recombinase RAD51 that forms a nucleoprotein filament on DNA during homologous recombination. The second utilizes freely diffusing MutS sliding clamps that form during mismatch repair, along with the natural thermal motions of these proteins and the wrapped DNA.

27


Epigenetic inheritance of a UV hyper-resistance phenotype in Saccharomyces cerevisiae

Jeffrey S. Thompson

Rachel M. Reardon, LauraAnn H. Schmidberger, Amanda K. Walsh, Adriane E. Thompson, and

Jeffrey S. Thompson

Department of Biology, Denison University, Granville, Ohio

Exposure to DNA damaging agents activates a variety of cell-cycle checkpoint and DNA repair activities, collectively referred to as the DNA damage response (DDR). Upon the repair of DNA damage, DDR is deactivated, and expression of relevant genes returns to pre-damage levels. However, we have found that baker’s yeast cells retain an enhanced capacity to survive DNA damage following an initial exposure to ultraviolet (UV) radiation. Pre-exposed cells exhibit significantly increased survival frequency following a secondary UV exposure compared to unexposed controls, the degree of which depends on the time between the two exposures. Maximal effects (~200-fold increased survival) were found after a 4-hour incubation period, but significant differences were found as late as 16 hours after the initial exposure, corresponding to ~8-10 cellular generations. This “hyper-resistance” phenotype persists well past the time required to repair the initial damage, and furthermore, the phenotype is observed in cell populations from which the original exposed mother cells were removed, suggesting an epigenetic mechanism. DNA repair kinetics in pre-exposed cells were indistinguishable from those in unexposed cells, however we found that absolute DNA damage levels accrued during the second UV exposure were reduced to ~30-40% in pre-exposed cells relative to the unexposed controls, indicating that increased survival is a result of reduced damage levels. Transcriptome analysis of pre-exposed cells revealed over-expression of genes functionally enriched in carbohydrate metabolism and cell wall synthesis, implicating changes in cell wall structure and/or composition in the protective properties in pre-exposed cells. Lastly, we have found that histone post-translational modifications H3K4 methylation and H3K56 acetylation are important for the hyper-resistance phenotype, suggesting that DNA damage-induced histone modification changes may act as epigenetic markers to propagate this phenotype in descendant cells.

28


Mismatch-repair signature mutations modulate gene enhancer activity across colorectal cancer epigenomes

Stevephen Hung

Stevephen Hung1

, Alina Saiakhova1

, Devin Neu1

, Zachary Faber1

, Cynthia Bartels1

, Ian Bayles1

,

Gursimran Dhillon1

, Ellen Hong1

, Matthew Kalady3

, Sanford Markowitz1,2

,

& Peter C. Scacheri1

Department of Genetics and Genome Sciences1

, Department of Medicine2

, Case Western Reserve University, Cleveland, Ohio

Lerner Research Institute3

, Cleveland Clinic, Cleveland, Ohio The search for cancer driver mutations has largely focused on the 2% of the human genome that codes for genes. Commonly mutated genes have been found for many cancers, but far less is known about the prevalence of mutations in cis regulatory elements. We leveraged an approach that exploits gains in enhancer activity in tumor versus normal in combination with mutation detection from H3K27ac ChIP-seq data to pinpoint potential activating mutations in enhancer elements in colorectal cancer (CRC). Analysis of CRC specimens from all clinical stages revealed that samples of MSI subtype have a particularly high rate of indel mutations in active enhancers. In support of a functional role, enhancers with indels show evidence of positive selection and their target genes show elevated expression. Moreover, a subset of the enhancer indels is highly recurrent. The indels arise in short homopolymer tracts of A/T’s and generate sequences that closely resemble consensus motifs for the FOX family of pioneer transcription factors. We demonstrate the capacity of the noncoding indels to modulate enhancer activity through CRISPR/Cas9 inactivation of the MLH1 gene followed by H3K27ac ChIP-seq studies. Our results suggest that indel mutations in noncoding poly (A/T) sequences, previously presumed benign, frequently augment enhancer activity in the epigenomes of MMR- deficient CRC tumors and provide a selective advantage for tumor growth.

29


Pre-replicative complex protein ORCA/LRWD1 regulates homologous recombination at ALT-telomeres by modulating RPA binding.

Rosaline Hsu

Rosaline Hsu1, Yo-Chuen Lin1, Deepak Singh1, Yating Wang1, Vasudha Aggarwal2, Jaba Mitra2, Abhijith Matur1, Taekjip Ha2,3, Kannanganattu V. Prasanth1 and Supriya G. Prasanth1

1Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801 USA; 2Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore USA; 3Howard Hughes Medical Institute, Johns Hopkins University. Telomeres are repetitive sequences at the ends of linear chromosomes. In mammalian cells, telomeres are protected by the Shelterin complex that coordinates end protection with telomere replication. Dysfunctional telomeres result in genomic instability and cancer development. Cancer cells achieve immortalization by acquiring a telomere maintenance mechanism. Approximately 10~15% of human tumors, mostly mesenchymal origin, utilize a telomerase-independent mechanism termed Alternative Lengthening of Telomeres (ALT), which involves a homologous- recombination-mediated DNA replication. We have identified that the human Origin Recognition Complex-associated protein (ORCA/LRWD1) as well as several components of ORC are enriched at ALT-telomeres throughout the cell cycle. The extent of ORCA enrichment at ALT- telomeres directly correlates with the levels of the Shelterin components. The loss of ORCA induces the formation of ALT-associated PML bodies (APBs), shows elevated levels of RAD51 and robust accumulation of RPA at ALT-telomeres, and increased telomere sister chromatid exchange (T-SCE). Furthermore, cells lacking ORCA show increased frequency of global sister chromatid exchange, suggesting that ORCA plays a role in the inhibition of homologous recombination. The depletion of ORCA causes decreased H3K9me3 at the telomeres, increased TERRA RNA, and overall chromatin decondensation. Furthermore, ORCA directly interacts with the single stranded DNA binding protein RPA and modulates its binding to ssDNA. In summary, our findings suggest that ORCA represses unwanted homologous recombination.

30


Epigenetic changes associated with transgenerational epigenetic silencing of a maize transposon.

Damon Lisch

Department of Botany and Plant Pathology and Purdue Center for Plant Biology, Purdue

University, West Lafayette, IN

Although a great deal is known about the means by which transposable elements (TEs) are maintained in a silenced state, relatively little is known about how TEs are recognized and heritably silenced in the first place, and how silencing is reinforced over time. We use a model system that involves a naturally occurring variant of the MuDR transposon that can trigger epigenetic silencing of that transposon, which is maintained over multiple generations even in the absence of the initial trigger. Using this system, we have identified a class of small RNAs that initiate silencing due to interaction with one of the two transcripts produced by MuDR. We find that initiation of silencing does not require components of the RNA-directed DNA methylation (RdDM) pathway, and that silencing of MuDR can be maintained in RdDM mutant backgrounds even in the absence of DNA methylation. However, after multiple generations in these backgrounds, we find that expression and activity of the element can be restored. Finally, we find that the restoration of activity in these mutant backgrounds can be accelerated both during and after brief exposure to heat stress. We are currently investigating histone modifications that may be functioning to maintain TE silencing in the absence of DNA methylation, and the ways that these modifications may be altered under heat stress conditions. In addition, we are investigating the degree to which heat stress may affect various epimutant phenotypes that also appear after multiple generations in RdDM mutant backgrounds.

31


Epigenetic regulation of development phase transition in plants

Xuehua Zhong

Wisconsin Institute for Discovery & Laboratory of Genetics, University of Wisconsin-Madison, WI, USA

The ability of cells to perceive and translate versatile cues into differential chromatin and transcriptional states is critical for many biological processes. In plants, timely transition to a flowering state is crucial for successful reproduction. EARLY BOLTING IN SHORT DAY (EBS) is a negative transcriptional regulator that prevents premature flowering in Arabidopsis. We recently found that EBS contains bivalent bromo-adjacent homology (BAH)-plant homeodomain (PHD) reader modules that bind H3K27me3 and H3K4me3, respectively. A subset of EBS-associated genes was co-enriched with H3K4me3, H3K27me3, and the Polycomb repressor complex 2 (PRC2). Interestingly, EBS adopts an auto-inhibition mode to mediate its binding preference switch between H3K27me3 and H3K4me3. This binding balance is critical because disruption of either EBS-H3K27me3 or EBS-H3K4me3 interaction induces early floral transition. This study identifies a single bivalent chromatin reader capable of recognizing two antagonistic histone marks and reveals a distinct mechanism of interplay between active and repressive chromatin states.

32


Investigating the interaction between MED5 and CDK8 in Arabidopsis

Xiangying (Candy) Mao

Xiangying (Candy) Mao, Vikki Weake and Clint Chapple

Department of Biochemistry, Purdue University, IN, USA

Plant metabolic networks are precisely regulated by the spatial and temporal expression of suites of genes. Among the various transcription (co)factors, Mediator has been identified as a hub for transcription regulation. Using a forward genetic screen, our lab determined that MED5, an Arabidopsis Mediator tail subunit, is required for maintaining phenylpropanoid homeostasis. A semi-dominant mutant (ref4-3) characterized by a single amino acid substitution in MED5a (G383S) was isolated as a strong suppressor of phenylpropanoid pathway, indicated by decreased soluble phenylpropanoid metabolite accumulation, reduced lignin content and dwarfism. In contrast, knocking out MED5a and MED5b (med5a/5b) results in the accumulation of increased levels of phenylpropanoid pathway derivatives. Considering that the CDK8 kinase module is a repressive module in Mediator, we tested the hypothesis that Arabidopsis MED5 represses phenylpropanoid pathway by interacting with CDK8. To test this hypothesis, CDK8 knockout lines (cdk8-1) were crossed with ref4-3, and the phenylpropanoid content of the resulting double mutants was evaluated. In ref4-3 cdk8-1 plants, the concentration of sinapate esters and total lignin content are as low as they are in ref4-3, yet the growth defect in ref4-3 is largely rescued. To further determine the genes targeted by MED5 and CDK8 in maintaining proper plant growth, we performed an RNA-seq analysis, which showed that a majority of the genes involved in salicylic acid (SA) biosynthesis and signaling are up-regulated in ref4-3 compared to wild type and ref4-3 cdk8-1. Consistent with this observation, SA, which has been previously implicated in dwarfing in lignin-modified plants, is accumulated to elevated levels in ref4-3 but not in wild type and ref4-3 cdk8-1. Nevertheless, blocking SA biosynthesis is not sufficient to restore the growth deficiency of ref4-3, suggesting that the hyperaccumulation of SA is more likely to be an effect rather than a cause for its dwarf phenotype. At the molecular level, to elucidate how ref4-3 regulates downstream gene targets in a CDK8- dependent manner, we performed RNA polymerase II (Pol II) ChIP-seq analysis in wild type, ref4-3, cdk8-1 and ref4-3 cdk8-1. The Pol II ChIP-seq data provides additional information for us to identify the genes that are causative for the dwarfism of ref4-3. Taken together, this study identifies the genetic interaction between MED5 and CDK8 in Arabidopsis, which enhances our understanding in the function of Mediator in plant metabolism and its role in lignin-modification-induced dwarfism.

33


Converting DNA information into double-stranded RNA in a coupled reaction

Jasleen Singh

Jasleen Singh1, Vibhor Mishra

1,2, Feng Wang

1, Hsiao-Yun Huang

1,2, Craig Pikaard

1,2

1Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana

University, Bloomington, IN, USA 2Howard Hughes Medical Institute, Indiana University, Bloomington, IN, USA

In plants, 24nt siRNA-directed DNA methylation silences transposons, repeats and specific genes. Here, we demonstrate DNA-templated synthesis of 24nt siRNAs in vitro by multisubunit NUCLEAR RNA POLYMERASE IV (Pol IV), RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE3 (DCL3). Pol IV acts first, transcribing the template DNA and terminating soon after encountering the non-template DNA strand. The termination complex triggers RDR2 copying of Pol IV transcripts into duplex RNA, with second strands often including 3' non- templated nucleotides due to RDR2's terminal transferase activity. DCL3 cuts resulting duplexes from either end, tolerating 5' monophosphates or triphosphates and blunt or overhanging 3' ends, primarily yielding 24nt products. The results suggest explanations for why Pol IV-RDR2 transcripts are short, why siRNAs vary in size and often have DNA-mismatched 3' ends, and reveal a unique reaction mechanism in which DNA information is converted into dsRNA via the coupled reactions of DNA- and RNA-dependent RNA polymerases.

34


"PBRM1 and the recognition of histone acetylation during stress"

Emily Dykhuizen

Department of Medicinal Chemistry and Molecular Pharmacology,

Purdue University, West Lafayette, IN Polybromo1 (PBRM1) is a chromatin remodeler subunit highly mutated in cancer, particularly renal clear cell carcinoma. PBRM1 is a member of the SWI/SNF subcomplex, PBAF (PBRM1-Brg1/Brm Associated Factors) and is characterized by six tandem bromodomains. In adult mice and most cell lines PBRM1 is dispensable, making its role in tumor suppression elusive. Utilizing cellular models of normal and transformed epithelium, we have established a role for PBRM1 in epithelial cell maintenance through the expression of genes involved in cell adhesion, hypoxic response, metabolism, and apoptosis. The exact genes regulated by PBRM1 are cell line-dependent, but are generally regulated by stress response transcription factors such as FOXO and AP-1 in response to environmental cues. Further, we have established that the bromodomains of PBRM1 primarily recognize H3K14Ac, which is an acetylation mark uniquely increased at genes upon genomic and metabolic stress. Taken together, these results point to a model in which PBRM1 is targeted to sites of increased H3K14 histone acetylation and increases chromatin accessibility to allow for DNA binding by stress response transcription factors. Indeed, under high cellular stress conditions, we find that PBRM1 is required to restrict the accumulation of reactive oxygen species and initiate both pro-apoptotic and pro-survival pathways. Therefore, in the same cell line PBRM1 deletion promotes cell growth under favorable conditions, but is cytotoxic under conditions of high cellular stress. This context-specific function for PBRM1 in stress response provides an explanation for how PBRM1 deletion initiates cancer formation, but also increases the susceptibility of PBRM1-mutant tumors to cytotoxic therapies.

35


A Refined Model of Genome Nuclear Organization Using TSA-Seq

Andrew S. Belmont

Yu Chen1, Liguo Zhang1, Yang Zhang2, Yuchuan Wang3, Eva K. Brinkman4, Bas van Steensel4, Jian Ma2,3,5,6, Andrew S. Belmont1,5,6

1Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, 2Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, 3Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, 4Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1016 HM Amsterdam, the Netherlands, 5Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 6Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 We developed TSA-Seq to probe genome organization. By creating an exponential gradient of DNA labeling over an ~1.5-micron distance, Tyramide Signal Amplification (TSA) enables genome-wide measurement of relative chromosome loci distances to particular nuclear compartments. Combining Lamina and Speckle TSA-Seq, provides new insights into nuclear architecture: Lamina-Associated Domains (LADs) partition into subdomains of varying distance to the nuclear lamina. Inter-LADs vary in how far they protrude into the nuclear interior, with centers of transcriptional “hot-zones” mapping to the most interior location of an inter-LAD chromosome trajectory. Transcription hotzones mapping closest to nuclear speckles correspond to the A1 Hi-C subcompartment, and are enriched in super-enhancers, the most highly expressed genes, and genes with low transcriptional pausing. In K562 cells, ~5% of the genome maps within 500 nm of nuclear speckles in ~100% of cells. Various genomic activities align along a Nuclear Speckle-Lamina axis, which we show represents an ensemble average over different cells as well as different types of noncontiguous chromosome trajectories. Comparing cell lines, we observe both constitutive Speckle Associated Domains (SPADs), associated with high gene density and constitutively high transcription, and a smaller number of facultative SPADs, correlated with cell-type specific transcription. Additionally, rapidly inducible heat-shock genes are positioned within constitutive SPADs, perhaps for robust transcriptional activation. More generally, we have identified chromatin domains with Mbps-size that shift variable distances along this Nuclear Speckle- Lamina axis, with accompanying changes in transcriptional activity. Overall our initial analysis suggests that nuclear speckles serve as a major active compartment for constitutive transcription, while developmentally regulated genes move variable distances along this Nuclear Speckle-Lamina axis, providing a potentially novel transcriptional regulatory mechanism.

36


SETMAR: A NOVEL DNA-BINDING AND CHROMATIN LOOPING FACTOR

Alison M. Bates

Alison M. Bates, Qiujia Chen, Michael E. Fusakio, Ronald C. Wek, and Millie M. Georgiadis

Department of Biochemistry and Molecular Biology, Indiana University School of Medicine,

Indianapolis, Indiana About 50 million years ago, an Hsmar1 transposon invaded an early primate genome and inserted itself downstream of a SET methyltransferase gene, leading to the birth of a new chimeric protein now called SETMAR. While all other Hsmar1 sequences in the human genome have suffered inactivating mutational damage, the transposase domain of SETMAR has remained remarkably intact, suggesting that it has gained a novel, evolutionarily advantageous function. While SETMAR can no longer transpose itself throughout the genome, it has retained its ancestral sequence-specific DNA binding activity, the importance of which is currently unknown. To investigate this, we solved the crystal structure of DNA-bound SETMAR and performed ChIP-seq to examine SETMAR binding in the human genome. We also utilized RNA-sequencing to assess the effect of SETMAR on transcription and analyzed its transposase-derived chromatin- looping ability using chromosome-conformation-capture-on-ChIP (4C). The crystal structure of DNA-bound SETMAR confirmed sequence-specific recognition of Hsmar1 terminal inverted repeat (TIR) sequences through seven nucleobase-specific interactions. ChIP-seq showed that SETMAR binds extensively throughout the genome, amassing 7457 binding sites, 94% of which include a TIR sequence. RNA-seq indicated 177 genes that are differentially regulated by SETMAR, including repression of 17 histone genes, suggesting a possible role in chromatin dynamics. 4C analysis revealed numerous chromatin loops that form both intrachromosomal and interchromosomal connections. As previous studies have shown that SETMAR prevents chromosomal translocations, our findings raise the possibility of a novel mechanism whereby SETMAR influences the stability and 3-dimensional positioning of chromosomes in the nucleus. The prevalence of SETMAR binding in the human genome combined with its dimeric structure and DNA looping capacity suggest a novel role for SETMAR as a chromatin organizing factor.

37


INVESTIGATING THE IMPACT OF H1 BINDING ON CHROMATIN FIBER STRUCTURES AND DYNAMICS USING ALL-ATOM MOLECULAR DYNAMICS

SIMULATIONS

Francisco Rodríguez-Ropero

Francisco Rodríguez-Ropero and Jeff Wereszczynski

Department of Physics, Illinois Institute of Technology, Chicago, IL, USA Linker histones bind Nucleosome Core Particles (NCP) forming chromatosomes, which induces greater DNA compaction in chromatin fibers. However, precise molecular understanding of the impact of linker histones on the structure, mechanics, and dynamics of chromatin fibers is still lacking in the literature. In this contribution we will report results from 3 µs of fully atomistic Molecular Dynamics (MD) simulations of chromatin fibers formed by an octa-NCP structure, both with and without H1 linker histones bound in off-dyad positions. Our systems were built using as reference the 11 Å cryo-EM density map solved by Song et al. (Science, 2014, 344, 376) with 177 base pairs. Results show that inter-NCP stacking interactions are increased upon linker histone binding. H1 linker histones are tightly bound to the linker DNA due to the abundance of lysine amino acids, which prompts a local rearrangement of the DNA and reduces the flexibility of the linker DNA. These effects are translated into an increase in rigidity and compaction of the overall chromatin fiber when H1 linker histones are present in the system. Moreover, mutual correlation analyses of the systems with and without H1 show an enhancement of the correlated motions all along stacked NCPs. This suggests that H1 triggers a cascading stabilizing effect along the resulting chromatin fiber. We expect our findings to have direct implications in chromatin remodeling, epigenetics, and identification of histone posttranslational modification sites.

38


Epigenetic regulation through UHRF proteins

Scott B. Rothbart

Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI My lab is keen on understanding the complex relationship between DNA methylation and histone post-translational modifications (PTMs); two key epigenetic regulators of genome accessibility, interaction, and function. Within this broad framework, we question 1) how are the writers and erasers of chromatin modifications regulated, 2) how do nuclear proteins and their complexes interface with (i.e., read) epigenetic marks to perform their chromatin regulatory functions, and 3) how does deregulation of chromatin signaling contribute to human cancer? Several ongoing projects in the lab are focused on the UHRF family of E3 ubiquitin ligases. The pioneering member of this family, UHRF1, is a histone- and DNA-binding RING E3 ligase that controls a pathway responsible for maintaining up to 80% of the global DNA methylation found in mammalian cells. UHRF1 facilitates recruitment of DNMT1 to replicating chromatin through orchestrated recognition of histones and DNA, which converge on ubiquitination of histone H3, a binding site for DNMT1. UHRF2 shares structural homology with UHRF1, but surprisingly lacks functional redundancy as a DNA methylation regulator. Through comprehensive and comparative structure-guided biochemical and biophysical analysis of UHRF proteins, we are uncovering mechanisms of intraand inter-molecular crosstalk regulating the binding and enzymatic activities of these chromatin regulators and are revealing molecular details that connect UHRF proteins to the DNA methylation maintenance program.

39


The effect of nucleosome conformation on histone tail binding: Implications for chromatin signaling

Catherine Musselman

Department of Biochemistry, University of Iowa, Carver College of Medicine

Histone tails harbor a plethora of post-translational modifications (PTMs) that direct the function of chromatin regulators. Recognition of histone PTMs by these regulatory complexes is mediated through the action of reader sub-domains. The interaction of reader domains with modified histone tails has been extensively studied using peptide fragments of the tails. However, we have very little knowledge of how these domains associate with the full nucleosome. We are using NMR spectroscopy to investigate this, and have found that the conformation of the histone tails in the context of the nucleosome has a dramatic effect on reader domain binding. As a model system, we are investigating the interaction of the BPTF PHD finger with its known cognate modification, methylated lysine 4 on histone H3 (H3K4me3). Here, we show that the conformation adopted by the histone H3 tails within the context of the nucleosome is inhibitory to binding of the BPTF PHD finger to H3K4me3, as compared to histone peptides. Using NMR spectroscopy and MD simulations, we find that the H3 tails interact robustly but dynamically with nucleosomal DNA, and demonstrate that this inhibits PHD finger association. Modifications and mutations of the H3 tail outside the binding region increase the accessibility to PHD finger binding, indicating that PTM crosstalk can regulate reader domain binding by altering the nucleosome conformation. Together, our results demonstrate that the nucleosome context has a dramatic impact on signaling events at the histone tails, and highlights the importance of studying histone binding in the context of the nucleosome.

40


BMI1 localization to sites of DNA damage as a potential mechanism for development of cisplatin resistance

Shruthi Sriramkumar

Shruthi Sriramkumar1, Heather M. O’Hagan

1,2

1Medical Sciences, Indiana University School of Medicine, Bloomington IN, 47405, USA.

2Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, 46202, USA.

Background: Platinum based agents, cisplatin and carboplatin are most commonly used to treat ovarian cancer (OC) patients. These agents damage DNA by forming adducts with adjacent guanines. Resistance to platinum based agents is the major cause of mortality among OC patients. Aberrant DNA hypermethylation of genes and their subsequent transcriptional repression has been linked to cisplatin resistance in OC. However, the mechanism of initiation of these alterations is not known. Transient transcriptional repression occurs in the vicinity of DNA damage sites to promote repair. However, this transient transcriptional repression can persist at some loci causing stable silencing. We hypothesize that BMI1 ubiquitinates H2AX at K119 at sites of cisplatin-induced DNA damage and contributes to transcriptional repression. This recruitment occasionally causes stable gene silencing ultimately contributing to the development of cisplatin resistance.

Methods: Ovarian cancer cells were treated with IC50 dose of cisplatin and 8 hours later localization of BMI1 to sites of damage and H2AX ubiquitination was demonstrated by using immunofluorescence and western blot respectively. Gene expression changes were determined by qRT-PCR.

Results: Our preliminary data demonstrates BMI1 co-localization with the damage marker γH2AX and H2AX ubiquitination after cisplatin treatment.H2AX ubiquitination decreases when ATM is inhibited and on knockdown of NER proteins-XPA and CSB. We also demonstrate that candidate genes that are known to be silenced by DNA methylation in cisplatin resistant cells, are transcriptionally repressed following acute cisplatin treatment.

Conclusions: BMI1 localizes to sites of cisplatin-induced DNA damage where it ubiquitinates H2AX. A portion of this ubiquitination is dependent on ATM and NER proteins. We hypothesize that BMI1 localization is also dependent on ATM and NER proteins. Understanding the role of BMI1 in platinum resistance will enable us to design therapies to avert the development of drug resistant ovarian cancers.

41


Regulation of Human Sirtuin Deacylase Activity by Cellular Oxidants

Kelsey S. Kalous

Kelsey S. Kalous, Sarah L. Wynia-Smith, Michael D. Olp, Brian C. Smith

Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI

Sirtuins catalyze the NAD+-dependent deacylation of acyl-lysine residues, producing O- acyl-ADP-ribose and nicotinamide. Humans encode seven sirtuins (Sirt1-7) that are considered pro-survival proteins, and decreased sirtuin activity promotes aging-related diseases, including type-II diabetes. However, how sirtuin activity is inhibited during aging is largely unknown. We are defining the physiological mechanisms that regulate sirtuin activity post-translationally, as elucidation of these mechanisms will illuminate unexploited means to prevent disease- associated decreases in sirtuin activity. As oxidative stress increases with age, we focus on the regulation of sirtuin activity by post-translational modification by cellular oxidants.

We show that Sirt1 can be nitrosated by S-nitrosoglutathione (GSNO). Colorimetric Zn2+

loss and circular dichroism assays revealed Sirt1 nitrosation correlated with Zn2+-release and

loss of α-helical structure, suggesting the target of nitrosation is the Zn2+-tetrathiolate conserved

among sirtuins. Molecular dynamics simulations suggested Zn2+ loss due to Sirt1 nitrosation results in repositioning of the tetrathiolate subdomain away from the rest of the catalytic domain,

disrupting NAD+ and acetyl-lysine substrate binding. Furthermore, Sirt1 nitrosation was reversed upon exposure to thiol-based reducing-agents, resulting in restoration of Sirt1 activity. This

restoration was dependent on the presence of Zn2+, consistent with nitrosation of the Zn2+- tetrathiolate as the source of Sirt1 inhibition.

More recently, we found that nuclear sirtuins (Sirt1, Sirt2, Sirt6) are inhibited in vitro by nitric oxide (NO) and NO-derived oxidants, and are resistant to inhibition by oxidized glutathione, hydrogen peroxide, and hydrogen sulfide. Surprisingly, mitochondrial sirtuins (Sirt3 and Sirt5) displayed selective inhibition by peroxynitrite and were insensitive to all other assayed oxidants.

These data suggest that, despite conservation of the Zn2+-tetrathiolate across all sirtuins, S-

nitrosation does not universally inhibit sirtuins. Additionally, we observed a concentration- and time-dependent increase in Sirt6 expression in pancreatic beta cells in response to NO, suggesting that NO modulates Sirt6 expression in beta cells under inflammatory conditions.

42

POSTER SESSION – ODD NUMBERS

Poster

# First Name Last Name Abstract Title

1. Lama Alabdi Regulation of pluripotency by DNA methylation in F9 Embryonal carcinoma

3. Kortany Baker The Study of Epigenetic Mediated Azole Resistance

5. Alison Bates SETMAR: A NOVEL DNA-BINDING AND CHROMATIN LOOPING FACTOR

7. Elena Beketova Targeting PRMT5 as a novel approach for the treatment of castration-resistant prostate cancer

9. Panyue Chen Deciphering the role of N-terminal methylation in modulating yeast protein function including the multitasking stress response protein, Hsp31

11. Alison Chomiak Polycomb signaling as a therapeutic axis for enhancing epigenetic therapy in colorectal cancer

13. Katelyn Connelly Elucidating the role of the CBX8 chromodomain as a therapeutic target

15. Spencer Escobedo Chromatin remodeler Brahma is necessary for age dependent cell survival and visual behavior in Drosophila photoreceptors

17. Harrison Fuchs Interactions between the BPTF Bromodomain and Histone H4 tail in the context of the nucleosome

19. Christopher Goetz DISCOVERY AND DEVELOPMENT OF NOVEL LIGANDS FOR THE SECOND BROMODOMAIN OF POLYBROMO-1

21. Wei Guo Dissecting the maintenance of MuDR transposon silencing in maize

23. Youssef Hegazy Defining the mechanisms for R-loop formation in yeast

25. Rosaline Hsu Pre-replicative complex protein ORCA/LRWD1 regulates homologous recombination at ALT-telomeres by modulating RPA binding

27. Stevephen Hung Mismatch-repair signature mutations modulate gene enhancer activity across colorectal cancer epigenomes

29. Mohammad Kamran BEND3 regulates pluripotency by p21 mediated pathway

31. Peter Lewis Dysregulation of Polycomb silencing by oncohistones

33. Yo-Chuen Lin PCNA-mediated stabilization of E3 ligase RFWD3 at the replication fork is essential for DNA replication

35. Fengyi Mao Plk1 inhibition enhances the efficacy of BET epigenetic reader blockade in castration-resistant prostate cancer

37. Allison Mitchell FOXQ1 interacts with the KMT2/MLL core complex to promote transcriptional activation of the epithelial to mesenchymal transition (EMT) program

39. Andrew Morton Enhancer co-option on extrachromosomal oncogenic amplifications

41. Prabakaran Nagarajan Early Aging Phenotypes Associated With Haploinsufficiency Of Hat1 In Mice

43

POSTER SESSION – ODD NUMBERS

Poster


43. Fei Gao Epigenomic landscape, spatial conformation and function of regulatory elements of the PDGFRA-KIT locus in gastrointestinal stromal tumor (GIST) cells

45. Arpita Pal Aberrantly expressed microRNAs drive the development of acquired Erlotinibresistance in Non-Small Cell Lung Cancer (NSCLC)

47. Sarah Peck Profiling the impact of missense mutations on the proteome

49. Elizabeth Porter The Role of Polybromo1 in Stress Response

51. Wenjie Qi Modeling Aryl Hydrocarbon Receptor-mediated Gene Regulatory Networks

53. Rachel Reardon Exploring the role of histone modifications in epigenetic UV hyper-resistance of Saccharomyces cerevisiae

55. Francisco Rodriguez-Ropero

INVESTIGATING THE IMPACT OF H1 BINDING ON CHROMATIN FIBER STRUCTURES AND DYNAMICS USING ALL-ATOM MOLECULAR DYNAMICS SIMULATIONS

57. Ray Scheid Bivalent histone reader, EBS, regulates floral phase transition in Arabidopsis

59. Brian Smith Discovery of Brd4-selective inhibitors through a novel fragment screening strategy

61. Shruthi Sriramkumar BMI1 localization to sites of DNA damage as a potential mechanism for development of cisplatin resistance

63. Jason True Analysis of RNA Polymerase II protein-protein interactions as a consequence of FACT perturbation

65. Ruixin Wang PLK1-dependent phosphorylation of EZH2 contributes to its oncogenic activity in castration-resistant prostate cancer

67. Aaron Williams Investigating X-chromosome Inactivation in Human Embryonic Stem Cells

69. Zheng Xing Characterization of the mammalian DEAD-box protein DDX5 reveals functional conservation with S. cerevisiae ortholog Dbp2 in transcriptional control and glucose metabolism

71. Jiaxin Long The chromatin remodeler PIE1 contributes to loss of the repressive epigenetic mark H3K27me3 in plants lacking the chromatin remodeler PKL

44

POSTER SESSION – EVEN NUMBERS

Poster


2. Aktan Alpsoy GLTSCR1 and GLTSCR1L define a unique SWI/SNF subcomplex

4. Christopher Ball Nucleotide resolution analysis of RNA polymerase II initiation and pausing in human cytomegalovirus

6. Ian Bayles Ex vivo screen identifies CDK12 as an epigenetic-driven metastatic vulnerability in osteosarcoma

8. Samuel Bowerman Nucleosomal Inhibition of PHD-H3 Binding is Mediated by PTM Crosstalk: Support from Molecular Dynamics Simulations

10. Jerrin Cherian Mechanisms involved in repression of germline genes in somatic cells of C.elegans

12. Marissa Cloutier A Transgenerational Role for Polycomb Group Protein EED in Imprinted X-chromosome Inactivation

14. Evan Cornett A functional proteomics screen for lysine methyltransferase substrate selectivity reveals a role for SMYD2 in circadian clock regulation

16. Meghan Fealey Developmental regulation of chromatin compaction by C. elegans synMuv B proteins

18. Fei Gao Hypoxia-inducible factor 1 alpha (HIF1A) stimulates neuronal nitric oxide synthase (Nos1) transcription by modifying spatial chromatin organization

20. Inosha Gomes PRMT5 is a substrate of HDAC6

22. Humna Hasan “Small talk” between the Non-Small-Cell Lung Cancer cells and normal bronchial epithelial cells via extracellular vesicles lead to NSCLC progression

24. Casey Hooker Epigenetically-regulated CAZymes enable efficient degradation of untreated lignocellulose by anaerobic gut fungi for bioenergy production

26. Katlyn Hughes Altered RNA Polymerase II Transcription Dynamics in the Absence of Transcription Elongation Factor Spt4

28. Kelsey Kalous Regulation of Human Sirtuin Deacylase Activity by Cellular Oxidants

30. Ann Kirchmaier CDC7 modulates silencing via H4 K16 acetylation and the histone chaperone CAF-1

32. Chennan Li Identifying critical genes and microRNAs that when lost, can drive neoplastic transformation of non-cancerous lung cells.

34. Brianna Lupo The molecular basis of multivalent DNA binding by the BRM AT-Hook and bromodomain

36. Xiangying (Candy)

Mao Investigating the interaction between MED5 and CDK8 in Arabidopsis

45

POSTER SESSION – EVEN NUMBERS

Poster #

First Name Last Name Abstract Title

38. Emma Morrison Histone H3 Tail Conformation Regulates Nucleosome Association by the BPTF PHD Finger

40. Kaushik Muralidharan Role of miRNAs in opioid addiction and neuroplasticity

42. Devin Neu Identifying Determinants of Signature Enhancer Activation in Colon Cancer

44. Jake Owens PRMT5 is a novel epigenetic regulator of DNA repair genes and a therapeutic target to improve radiation therapy

46. Xiaoqing Michelle

Pan Roberts

Stability of whole-blood DNA methylation profiles under different storage durations and conditions

48. Lori Pile Regulation of central carbon metabolism by SAM synthetase and the transcriptional cofactor SIN3

50. Emily Putnam High-Throughput Locus-Specific DNA Methylation Validation Platforms in Aging Quantification Research

52. Ana-Maria Raicu Adaptation of a CRISPR Interference Method for Probing Chromatin Properties of Repressor Domains

54. Julio Sanchez Characterization of the novel DNA binding activity of the BRG1 AT-hook-bromodomain

56. Jasleen Singh Converting DNA information into double-stranded RNA in a coupled reaction

58. Erin Sorlien Analysis of the contribution of the chromatin remodeler and tumor suppressor chd5 to neural differentiation and tumor suppression in Danio rerio

60. Rochelle Tiedemann High-resolution epigenome mapping reveals unique genomic signatures of UHRF1-dependent DNA methylation inheritance

62. Jose Victorino CTD PHOSPHATASE Ssu72 STIMULATES READ-THROUGH AT NNS TERMINATED GENES

64. Tyler Weaver Structural basis for multivalent engagement of DNA and H3K27me3 by the CBX8 CD

66. Dustin Woods The effects of linker histone isoforms on the structure and dynamics of the chromatosome

68. Bingyu Yan Characterizing enhancer RNAs in adaptive immune cells

70. Ethan Zhang Identification of Novel HDAC1 Substrates Using a Mutant Trapping Strategy

46

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Documents

JUNE 10-12, 2018, PURDUE UNIVERSITY, WEST ......6 10:55 AM Peter Jones, Ph.D. (invited speaker) Van Andel Research Institute 11:15 AM Lama Alabdi (selected speaker) Purdue University