John Satterlee, Ph.D.

NIDA Council May 3, 2016

Outline

Ø What is the 4D nucleome? Why is it important?

Ø The Common Fund 4D Nucleome Program

There’s more to the genome than its sequence

Human Genome Project

Roadmap Epigenomics, ENCODE, IHEC

4D Nucleome

Mao et al, Trends Genet., 2011, 27: 295-306

Structures Within the Nucleus

Bolzer, et al 2005 Plos Biol. 3:e157

Chromosomal Territories

Nucleome = the organization of the nucleus in space & time (4D)

Alterations of genome organization are associated with:

• cancer • premature aging syndromes• learning and memory

Nuclear organization is dynamic

A CRISPR Image of the Nuclear Genome

The CRISPR/Cas system can be used to:Ø Test regulatory functions

Ø Image genetic elements dynamically in live cells

Imagingtelomere

dynamics:(Stan Qi lab, UCSF)

Chen et al., 2013 Cell 155:1479-91

http://homer.salk.edu/homer/interactions/circos.html

Assaying and Visualizing Chromosomal Interactions

Hi-C assayChia-Pet assay

Maps suggest that the genome is organized in physically defined domains/loops.

Connections:Within chromosomesBetween chromosomes

>80% of disease-associated genetic variants reside in noncoding regulatory sequences with unknown targets.

Chromatin Architecture in HIV Infection

Nuclear Architecture dictates HIV-1 integration site selection. Marini et al. 2015 Nature. 521:227-31.

ØPrefers transcriptionally active regions

ØAvoids nuclear-lamin regionsassociated w/ inactive chromatin

Ø Integrates near nuclear pores

2199 Inactive Olfactory Receptors sequestered within the nucleus

1 Active Olfactory Receptor Allele withRNA expression

Nuclear Architecture Critical for Olfactory Receptor Allele Expression

The mouse genome encodes 1100 different olfactory receptor genes (2200 alleles)

Only 1/2199 olfactory receptor alleles is expressed in a single olfactory neuron nucleus

Lomvardas lab, Columbia University Clowney, et al. 2012 Cell, 151:724-737

Bharadwaj et al. Neuron 2014 84:997-10008

Conserved Chromatin Architecture Regulates Gene Expression & Cognition

LOW

370KbTSS

450Kb

450kb1TSS

3’

5’

370Kb

NRF-1

AP1CTCF

5’

3’

No GRIN2B expression

GRIN2B expression

TSS

5’

3’

SE

TD

B1

370Kb

450KbNRF-1

AP1CTCF

H3K9me3

HP1

High Low

370KbTSS

450Kb

450kb1TSS

3’

5’

370Kb

NRF-1

AP1CTCF

5’

3’

No GRIN2B expression

GRIN2B expression

TSS5’

3’S

ET

DB

1

370Kb

450KbNRF-1

AP1CTCF

H3K9me3

HP1

High Low

GRIN2BGeneExpression

370KbTSS

450Kb

450kb1TSS

3’

5’

370Kb

NRF-1

AP1CTCF

5’

3’

No GRIN2B expression

GRIN2B expression

TSS

5’

3’S

ET

DB

1

370K

b

450KbNRF-1

AP1CTCF

H3K9me3

HP1

High Low

HIGH

NONE

GRIN2BGeneExpression

GRIN2B=NMDAglutamatereceptorsubunit

Akbarian lab, Mt. Sinai, R01DA036984

Chromatin Remodeling in Substance Abuse

Wood lab, UC Irvine, R01DA025922 Vogel-Ciernia et al. 2013 Nat Neuro. 16:552-61

BAF chromatin remodeling complex

Changes DNA/nucleosome structure

Knockout BAF53b neuronal-specific subunit

ØRequired in hippocampus in adult neurons for long-term (but not short-term) memory tasks

ØBAF53b required for cocaine-associated memories (in press)

ØStabilizes long-term potentiation (LTP)

Outline

Ø What is the 4D nucleome? Why is it important?

Ø The Common Fund 4D Nucleome Program

Glycoscience

4DNucleome

LibraryofIntegratedNetwork-

BasedCellularSignatures(LINCS)

SingleCell

Analysis

CurrentCommonFundPrograms

EnhancingtheDiversityoftheNIH-Funded

Workforce

PROMIS:ClinicalOutcomesAssessment

NIHCenterfor

RegenerativeMedicine

RegulatoryScience

MolecularLibraries

andImaging

HumanMicrobiome

ProteinCapture

PioneerAwardsNewInnovatorAwardsTransformativeResearchAwardsEarlyIndependenceAwards

BioinformaticsandComputational Biology

BuildingBlocks,BiologicalPathways

AndNetworksGenotype-Tissue

Expression

Nanomedicine

ScienceofBehaviorChange

GulfOilSpillLongTermFollowUp

GlobalHealth

KnockoutMouse

Phenotyping

BigDatatoKnowledge(BD2K)

HCSResearchCollaboratory High-Risk

ResearchNIH

Common Fund

HealthEconomics

Epigenomics

http://commonfund.nih.gov/

Metabolomics

UndiagnosedDiseasesNetwork

ExtracellularRNA

Communication

Strengtheningthe

BiomedicalResearchWorkforceIlluminatingthe

DruggableGenome

StimulatingPeripheralActivitytoRelieveConditions

(SPARC)

Co-chairs:Roderic Pettigrew NIBIBDinah S. Singer NCIPhil Smith NIDDK

Working Group Coordinators:Olivier Blondel NIDDKRichard Conroy NIBIBJudy Mietz NCI

Common Fund Program Leaders:Patricia Labosky OSCAnanda Roy OSC

4DN Program Director:Lisa Chadwick NIEHS

4DN Program Analyst:Iddil Bekirov NIDDK

Working Group:David Balasundaram CSRTerry Bishop NIDDKAnthony Carter NIGMSSean Hanlon NCIRebecca Lenzi OSCMike Pazin NHGRILisa Postow NHLBIMatt Reilly NIAAARobert Riddle NINDSJohn Satterlee NIDAGeetha Senthil NIMHJessica Smith OSCJose M. Velazquez NIA

4D Nucleome NIH Common Fund Program

Goals to understand:

1. The principles underlying nuclear organization of mammalian genomes in space and time

2. The role that nuclear organization plays in gene expression and cellular function

3. How changes in nuclear organization affect normal development and disease

4D Nucleome NIH Common Fund Program

https://commonfund.nih.gov/4dnucleome/index

Building the Network

Epigenome(2005-2015)

4D Nucleome(2015-2020)

Common Fund 4D Nucleome Program

Genome(1990-2005)

Next generation tools: to explore the relationship between genome organization and function

• Imaging (NIBIB) • Nucleomics (NHLBI)• Nuclear bodies (NIDA)

Reference maps: of the 4D organization of the genome in a variety of human cells/tissues and cell states

• Nuclear Org. & Function Centers (NIDDK)• Data Coordination/Integration Center (NCI)• Organizational Hub (NCI)

Study of Nuclear Bodies and Compartments (U01)

Contact PIs:

Clifford Brangwynne, PrincetonLarry Gerace, ScrippsMark Groudine, HutchMitchell Guttman, CaltechPaul Kaufman, U MassStavros Lomvardas, Columbia

Develop tools & technologies to investigate the structure and function of nuclear bodies/domains

NIDA

Nucleomics Tools (U01)

Contact PIs:Peter Fraser, Babraham InstituteMitchell Guttman, CaltechErez Lieberman-Aiden, BaylorJohn Lis, CornellArjun Raj, U Penn

Develop & validate novel technologies to investigate the 4D organization of the genome

4D Nucleome Imaging Tools (U01)

Contact PIs:

Joerg Bewersdorf, YaleLong Cai, CaltechJan Ellenberg, HeidelbergThomas Gregor, PrincetonDavid Grunwald, U Mass

Kit Lam, UC DavisJan Liphardt, StanfordClodagh O’Shea, Salk InstituteRobert Singer, Albert Einstein

Develop & validate imaging technologies to visualize the structural/functional organization of the genome

and its dynamics

Nuclear Organization and Function Interdisciplinary Consortium (NOFIC) (U54)

Frank Alber, USCAndrew Belmont, U of IllinoisJob Dekker, U MassBing Ren, UCSDYijunRuan, Jackson LabJay Shendure, U Washington

Contact PIs:

Technology development and data production to understand 4D Nucleome structure/function

4D Nucleome Network Data Coordination and Integration Center (DCIC) (U01)

Contact PIs:Peter Park, Harvard(Data coordination and integration)Ting Wang, Washington University(Data visualization tools)

Collect, store, curate, & display data, metadata, and analysis tools

Disseminate to the scientific community

4D Nucleome Network Organizational Hub (U01)

Contact PI: Sheng Zhong, UCSD

Administrative infrastructure. Develops and maintains the 4DN Portal, organizes outreach

activities, coordinates the Opportunity Pool of funds.

Potential U.S. and International Partnerships

QUESTIONS?