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SwedishEpigeneticsandChromatinMeetingEpiChrom2017

November30–December1,2017Rudbecksalen

DagHammarskjöldsväg20Uppsala

Artworkkindlyprovidedby:Dr.MhairiTowler-UniversityofDundee/Vivomotion(www.vivomotion.co.uk),LinkLiandDr.PaulHarrison-UniversityofDundee

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Day1

8:00 Registrationandcoffee8:30 Welcomeaddress8:40 SessionI:UnderstandingEpigeneticsI8:40 UnderstandingthenexusbetweenlncRNAsandchromatin-levelgeneexpression

ChandrasekharKanduri,UniversityofGothenburg9:20 AmicroarrayscreenidentifiesnovelTGFbeta-regulatedlongnon-codingRNAs

PanagiotisPapoutsoglou,UppsalaUniversity9:40 TheChromatinremodelingcomplexB-WICHisrequiredforDNAPolItranscriptionactivationby

glucosestimulationYuanGuo,StockholmUniversity

10:00 Coffeeandsandwiches10:30 SessionII:Epigeneticsinsolidtumors10:30 Tissue-typespecificfunctionalannotationoftranscriptionfactormotifsforprioritizationofnoncoding

variantsHusenUmer,UppsalaUniversity

10:50 ExosomesreleasedbypediatricgliomastemcellsinducegeneexpressionchangesinneuralcellsAgotaTuzesi,UniversityofGothenburg

11:10 OrthotopictransplantationofpediatricgliomastemcellsinmicemirrorstheclinicalcourseofthepatientAnnaWenger,UniversityofGothenburg

11:30 Coffeebreak11:50 SessionIII:Epigeneticsinhematologicalmalignancies11:50 Adistinctgeneregulatorynetwork,establishedindependentofcodingmutations,underpinstheCLL

phenotypeAylaDePaepe,KarolinskaInstitutet

12:10 DiscoveryofnewmolecularsubgroupsinpediatricALLusingDNAmethylationclassificationandRNA-sequencingYanaraMarincevic-Zuniga,UppsalaUniversity

12:30 Genome-wideDNAmethylationprofilinginchroniclymphocyticleukemiapatientscarryingstereotypedB-cellreceptorsLarryMansouri,UppsalaUniversity

12:50 Epigeneticco-regulationasapotentialtherapeutictargetinmultiplemyelomaAlbaAtienzaPárraga,UppsalaUniversity

13:10 Lunchandposters14:15 Immunememory

HenkStunnenberg,RadboudInstituteforMolecularLifeSciences(RIMLS),Nijmegen,TheNetherlands

15:15 Coffeeandsweets15:50 SessionIV:Epigeneticsandimmunity15:50 ReactivationpotentialofHIV-1inprimaryCD4Tcellsdependonthechromatinmicroenvironment

PeterSvensson,KarolinskaInstitutet16:10 MajortranscriptionalchangesobservedintheFulani,anethnicgrouplesssusceptibletomalaria

JaclynQuin,StockholmUniversity16:30 EnhancerregulationbyGPS2modulatesmacrophageinflammation

ZhiqiangHuang,KarolinskaInstitutet16:50

UtilizingepigenomicstounderstandneurodegenerationinMultipleSclerosis:whataretheneuronstellingus?LaraKular,KarolinskaInstitutet

17:10 Mingle

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Day 2

8:30 SessionV:UnderstandingEpigeneticsII8:30 DecipheringthecooperativityofPolycombrepression

YuriSchwartz,UmeåUniversity9:10 TargetingPolycombrepressivecomplexesthroughevolutionaryconservedDNAelements

JuanIgnacioBarrasaLopez,UmeåUniversity9:30 DevelopmentalpatterningandgeneregulationbytheBEN-solofamily

QiDai,StockholmUniversity9:50 ThefutureofepigeneticsatSciLifeLab?SimonElsässer,KarolinskaInstitutet10:10 Coffeeandsandwiches10:40 SessionVI:Epigeneticsacrossspecies10:40 EctopicapplicationofH3K9me2establishespostzygoticreproductiveisolationinArabidopsis

HuaJiang,SwedishUniversityofAgriculturalSciences11:00 ImprintedgeneregulationbythepaternallyexpressedgenePHERES1inArabidopsis

RitaBatista,SwedishUniversityofAgriculturalSciences11:20 GeneticdissectionofDrosophilaHDAC3function

MinTang,StockholmUniversity11:40 C12D8.1:AnegativeregulatorofRNAiinheritanceinCaenorhabditiselegans

BenjaminHolmgren,UppsalaUniversity12:00 Lunchandposters13:00 ComputationalEpigenomicApproachesforDecipheringtheNon-codingHumanGenome

JasonErnst,UniversityofCalifornia,LosAngeles(UCLA),USA14:00 Coffeebreak14:20 SessionVII:Epigenomics14:20 MechanisticInsightsintoAutoinhibitionoftheOncogenicChromatinRemodelerALC1

SebastianDeindl,UppsalaUniversity14:40 Identificationofoligodendrocytelineagestateswithsingle-cellATAC-seq

EneritzAgirre,KarolinskaInstitutet15:00 Protein-codingsequenceexclusionbyalternativetranscriptionstartsiteusageacrossthehumanbody

WenboDong,KarolinskaInstitutet15:20 Nascenttranscriptionplasticityinmouseembryonicstemcells

RuiShao,KarolinskaInstitutet15:40 Coffeeandsweets16:10 SessionVIII:Epitools16:10 Chromatrap®;Amoreefficient,sensitive&robustmethodofchromatinimmunoprecipitation

(commercial)LindsayParkes

16:25 ActiveMotif,enableschromatinandgeneregulationresearch(commercial)SarantisChlamydas

16:40 Anovelmethodologyforidentifyinggenome-wideRNA-chromatininteractionsAlessandroBonetti,KarolinskaInstitutet

17:00 ModellingthedynamicsofepigeneticmemoryLudvigLizana,UmeåUniversity

17:20 Closingremarks

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Posters EpiChrom 2017 Day 1 1

SingleCRISPR-Cas9knockoutofEMT-relatedtranscriptionfactorsfailstoinduceepithelialreversionofmesenchymalbreastcancercellsVarunMaturi,UppsalaUniversity

2 IdentificationoflncRNAassociatedwithoutcomeinacutemyeloidleukemia(AML)AnneNeddermeyer,UppsalaUniversity

3 MechanisticcharacterizationofHDACimediatedKITdownregulationinsystemicmastocytosisHaniAbdulkadirAli,KarolinskaInstitutet

4 Functionalevaluationofnon-codingmutationinChronicLymphocyticLeukemiaLuciaPenaPerez,KarolinskaInstitutet

5 Fromcellstodatain24hours-High-ThroughputChIPmentationonultra-lowcellnumbersCharlotteGustafsson,KarolinskaInstitutet

6 RROSETTA:atoolkitforcreatingroughsetmodelsMateuszGarbulowski,UppsalaUniversity

Posters EpiChrom 2017 Day 2

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AlternativesplicingandSWI/SNFchromatinremodelingcomplexAntoniGanezZapater,StockholmUniversity

2 DissectionofGPS2-PPARapathwaysgoverninghepaticlipidmetabolismNingLiang,KarolinskaInstitutet

3 InvestigatingthefunctionofBEN-solotranscriptionfactorsinthedevelopingDrosophilaCNSMalinUeberschär,StockholmUniversity

4 SPlintedLigationAdapterTagging(SPLAT),anovellibrarypreparationmethodforwholegenomebisulphitesequencingAmandaRaine,UppsalaUniversity

5 MonitoringoftheepigeneticstateinlivecellsCeciliaBergqvist,StockholmUniversity

6 Improvedtreatmentsofpediatricbraintumorsusingepigeneticdrugs?SusannaLarsson,SahlgrenskaCancerCenter/UniversityofGothenburg

7 LSD1modulationbyallostericligandsJohanWinquist,Beactica

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Thursday, November 30th 2017

Session I: Understanding Epigenetics I Chair:HelenaJernberg-Wiklund

Invitedspeaker:

ChandrasekharKanduri

Dr.ChandraKanduriisaProfessorattheDepartmentofMedicalBiochemistryand Cell Biology, Institute of Biomedicine, University of Gothenburg,Gothenburg. He holds a doctoral degree from the Banaras Hindu University,India and did his postdoctoral work at the Department of Development andGenetics, Uppsala University. He is a MHF1-Vetenskapsrådet-Medicin panelmember and a reviewer for AICR, ESF, EURYI (European Young InvestigatorAward), The Netherlands organization for Scientific Research (NWO), FRMFrance,INSERMFranceandSwissNationalFoundation.

Hisworkexploresthefunctionoflong-noncodingRNAsintheepigeneticregulationoftranscriptionduring development and disease, and aims at developing lncRNA-based therapeutics in thetreatmentofcancer.

Understanding the nexus between lncRNAs and chromatin-level gene expression

Chromatin is organized into active and inactive compartments with distinct epigenetics codes.These active and inactive chromatin-specific histone modifications are defined by regulatoryinteractions between DNA sequences and chromatin remodelers in a tissue and developmentalstage dependent manner. However, it is not clear how chromatin remodelers are targeted tospecificchromatinregionsacrossthegenome.RecentevidencessuggestthatlncRNAsconstituteanimportant feature in the targeting of chromatin remodelers across the genome. Thus there is agrowinginteresttoaddressthefunctionalcontributionoflncRNAsinthesub-compartmentalizationof the eukaryotic genome. Characterization of chromatin-associated lncRNAs in functionallydemarcatedchromatincompartmentsmayhelpusbetterunderstandthefunctionalnexusbetweenlncRNAs and epigenetic states of the chromatin. Towards this broader aim, we have optimizedchromatinRNAimmunoprecipitation(ChRIP),toprofilechromatinassociatedRNAtranscriptsfromdifferentchromatincompartmentsacrossthegenome.ByusingChRIPtechnique,wecharacterizedlncRNAsthatarefunctionallyassociatedwithactive(enrichedwithahistonemodificationH3K4me2andachromatinreaderandH3K4-specificmethyltransferaseWDR5)andinactive(enrichedwithahistone modification H3K27me3 and H3K27-specific methyltransferase EZH2) chromatincompartments.ByperformingmechanisticinvestigationsonahandfulofselectedcandidatesfromtheactiveandinactivechromatinassociatedlncRNAs,wehavecharacterizedmechanismsbywhichtheyinfluencetargetgeneexpressionincisortransviatargetingchromatinremodelers.

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A microarray screen identifies novel TGFβ-regulated long non-coding RNAs

PanagiotisPapoutsoglou1,YutaroTsubakihara1,Carl-HenrikHeldin1andAristidisMoustakas11DepartmentofMedicalBiochemistryandMicrobiology,ScienceforLifeLaboratory,UppsalaUniversity,Uppsala,Sweden

The transforming growth factor beta (TGFβ) signaling pathway plays crucial roles in embryonicdevelopment, cellular homeostasis and tumor progression. TGFβ signals via the activation ofeffectorSmadproteins,Smad2andSmad3,whicharephosphorylatedbythetypeITGFβreceptor.Smad2/3formcomplexwiththecommonSmad(Smad4)andtranslocateintothenucleus,engagingintheregulationofgeneexpression.Longnon-codingRNAs(lncRNAs)aretranscripts, longerthan200nucleotides, lacking inproteincodingpotential.Theymainlyparticipate in themodulationofgene expression at the transcriptional or post-transcriptional level by interacting with genomicregions,RNAmoleculesorproteins.AlthoughthebiologyoflncRNAshasbeenextensivelystudiedoverthelastyears,theirmechanismsoffunction,aswellastheirinvolvementinTGFβsignalingarenot fully understood. In this study, we aimed to elucidate novel lncRNAs, whose expression isregulatedbyTGFβsignaling.OurmicroarrayexperimentrevealedseveralTGFβ-targetlncRNAsandamongthem,wefocusedonthegeneadjacenttotheTGFB2locus,namedasTGFB2antisenseRNA1 (TGFB2-AS1),which is induced by TGFβ. Both Smad and protein kinase signaling pathways areimportantfortheinductionofTGFB2-AS1expression.UsingRNAinsituhybridizationweobservedapredominant nuclear localizationof the TGFB2-AS1 transcript.Depletionof TGFB2-AS1 enhancedthe TGFβ/Smad-mediated transcriptional responses, aswell as theexpressionof the TGFβ-targetgenes fibronectin, SMAD7 and PAI-1. On the other hand, cells stably over-expressing TGFB2-AS1showed reduced fibronectin and SMAD7expression levels.Moreover, TGFB2-AS1 attenuated theTGFβ-inducedcellgrowtharrestinhumanimmortalizedkeratinocytes.Collectively,weidentifiedanovelTGFβ-targetlncRNAwithaninhibitoryroleonTGFβsignalingoutput,suggestingthatTGFB2-AS1isapartofanauto-regulatorynegativefeedbackloopthatbalancesTGFβ-mediatedresponses.

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The Chromatin remodeling complex B-WICH is required for DNA Pol I transcription activation by glucose stimulation

Anna Rolicka1, Yuan Guo1, Antoni Zapater Ganez1, Jaclyn Quin1, Anna Vintermist1,FatemehSadeghifar1,MarieHenriksson2andAnn-KristinÖstlundFarrants11DepartmentofMolecularBiosciences,TheWenner-GrenInstitute,StockholmUniversity2DepartmentofMicrobiology,TumorandCellBiology,KarolinskaInstitute

The Chromatin remodeling complex B-WICHwith its core sub-units SNF2h, theWilliamSyndrome Transcription Factor (WSTF) and nuclear myosin (NM1), is involved intranscription of ribosomal genes and associates with the RNA pol I machinery in thenucleolus.InRNApolItranscription,B-WICHremodelschromatinlocallyatthepromoterregion andwhich leads to an increasedhistoneH3acetylation.Our recent results haveshown that B-WICH sub-unit WSTF plays an important role in glucose regulated rDNAtranscription. We have observed increased chromatin accessibility upon glucosestimulationwhichisnotobservableinabsenceofWSTF.Furthermore,wehaveobservedincreasedpresenceofthePolImachinery,H3HATSandc-MYCatrDNApromoterregion.Theunderlyingmechanismof the“closed”chromatinstate isnotknown.TheATPase inthesilencingcomplexNuRD(CHD4)whichrepressesrRNAtranscriptionwasstillpresentatthepromoteruponglucosestimulationinWSTFKDcells.

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Session II: Epigenetics in solid tumors Chair:AntoniaKalushkova

Gene regulatory defects in a pan-cancer cohort of 2,515 samples

HusenM.Umer1,JanKomorowski1,2,ClaesWadelius31ScienceforLifeLaboratory,DepartmentofCellandMolecularBiology,UppsalaUniversity,Uppsala,Sweden2InstituteofComputerScience,PolishAcademyofSciences,Warsaw,Poland3ScienceforLifeLaboratory,DepartmentofImmunology,GeneticsandPathology,UppsalaUniversity,Uppsala,Sweden

Thenoncodinggenomecontains thevastmajorityof somaticmutations identified froma cancergenome. While very few of the mutations are expected to be cancer drivers, those affectingregulatoryelementshavethepotentialtohavedownstreameffectsongenederegulationthatmaycontributetocancerprogression.Toidentifypotentialregulatorymutations,wescreenedsomaticmutations in a pan-cancer cohort of 2,515 cancerwhole genome sequences.We found a highlysignificant positive selection for regulatorymutations in transcription factor motifs across manycancer types. Overall, 10,806 mutated functional regulatory elements were identified in 2,263tumorsamplescontaining25,454candidatefunctionalregulatorymutations(CFRMs).409elementswerehighlyenrichedforsomaticmutations.OuranalysisindicatedsixorfewerCFRMspertumorin50%ofthesamplesandanaverageofelevenCFRMspertumor.Ourresultsprovideadetailedviewoftheroleofregulatorymutationsincancergenomes.

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Exosomes released by paediatric glioma stem cells induce gene expression changes in neural cells

ÁgotaTűzesi1,TeresiaKling1,AnnaWenger1,TaralRLunavat2,SuChulJang2,BertilRydenhag3,JanLötvall2,StevenM.Pollard4,AnnaDanielsson5andHelenaCarén11Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy,UniversityofGothenburg,Gothenburg,Sweden2KreftingResearchCenter,DepartmentofInternalMedicineandClinicalNutrition,UniversityofGothenburg,Gothenburg,Sweden3Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University ofGothenburg,Gothenburg,Sweden4MRCCentreforRegenerativeMedicine,UniversityofEdinburgh,EdinburghbioQuarter,5LittleFranceDrive,Edinburgh,UK5Sahlgrenska Cancer Center, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University ofGothenburg,Gothenburg,Sweden

Background:Most cells, including cancer stem cells, release different-sized vesicles that containgeneticmaterialandhavean importantrole incell–to-cellcommunication.Themoststudiedandsmallest in size of these extracellular vesicles are the exosomes.MicroRNAs (miRNAs) are smallnon-codingRNAs(19-25nucleotideslong)withmRNAsilencingfunction.MiRNAscanbeenclosedinextracellularvesiclesandtransferredfromcelltocell.A driving force behind pediatric high grade gliomas (HGG) is thought to be cancer stem cells.Epigeneticchanges,suchasthoseinducedbymiRNAs,haveanimportantroleinthegenerationandmaintenance of cancer stem cells. However, we have limited knowledge of the involvement ofexosomalmiRNAsreleasedbypediatricgliomastemcells(GSC) intothetumormicroenvironmentandtherebyinfluencingthepropertiesofneighboringcells.

Methods: We explored the expression of miRNAs in GSC and in exosomes derived therefrom,compared to normal neural stem cells (NSC) and corresponding exosomes, using miRNAmicroarrays. Further,we studied theGSC exosomalmiRNAs effect onNSCwith gene expressionanalysisusingTaqManLowDensityArray(TLDA)cards.

Results:Whereas cellular miRNAs were similar in normal and tumor cells, the exosomal miRNAprofiles differed, and our study identified several differentially expressed miRNAs. Of particularinterestismiR-1290andmiR-1246,whichhavepreviouslybeenlinkedto‘stemness’andinvasioninother cancers. We demonstrate that GSC-secreted exosomes influence the gene expression ofreceivingNSCs,particularlytargetinggeneswitharoleincellfateandtumorigenesis.

Conclusions:ThisstudyshowsthatGSCexosomescouldinfluencemalignantfeaturesofHGG.

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Orthotopic transplantation of pediatric glioma stem cells in mice mirrors the clinical course of the patient

AnnaWenger1,SusannaLarsson1,SandorDósa2,TeresiaKling1,HelenaCarén11Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy,UniversityofGothenburg2DepartmentofPathology,SahlgrenskaUniversityHospital

Background: The leading cause of cancer-related mortality among children is brain tumors andglioblastomamultiforme(GBM)hastheworstprognosis.Epigeneticderegulationisbelievedtobeadriver as these patients have few mutations compared to adults. New treatments are urgentlyneededbutfewpre-clinicalinvivomodelsexist.Oneapproachofgeneratingtheseistotransplanttumor tissue intomice, but it yields highly variable results and requires serial passaging inmice,which is time-consuming, expensive and ethically questionable.Wehave therefore established acellline-basedorthotopicmousemodelrepresentativeofthepatienttumor’smethylome.

Methods: Patient-derived cancer stem cell (CSC) lines from pediatric GBM were orthotopicallytransplanted into immunodeficient mice. The xenograft tumors were evaluated by histology forgliomafeatures.Genome-wideDNAmethylationanalysiswasperformedontheCSC,xenograftandpatienttumors.

Results:AllCSC lines initiated tumorsand thesurvivalof themicecorrelatedwith thesurvivaloftheirrespectivepatient.ThexenografttumorshadkeygliomafeaturesandwereclassifiedasGBMby histology andmethylation profiling. Themethylation profile of the xenograft tumor clusteredtogetherwith thepatient tumor (<3%ofCpG sites changedmethylation status) and the injectedCSCline.

Conclusions:Wehaveestablisheda robust and reproducible xenograftmodel forGBMbasedonprimaryCSClines.Thexenografttumorsaccuratelyreflectedthepatienttumorsandmirroredtheclinicalcourseofthepatient.Thismodelisthereforeidealforelucidatingthemethylome’sroleintumorsandaccuratelypredictingpatientresponseinpre-clinicalstudies.

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Session III: Epigenetics in hematological malignancies Chair:AndreasLennartsson

A distinct gene regulatory network, established independent of coding mutations, underpins the CLL phenotype

AleksandraKrstic1*,AylaDePaepe1*,CharlotteGustafsson1,KristinaSonnevi2,XaozeLi1,ShabnamKharazi1, Minna Taipale3, Minna Suomela1,2, Kenian Chen4, Malin Larsson5, Dag Ahrén6, RuthClifford7,EvaHellqvist1,EvaKimby1,2,YinLin4,AnnaSchuh8andRobertMånsson1,2*Theseauthorscontributedequallytothiswork1CenterforHematologyandRegenerativeMedicine,KarolinskaInstitutet,Stockholm,Sweden2HematologyCenter,KarolinskaUniversityHospital,Stockholm,Sweden3DepartmentofMedicalBiochemistryandBiophysics,KarolinskaInstitutet,Stockholm,Sweden4BaylorInstituteforImmunologyResearch,BaylorScott&WhiteResearchInstitute,Dallas5NBIS,LinköpingUniversity,Linköping,Sweden6NBIS,LundUniversity,Lund,Sweden7HaematologyDepartment,UniversityHospitalLimerick,Limerick,Ireland8DepartmentofOncology,UniversityofOxford,Oxford,UnitedKingdom

Chroniclymphocyticleukemia(CLL)patientspresentawiderangeofchromosomalaberrationsandmutations;still theyarepresentedwithaCLLphonotype.Hereweshowthat,despitethe lackofgeneticconsistency,wefoundaconsistentepigeneticsignatureforCLLusingChIP-seqandATAC-seq.Weidentifiedbothpromoter-proximalanddistalregulatoryelementswithhistoneChIP-seqforfreshlysortedperipheralbloodB-cells fromCLLpatientsandhealthycontrols.ToavoiddetectingnormalB-cellvariation,weuseduptofivedifferenthealthymatureB-cellpopulationstocontrastwith CLL. In this way we detected a set of CLL specific regulatory elements showing consistentchange between CLLs and our selection of normal B-cell populations. Linking these epigeneticchangeswiththeindividualsowngeneexpressiondeterminedbyRNA-seq,resultedinasetofCLLaberrant genes potentially deregulated by epigenetic changes. Based on ATAC-seq guidedmotifprediction in distal regulatory elementswith deviating activity in CLL,we generated networks ofpredictedchangesintranscriptionfactorusageandthegenesthesearepotentiallyderegulatinginCLL.Inaddition,ourdatacanalsodistinguishbetweentheusageofregulatoryelementsinthetwomajorCLLsubgroups,showingsignaturesspecificforIGHVmutatedandunmutatedCLL.Theresultis an exploration of regulatory elements in CLL and the proposed links these have to geneexpressionandtranscriptionfactorusage.

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Discovery of new molecular subgroups in pediatric ALL using DNA methylation classification and RNA-sequencing

YanaraMarincevic-Zuniga1,SaraNystedt1,SaraNilsson1,JohanDahlberg1,TrondFlaegstad2,MatsHeyman3, Kjeld Schmiegelow4, Kim Vettenranta5, Erik Forestier6, Gudmar Lönnerholm7, Ann-ChristineSyvänen1andJessicaNordlund11Dept.ofMedicalSciences,UppsalaUniversity2Dept.ofPediatrics,TromsøUniversityandUniversityHospital3ChildhoodCancerResearchUnit,KarolinskaInstitutet,AstridLindgrenChildren’sHospital,KarolinskaUniversityHospital4PediatricsandAdolescentMedicine,Rigshospitalet,and theMedicalFaculty, InstituteofClinicalMedicine,UniversityofCopenhagen5DivisionofHematology-OncologyandStemCellTransplantation,Children'sHospital,UniversityofHelsinki6Dept.ofMedicalBiosciences,UniversityofUmeå,7Dept.ofWomen’sandChildren’sHealth,UppsalaUniversity

Pediatricacutelymphoblasticleukemia(ALL)iscytogeneticallysub-groupedbasedonthepresenceoflarge-scalegenomicrearrangementssuchastranslocationsgivingrisetofusionsornon-randomgain/loss of chromosomes. Many of these alterations are recurrent in ALL and associated withsubtype-specific DNAmethylation (DNAm) profiles.We designedDNAm classifiers to predict thecytogeneticsubtypeofALLsamplesthatcomprisesevenofthecommonALLsubtypes1.

Herein, we evaluate the performance of the classifiers in an independent cohort of ALL patientsamples.Theclassifiersaccuratelypredictedsubtype-membershipof89%ofthesamples,achievingameansensitivityof0.91andspecificityof0.99.Wealsousedtheclassifierstoscreenforsubtype-membershipof116additionalALLpatientswithundefined/otherkaryotypesatdiagnosis(denotedBCP-other).Over60%ofthesecaseswerere-classifiedintoaknownsubtypebasedon“subtype-like” DNAm patterns. In depth analysis of “subtype-like” samples is currently on-going byintegrating theDNAmpredictionwith copynumberanalysis andRNA-sequencing.Moreover, thenewemergingsubgroupsinBCP-othercharacterizedbyfusionsinvolvingDUX4andZNF384arealsoassociatedwithdistinctDNAmprofiles2.WearedesigningandimplementingnewDNAmclassifierstoscreenforthesetwosubgroupsinBCP-otherpatients.

Together,ourDNAm-basedclassificationprovidesimproveddelineationoftheheterogeneousBCP-othergroup.Preliminary results fromtheclassifiers confirm thatDNAm isa robustandpowerfulepigeneticmarkerthatcouldserveasacomplementtocurrentdiagnosticmethods.TheclassifiercouldpotentiallybeusedasatooltodiscovernovelmolecularALLsubtypes.

1. NordlundJetal.,Clin.Epigenetics,20152. Marincevic-Zunigaetal.,J.Hematol.Oncol.,2017

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Genome-wide DNA methylation profiling in chronic lymphocytic leukemia patients carrying stereotyped B-cell receptors

Larry Mansouri1*, Sujata Bhoi1*, Giancarlo Castellano2, Lesley-Ann Sutton1, NikosPapakonstantinou3, Ana Queirós4, Panagiotis Baliakas1, Sara Ek5, Venera Kuci Emruli5, KarlaPlevova6,7, Stavroula Ntoufa3, Zadie Davis8, Emma Young1, Hanna Göransson-Kultima9, AndersIsaksson9, Karin E. Smedby10, Gianluca Gaidano11, Anton W. Langerak12, Frederic Davi13, DavideRossi14,DavidOscier8,SarkaPospisilova6,7,PaoloGhia15,EliasCampo2,KostasStamatopoulos3,José-IgnacioMartín-Subero4**andRichardRosenquist1,16**Contributedequally1DepartmentofImmunology,GeneticsandPathology,ScienceforLifeLaboratory,UppsalaUniversity,Sweden2HematopathologyUnit, Hospital Clinic, Institut d'Investigacions BiomèdiquesAugust Pi i Sunyer (IDIBAPS),University ofBarcelona,Barcelona,Spain3InstituteofAppliedBiosciences,CentreforResearchandTechnology-Hellas,Thessaloniki,Greece4Biomedical Epigenomics Group, Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), University ofBarcelona,Barcelona,Spain5DepartmentofImmunotechnology,LundUniversity,Sweden6DepartmentofInternalMedicine–HematologyandOncology,UniversityHospitalBrnoandFacultyofMedicine,MasarykUniversity,Brno,CzechRepublic7Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, CzechRepublic8DepartmentofMolecularPathology,RoyalBournemouthHospital,UK9DepartmentofMedicalSciences,CancerPharmacologyandComputationalMedicine,UppsalaUniversity,Sweden10DepartmentofMedicine,ClinicalEpidemiologyUnit,KarolinskaInstitutet,Stockholm,Sweden11DivisionofHematology,DepartmentofTranslationalMedicine,UniversityofEasternPiedmont,Novara,Italy12DepartmentofImmunology,ErasmusMC,UniversityMedicalCenterRotterdam,theNetherlands13Pitie-SalpetriereandUniversityPierreandMarieCurie,Paris,France14Hematology Department, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona,Switzerland15DivisionofExperimentalOncology,UniversitàVita-SaluteSanRaffaeleandIRCCSSanRaffaeleScientificInstitute,Milan,Italy16DepartmentofMolecularMedicineandSurgery,KarolinskaInstitutet,Stockholm,Sweden.

Inrecentyears,subsetsofchroniclymphocyticleukemia(CLL)patientscarryingstereotypedB-cellreceptors(BcRs)havebeenidentifiedthatshareclinicobiologicalfeaturesandoutcome.Using450Kmicroarrays, we investigated 176 CLL cases assigned to 8 major subsets including the clinicallyaggressive IGHV-unmutated(U-CLL)subsets#1,#3,#5,#6,#7and#8,the indolent IGHV-mutated(M-CLL) subset #4, as well as subset #2, which displays mixed IGHV mutation status and pooroutcome. In addition, we included non-subset CLL (n=325), subgrouped based on the recentlyproposedepigeneticclassificationofCLL,i.e.naïve-likeCLL(n-CLL),memory-likeCLL(m-CLL),andathird intermediate CLL subgroup (i-CLL), as well as sorted normal B-cell populations at differentstages of differentiation. Overall, unsupervised analysis revealed that all U-CLL subsets clusteredwith n-CLL, subset #4 clustered with m-CLL, while subset #2 clustered separately with i-CLL.Accordingly, supervised analysis revealed a limited number of CpG sites that were differentiallymethylated when comparing each U-CLL or M-CLL subset versus non-subset cases. In contrast,almost all subset #2 cases clustered separately from i-CLL, indicating that this subset mightrepresent a distinct subgroup of i-CLL. Additionally, we observed significant differences inepigenetic‘burden’insubset#1and#2vs.non-subsetcases,inlinewiththeirverypooroutcome.Inconclusion,whileU-CLLandM-CLLsubsetsgenerallyclusteredwithn-CLLandm-CLLcategories,respectively,implyingcommoncellularorigins,subset#2emergedasthefirstdefinedmemberofi-CLL,whichalludestoadistinctcellularoriginforthissubgroupofpatients.

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Epigenetic co-regulation as a potential therapeutic target in multiple myeloma

AlbaAtienzaPárraga1,KlevDiamanti2,AronSkaftason1,LoganLaurent1,MohammadAlzrigat1,AnqiMa3,JianJin3,JoséIgnacioMartín-Subero4,AndreasLennartsson5,JanKomorowski2,FredrikÖberg1,HelenaJernberg-Wiklund1*andAntoniaKalushkova1**Indicateslastco-authors1Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratoriet, UppsalaUniversity,Uppsala,Sweden2Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala Biomedicinska Centrum, UppsalaUniversity,Uppsala,Sweden3DepartmentsofPharmacologicalSciencesandOncologicalSciences, IcahnSchoolofMedicineatMountSinai,NewYork,NY,USA4Department of Pathology, Hematopathology Section, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi iSunyer(IDIBAPS),UniversityofBarcelona,Barcelona,Spain5DepartmentofBiosciencesandNutrition,KarolinskaInstitutet,Stockholm,Sweden.

Although multiple myeloma (MM) is a largely heterogeneous malignancy, we found anunderexpressed gene profile enriched in H3K27me3 targets as a common denominator amongpatients.WehavethereforeevaluatedtheimpactofH3K27me3genesilencinginMM,aswellasitsmoleculartargetsandtheroleofotherpotentialepigeneticcollaborators.RemovalofH3K27me3viaEZH2 inhibition led toapoptosis inMMcells.Among the reactivated targets,we foundgeneswithaknowntumorsuppressorfunctioninMMaswellasmiRNAsshowntobeunderexpressedinMM.InsilicopredictionidentifiedtheIRF4,BLIMP1andXBP1genes,withoncogenicrolesinMM,as targets of the reactivated miR-125a-3p and miR-320c. Strikingly, integrative analysis of theH3K27me3 targets and gene expression data showed that only bivalent genes (i.e. marked byH3K27me3 and H3K4me3) became active upon EZH2 inhibition, pointing towards additionalsilencingmechanisms.DNAmethylationandH3K27me3co-localizedatB-cellenhancers,suggestinga role of these two machineries at regulatory regions in MM. Combined treatment with DNAdemethylating agents and an EZH2 inhibitor synergistically reduced MM proliferation. Our datahighlightthemultifacetedroleofH3K27me3,aloneorincollaborationwithotherepigeneticmarks,ingeneregulationinMM

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KEYNOTE SPEAKER

HenkStunnenberg

Henk Stunnenberg is full professor at the Science andMedical facultyand head of theDepartment ofMolecular Biology andDirector of theRadboud Institute forMolecular Life Sciences of the Science faculty atRadboudUniversity,Nijmegen.HeismemberofEMBO,wasthechairofScientific Steering Committee of the International Human EpigenomeConsortium(IHEC),heisamemberoftheCouncilofScientistsofHumanFrontier Science Program Organization (HFSPO), Program Committeemember for the International Cancer Genome Consortium (ICGC) and

memberoftheOrganizingCommitteeoftheHumanCellAtlas.

Hisresearchaimsatunravelingthemolecularbasisofdevelopmentanddifferentiationemanatingfromthegenomeandepigenomeinthecontextofhealthanddiseasewithemphasisoncancerandmostrecentlyonimmunedisease.State-of-the-arttechnologicaldevelopmentsareappliedrangingfrom single molecule studies through to genome wide elucidation of genetic and epigeneticpathwaysandmechanisms.Heaimstodefinethequantitativeframeworkaroundthedynamicsoftheepigenomeanditsdeterminantsandtheirtranslationintoregulatorymodelsofdiseases.

Immune memory

Innate immunememory is thephenomenonwhereby innate immunecells suchasmonocytesormacrophagesundergofunctionalreprogrammingafterexposuretomicrobialcomponentssuchasLPS.Weappliedanintegratedepigenomicapproachtocharacterizethemoleculareventsinvolvedin LPS-induced tolerance in a time dependent manner. Our hypothesis-free analyses identifiedspecificpathwaysdysregulatedinnaïvemacrophagesandsuchderivedfrommonocytesexposedtoLPS. Transcriptional inactivity in response to a second LPS exposure in tolerizedmacrophages isaccompaniedwith failure todepositactivehistonemarksatpromotersof tolerizedgenes.Takentogether,weunveiledthatinnateimmunememoryinmonocytesandmacrophagesiswrittenintheepigenome.

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Session IV: Epigenetics and immunity Chair:GoncaloCastelo-Branco

Reactivation potential of HIV-1 in primary CD4 T cells depend on the chromatin microenvironment

J.PeterSvensson11DepartmentofBiosciencesandNutrition,KarolinskaInstitutet

OnceHuman ImmunodeficiencyVirus-1 (HIV-1) infectsa cell, theviral genomecan integrate inahostchromosome.Upon integration, theviral sequence ispackaged intochromatin,and insomecells, the proviral chromatin then becomes silenced.When the viral proteins are degraded, thelatentcell is indistinguishable fromanuninfectedcellandescapes the immunesystemaswellascurrent drugs. However, using host factors, at any time can the provirus reactivate andsubsequentlyre-infectneighboringcells.ThisreservoiroflatentlyinfectedcellsisthemainobstacletoacureforHIV/AIDS.

Wehavedetermined that theepigeneticmicroenvironmentprovidesapredictor for viral latencyreversal. Using primary CD4+ T lymphocytes infected with a reporter virus, we are able todistinguish between productive, reactivatable latent and truly latent cell populations. We havefollowed the maturation of proviral chromatin during the months following infection anddetermined how it affects the reactivation potential of the provirus. We also identified HIV-1integrationsitesbysequencingtheflankinghostregionsandfoundthatthethreepopulationsarefoundindistinctchromatinsettings.Whereasthetruly latentprovirusesare integratedinregionsmarked by several heterochromatic marks, the reactivatable portion is integrated in sites moreoftenassociatedwithactivechromatinmarks.

These results are important in that theyprovide clues to improve therapyofoneof the globallymostdevastatinghuman infections today. Insteadof focusingoneliminating theentire reservoir,focus may instead be shifted to finding drugs targeting the distinct cell population with areactivatableprovirus.

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Major transcriptional changes observed in the Fulani, an ethnic group less susceptible to malaria

JaclynQuin1*,IoanaBujila1*,MariamaChérif2,3,GuillaumeS.Sanou2,YingQu4,ManijehVafa5,AnnaRolicka1¤,SodiomonB.Sirima2,MaryA.O’Connell6,AndreasLennartsson4,MaritaTroye-Blomberg1,IssaNébié2andAnn-KristinÖstlundFarrants1*Theseauthorscontributedequallytothiswork.1DepartmentofMolecularBiosciences,TheWenner-GrenInstitute,StockholmUniversity2CentreNationaldeRechercheetdeFormationsurlePaludisme,BurkinaFaso3UniversitéPolytechniquedeBoboDioulasso,BurkinaFaso4DepartmentofBiosciencesandNutrition,KarolinskaInstitute5InfectiousDiseasesUnit,DepartmentofMedicine,KarolinskaInstitute6CentralEuropeanInstituteofTechnology,CzechRepublic

The Fulani ethnic grouphas relatively better protection fromPlasmodium falciparummalaria, asreflectedbyfewersymptomaticcasesofmalaria,lowerinfectionrates,andlowerparasitedensitiescomparedtosympatricethnicgroups.However,thebasisforthislowersusceptibilitytomalariabytheFulaniisunknown.TheincidenceofclassicmalariaresistancegenesarelowerintheFulanithaninothersympatricethnicpopulations,andtargetedSNPanalysesofothercandidategenesinvolvedinthe immuneresponsetomalariahavenotbeenabletoaccount fortheobserveddifference inthe Fulani susceptibility toP.falciparum. Therefore,wehaveperformedapilot study to examineglobaltranscriptionandDNAmethylationpatternsinspecificimmunecellpopulationsintheFulanitoelucidatethemechanismsthatconferthelowersusceptibilitytoP.falciparummalaria.Whenwecompared uninfected and infected Fulani individuals, in contrast to uninfected and infectedindividuals from the sympatric ethnic group Mossi, we observed a key difference: a strongtranscriptionalresponsewasonlydetectedinthemonocytefractionoftheFulani,whereover1000genesweresignificantlydifferentiallyexpresseduponP.falciparuminfection.

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Enhancer regulation by GPS2 modulates macrophage inflammation

ZhiqiangHuang1,SaioaGoñi1,MinnaU.Kaikkonen2,RongrongFan1,AnastasiosDamdimopoulos1,TomasJakobsson1,CliveD’Santos3,JasonCarroll3,NicolasVenteclef4,EckardtTreuter11Department of Biosciences and Nutrition, Center for Innovative Medicine (CIMED), Karolinska Institutet, CampusFlemingsberg,14157Huddinge,Sweden2A.I.VirtanenInstitute,UniversityofEasternFinland,70211Kuopio,Finland3CancerResearchUKCambridgeInstitute,UniversityofCambridge,CB20RE,UK4SorbonneUniversités.UniversitéPierreetMarie-Curie,INSERM,Paris,France

Transcriptionfactorsandco-regulatorscoordinatemacrophageinflammation.Ourrecentworkhasidentified a key role of a GPS2-containing co-repressor complex in suppressingmetabolic stress-induced macrophage inflammation via epigenomic mechanisms1. In the current study, wesystemically investigated the role of enhancers in GPS2-mediated repression with a particularemphasisonCcl2(Mcp-1).ChIP-seqandmicroarraydataindicatethatGPS2isrecruitedtoenhancerlociofmostup-regulatedgenesinGPS2KOmacrophages.GPS2wasreleasedupontreatmentwithLPS (a TLR4 agonist) at those enhancers. GPS2 ablationwas correlatedwith increased enhanceractivity, as judged by measuring H3K27 acetylation (by ChIP-seq) and enhancer RNA (eRNA)expression (by GRO-seq). We further identified the functionally important GPS2-regulatedenhancers at theCcl2 locusbydepleting specific enhancersusingCRISPR/Cas9.DepletionofonedistalenhancerledtoreducedH3K27acetylationatallotherCcl2enhancers,alongwithdecreasedeRNA expression, suggesting interaction of these enhancers. Intriguingly, inhibition of oneenhancer-derived eRNA (by antisense LNA GapmeR) significantly abolished LPS-induced Ccl2transcriptionandhadamajor impacton theGPS2KOeffectsat theCcl2 locus.Overall,ourdatasuggesttheinvolvementofeRNAsinmodulatingpro-inflammatorygeneresponsesinmacrophageswith a specific role of the GPS2 co-repressor complex in regulating eRNA expression at keyenhancers.

1. Fan,R.,Toubal,A.,Goni,S.,Drareni,K.,Huang,Z.,Alzaid,F.,Ballaire,R.,Ancel,P.,Liang,N.,Damdimopoulos,A.,et al. (2016). Lossof the co-repressorGPS2 sensitizesmacrophageactivationuponmetabolic stress inducedbyobesityandtype2diabetes.NatMed22,780-791.

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Utilizing epigenomics to understand neurodegeneration in Multiple Sclerosis: what are the neurons telling us?

Lara Kular1, Maria Needhamsen1, Milena Z Adzemovic1, Tatiana Kramarova1, David Gomez-Cabrero2,EwoudEwing1,JesperTegnér2,FredrikPiehl1,LouBrundin1andMajaJagodic11DepartmentofClinicalNeuroscience,CenterforMolecularMedicine,KarolinskaInstitutet,Stockholm,Sweden2Department ofMedicine, Unit of ComputationalMedicine, Center forMolecularMedicine, Karolinska Institutet, Solna,Sweden.

MultipleSclerosis(MS)isachronicinflammatorydiseasecharacterizedbyautoimmunedestructionofmyelin andneurons in the central nervous system. Today,MS is oneof the leading causesofneurologicaldisabilityinyoungadults.Currenttreatmentsactbroadlyontheimmunesystemandtheyareeffective incontrolling the inflammatorystageofdiseasewhile thereareno treatmentsthatprevent sustainedneuronal lossanddiseaseprogression.Although thecauseofMSremainsunknown,vastepidemiologicaldataestablishMSasacomplexdisease influencedbygeneticandenvironmentalfactors.Epigeneticmechanisms,suchasDNAmethylation,orchestrateactivityofthegenome in response to environmental cues and may provide better understanding of diseasepathogenesis.OneofthemainchallengeswithstudyingdiseasessuchasMSisthelimitedaccesstothe target tissue - the brain. Recent progress in development of methods to survey epigeneticmodifications,and fromthem infergenomeactivity,openeduppossibilities to studybrain tissueandmechanismsthatunderlieneuronallossinMSpatients.

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Friday, December 1st 2017

Session V: Understanding Epigenetics II Chair:SebastianDeindl

Invitedspeaker:

YuriB.Schwartz

Dr. Yuri Schwartz is associate professor of genetics at the Department ofMolecular Biology, Umeå University. He produced one of the best high-resolutiongenome-widemapsofPolycombregulationinDrosophilaandmadeimportantcontributionstounderstandcross-talkbetweendifferentPolycombcomponents in flies and human cells. He co-founded the EpiCoN initiative(Epigenetic Cooperation Norrland, www.epicon.nu), which aims to fostergroundbreakingepigeneticsresearchinNorthernSweden.

Deciphering the cooperativity of Polycomb repression

TatyanaG.Kahn,SarinaR.Cameron, Juan I.Barrasa,EshaghDorafshan, JanaŠmigová,AlexanderGlotovandYuriB.SchwartzDepartmentofMolecularBiology,UmeåUniversity,Sweden

Polycombproteins are epigenetic repressors that regulatemanyof the same keydevelopmentalgenes in insectsandvertebrates.Polycombproteinsact inconcertas largecomplexesofthetwotypes: PRC1 and PRC2. The lattermethylate Lysine 27 of histoneH3 (H3K27) and tri-methylatedH3K27transmitsepigeneticmemoryoftherepressedstatewhencellsdivide.HowthepresenceofH3K27me3translatesintoadvantagefortherepressionisnotveryclear.WorkingwithDrosophilamodel,wefindthatH3K27me3isnotessentialtotargetPRCcomplexestospecificgenes.InsteadithelpsPRCcomplexesanchoredatPolycombResponseElements(PREs)tointeractwithsurroundingchromatin.WealsofindthatPRC1canbindPREsintheabsenceofPRC2but,atmostPREs,PRC2requiresPRC1tobetargeted.OurstudiesonhumanculturedcellsfurthersuggestthattargetingofPRC1bycompactDNAelements isanevolutionarilyold featureofPolycombrepression.We findthatcoordinatedrecruitmentofmammalianPRC1andPRC2complexesinvolvesacombinationofaspecialized PRC1 targeting element (PTE) and an adjacent CpG-island, which together act asmammalianPolycombResponseElements.

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Targeting Polycomb repressive complexes through evolutionary conserved DNA elements

BarrasaJI1,KahnTG1,CameronSR1,RusseilJ1,DeplanckeB1,SchwartzYB11DepartmentofMolecularBiology,UmeåUniversity,Sweden

Polycomb group proteins are transcriptional repressors with a key role in the development ofmulticellular organisms.Miss-expression of Polycomb proteins is known to cause developmentalabnormalities and is also linked to several types of cancer. Polycombproteins formmultiproteincomplexes to repress transcriptionat specific targetgenes,but themechanisms involved in theirrecruitmentinmammalsarepoorlyunderstood.First,andincontrasttothewell-knownDrosophilaPolycomb Response Elements (PREs), no specific DNA elements have been identified to recruitmammalian Polycomb complexes. And second, considering that is unclear whether Polycombproteins can themselvesbindDNA,noDNAbindingpartnershavebeenunambiguously linked tothetargetingofPolycombcomplexes.ThehistonemodificationsdepositedbyPolycombRepressiveComplexes1and2(PRC1andPRC2),H2AK119UbandH3K27me3respectively,areassociatedwithtranscriptionalrepressionbutneitherofthemissufficienttorecruitPRCcomplexestotheirtargetgenes.

WehaverecentlyestablishedtheCyclinD2(CCND2)oncogeneasamodeltounravelsomeofthesequestions1.Wehaveidentifieda1kbDNAelementupstreamofthehumanCCND2genepromoterthat autonomously recruits PRC1 but very little PRC2. This PRC1 targeting element (PTE), incollaborationwithaproximalCpG islandspecialized inPRC2 recruitment, resembles the functionand modular structure ofDrosophila PREs. Here we demonstrate that these DNA elements areevolutionary conserved inmouse anduse this system to identify potentialDNAbindingpartnersinvolvedintherecruitmentofPRCcomplexestotheirtargetgenes.

1. Cameron SR,Nandi S, Kahn TG, Barrasa JI, Stenberg P, Schwartz YB. 2017.PTE, a novelmodule ofmammalianPolycombResponseElements.bioRxivdoi:https://doi.org/10.1101/177097

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Developmental patterning and gene regulation by the BEN-solo family

JiayuWen1,MalinUeberschär3,BrianJoseph1,TsutomuAoki2,PaulSchedl2,EricLai1,QiDai31ProgrammeofDevelopmentalBiology,MemorialSloanKetteringInstitute2DepartmentofMolecularBiology,PrincetonUniversity3DepartmentofMolecularBioscience,theWenner-GrenInstitute,StockholmUniversity

Background:Geneexpression is regulatedbythe interplaybetweenchromatin factors,sequence-specifictranscriptionfactors(TFs)andgeneraltranscriptionmachinery.Westudyanovelfamilyofproteins, the BEN-solo family that can not only act as TFs but also as insulator proteins. The flygenome encodes three BEN-solo proteins, namely Insensitive (Insv), Bsg25A (Elba1) and CG9883(Elba2).InsvpromotessensoryorgandevelopmentthroughinteractingwithNotchsignaling,anditcanbind toa specificpalindromicDNAsequence tomediate transcriptional repression.AlthoughElba1andElba2areabletobindthesameInsvmotif,theyalsoheterotrimerizewiththeirobligateadaptorElba3torecognizeasimilarbutasymmetricmotifintheFab-7insulator.

Results: Using genome-wide approaches, we found that the binding regions of the three Elbaproteins overlap throughout the genome. Different from Insv binding loci that represent classicenhancer-type, Elba-bound regions are enriched for active histone marks at promoters and +1nucleosomes.As+1nucleosomewasshowntoregulateRNApolymeraseIIpausing,wecomparedElba-occupied regionswith paused promoters, and found high correlation between Elba bindingandpausing.CandidatetargetgenesboundbyElbabecameup-regulatedinelbamutants.

Conclusions:We separated the functionalities between Insv and the Elba type of BEN proteins,Elba1andElba2.Unexpectedly,wefoundthattheElbacomplexmayinteractwith+1nucleosomestoregulatetranscription(and/ortofunctionas insulators).WespeculatethatbindingbytheElbaproteins may be a novel type of mechanisms that regulates Pol II activities (e.g., pausing) intranscription.

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Session VI: Epigenetics across species Chair:Ann-KristinÖstlundFarrants

Ectopic application of H3K9me2 establishes postzygotic reproductive isolation in Aradibopsis

HuaJiang1,JordiMoreno-Romero1,JuanSantos-González1andClaudiaKöhler11DepartmentofPlantBiology,UppsalaBioCenter,SwedishUniversityofAgriculturalSciencesandLinneanCenterforPlantBiology,Uppsala,Sweden

Understanding themechanisms bywhich populations become reproductively isolated is amajorgoal of evolutionary biology. Postzygotic reproductive isolation in response to hybridizations ofplants thatdiffer inploidy (interploidyhybridizations) is amajorpath for sympatric speciation inplants. This mechanism is manifested in the endosperm, a dosage sensitive tissue supportingembryogrowth.Deregulatedexpressionofapaternally-expressedimprintedgene(PEG),ADMETOS(ADM), underpin the interploidy hybridization barrier in the endosperm inArabidopsis thaliana1.Moreover,threeadditionalPEGs,SUVH7,PEG2,andPEG9werealsofoundtoestablishinterploidyhybridizationbarriersintheendosperm2,revealingthatPEGsplayamajorroleasspeciationgenesin plants. However, themechanisms of their action remained unknown. Here, I will discuss ourlatestfindingthatADMinteractswithanAT-richDNAbindingproteinandectopicallyrecruitstheheterochromatic mark H3K9me2 to AT-rich transposable elements (TEs), causing deregulatedexpressionofneighboringgenes3.OurdatasuggeststhatreproductiveisolationasaconsequenceofepigeneticregulationofTEsisaconservedfeatureinanimalsandplants.

1. KradolferD,WolffP,JiangH,SiretskiyA,KöhlerC.(2013).AnimprintedgeneunderliespostzygoticreproductiveisolationinArabidopsisthaliana.DevCell.26:525-535.

2. Wolff P, Jiang H,Wang G, Santos-Gonzàlez J, Köhler C (2015). Paternally expressed imprinted genes establishpostzygotichybridizationbarriersinArabidopsisthaliana.eLife.10074.

3. JiangH,Moreno-RomeroJ,Santos-GonzálezJ,DeJaegerG,GevaertK,VanDeSlijkeE,KöhlerC. (2017).Ectopicapplication of the repressive histone modification H3K9me2 establishes post-zygotic reproductive isolation inArabidopsisthaliana.Genes&Dev.31:1272-1287.

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Imprinted gene regulation by the paternally expressed gene PHERES1 in Arabidopsis thaliana

Rita A. Batista1, DuarteD. Figueiredo1, JordiMoreno-Romero1, Charlotte Siemons1, Juan Santos-González1andClaudiaKöhler11DepartmentofPlantBiology,UppsalaBioCenter,SwedishUniversityofAgriculturalSciencesandLinneanCenterforPlantBiology,Uppsala,Sweden

In flowering plants, seed development is initiated by the fertilization of the maternal egg andcentral cells by two paternal sperm cells, leading to the formation of the embryo and theendosperm,respectively.Theendospermisaproliferatingtissuethatnourishestheembryoduringits development, thus being functionally analogous to the mammalian placenta. Contrary tomammals,genomicimprintinginfloweringplantsseemstoberestrictedtotheendospermanditsdisruption is correlated with failure of endosperm development, which consequently leads toembryoarrest.Therefore,it is importanttounderstandindetailthemechanismsestablishingandregulatinggenomicimprinting.

In this work we found that dysregulation of PHERES1, a MADS-box transcription factor and apaternallyexpressedgene(PEG),iscorrelatedwithendospermfailureandthereforewesetouttocharacterize the functions of this PEG. We found that PHE1 controls the expression of otherimprintedgenes,especiallyPEGs,providinganexampleofimprintedtrans-regulationofimprintedgenes. In the particular case of PEG targets, we observe that the binding of PHERES1 occurs innarrow regions devoid of DNA methylation and repressive histone marks in the otherwiseepigeneticallyrepressedmaternalallele.WealsoobservethatPHERES1bindingsitesarefrequentlycontained in transposable elements, specifically in RC/Helitrons, which have been previouslyimplicated in imprinting establishment. Thus, this work provides evidence for moleculardomestication of transposable elements, and adds a layer of complexity in imprinted generegulation.

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Genetic dissection of Drosophila HDAC3 function

MinTang1,OlgaShilkova1andMattiasMannervik11DepartmentofMolecularBiosciences,TheWenner-GrenInstitute,StockholmUniveristy

Controloftranscriptionestablishesthegeneexpressionprogramsthatdefineacellanddirectscelldifferentiation. Histone deacetylases (HDACs) influence transcriptional regulation by catalyzingdeacetylationofhistones.Here,wetakeadvantageofDrosophilaasanexcellentmodeltostudythebiological function of HDAC3 in early embryo patterning and in brain development. The histonedeacetylaseHDAC3isbelievedtoregulategenetranscriptionbyitscatalyticactivityandbyformingacomplexwiththeco-repressorNCoR/SMRT.Usingtransgenicknock-downofHDAC3inthefemalegermline, we showed that depletion of maternal HDAC3 caused a failure in embryo hatching,various cuticle defects, and de-repression of sog gene expression in the mesoderm where it isnormally silenced by the Snail repressor. The phenotypes were partially rescued by a miRNA-resistantwttransgene.Site-directedmutagenesisofHDAC3wasperformedtodistinguishbetweena catalytic function and complex formation with the co-repressor NCoR/SMRT. Three differentmutations have been introduced based on mammalian HDAC3. A Y303F mutation renders theenzymeinactive,butdoesnotaffecttheinteractionbetweenHDAC3andthedeacetylaseactivationdomain (DAD) inNCoR/SMRT.TheK26Amutationandacombinationofmutations (HEBI)disruptthe interaction with DAD to different extents, and also impair deacetylase activity. These site-directedmutantmiRNAresistanttransgenesrescuedtheHDAC3phenotypetodifferentlevels.WealsogeneratedaHDAC3nullmutantaswellassite-directedknock-inmutants,andcharacterizedanopticlobephenotypeinthird-instarlarvalbrainsfromthedifferentmutants.Together,ourresultsshow thatHDAC3 function is not redundantwith other histonedeacetylases, but is essential forspecificdevelopmentalprocesses,andpartiallyindependentofcatalyticactivity.

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C12D8.1: A negative regulator of RNAi inheritance in Caenorhabditis elegans

BenjaminHolmgren1,LinneaBäckström1,YaniZhao1,andAndreaHinas11DepartmentofCellandMolecularBiology,UppsalaUniversity

InthenematodeCaenorhabditiselegans,RNAinterference(RNAi),sequence-specificgenesilencingmediatedbysmallRNAs,canbepassedonfromparenttooffspring.InheritanceofexogenousRNAiis limited, leading to progressivelyweaker silencing and restoration of target gene expression topre-silencing levels within a few generations. This loss of silencing has been suggested to beimportant forkeepinggeneexpressionplasticity,enablinganimals toquicklyadapt tochanges inthe environment. However, very little is known about the underlyingmechanisms that regulatepersistence of inheritance. In this study, we initially used bacteria-mediated (feeding) RNAi tosilenceasetofsevengenesidentifiedinayeasttwo-hybridscreenusingtheRNAtransportproteinSID-5 as bait. Target gene knockdown was followed by feeding RNAi against body wall muscle-expressed GFP, where three out of seven tested genes displayed reduced GFP RNAi efficiencycomparedtocontrolanimals.Oneofthesegenes,C12D8.1,waschosenforfurtherstudies.C12D8.1encodes a putative RNA- binding protein of the conserved Far upstream binding protein (FBP)family, which affects transcription and RNA metabolism in mammals. We found that aC12D8.1::mCherrytranslationalfusionproteincanlocalizetoboththenucleusandtocytoplasmic,oftenperinuclear,foci.Uponfurther investigationoftheeffectofC12D8.1onRNAiefficiency,wediscovered that twostrainscarryingdifferentputative lossof functionC12D8.1mutationsdonotphenocopytheC12D8.1RNAiknockdown,but insteaddisplayenhancedRNAi.Aseriesof feedingRNAiexperimentsindicatethatC12D8.1mutantshavestrongerinheritanceofexogenousRNAithanwildtypeworms.However,C12D8.1mutantswithinheritedRNAiwillmountaweakerresponsetoasecondroundofRNAiagainstadifferenttargetgene.Takentogether,thissuggeststhatC12D8.1negatively regulates inheritance of RNAi, thereby facilitating a dynamic epigenetic response tochangesintheenvironment.

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KEYNOTE SPEAKER

JasonErnst

Jason Ernst joined the faculty atUCLA in theDepartment of BiologicalChemistry, the Computer Science Department, and the BioinformaticsProgramin2012.Priortothat,hewasapostdoctoralfellowinManolisKellis' Computational Biology Group in the Computer Science andArtificial Intelligence Laboratory at MIT and affiliated with the BroadInstitute. In 2008, Jason completed a PhD advised by Ziv Bar-Josephwhere he was part of the Systems Biology Group, Machine LearningDepartment, and School of Computer Science at Carnegie Mellon

University.HeisamemberoftheeditorialboardatGenomeResearchandhasbeenaprogramco-chair for the ISMB Regulatory Genomics Special Interest Group (RegGenSIG) meeting. He is arecipientofaSloanFellowship,NIH-AvenirAward,NSFCareerAward,NSFPostdoctoralFellowship,aSiebelScholarship,andaGoldwaterScholarship.

Computational Epigenomic Approaches for Deciphering the Non-coding Human Genome Understanding the human genome sequence and in particular the vast non-coding regions is acentralchallengeformodernmolecularbiologywithprofoundimplicationstowardsunderstandingthegeneticbasisofdisease.WhileunderstandingthegenomebydirectlyreadingtheprimaryDNAsequenceisextremelychallenging,thepresenceofepigeneticmarksontopofthesequenceholdsgreatpromisetoaidourunderstandingofthegenome.Technologicaladvancesinsequencinghasmadeitpossibleinasingleexperimenttogeneratetensofmillionsofdatapointsonthelocationofaepigeneticmarkacrossthegenomeinaspecificcelltype,whichraisesanumberofcomputationalchallengesandopportunities.InthistalkIwillfirstdescribeamethodthatIpreviouslydeveloped,ChromHMM, that learns de novo combinatorial and spatial patterns from maps of multipleepigeneticmarksusingamultivariatehiddenMarkovmodel.Thesepatternscorrespondtodifferentclassesofgenomicelements,which Ihavethenusedtoprovideacell typespecificannotationofthe human genome. I will then describe a combined computational modeling and experimentalapproach,Sharpr-MPRA,that inhigh-throughputcantestputativeregulatoryelementsof interestidentified based on epigenomics patterns and identify within them at high resolution basesactivatingorrepressinggeneexpression.Finally,Iwilldescribeamethod,ChromImpute,toimputemapsofepigeneticmarksthatIhaveappliedinthecontextoftheRoadmapEpigenomicsprojecttocomputationally predict over 4000 epigenomic datasets vastly accelerating the coverage of thehuman epigenome while providing overall more robust maps than have been obtainedexperimentally.

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Session VII: Epigenomics Chair:JanKomorowski

Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1 MolecularCell,inpress

LauraC.Lehmann1,3,GraemeHewitt2,3,ShintaroAibara4,AlexanderLeitner5,EmilMarklund1,SarahL.Maslen6,VarunMaturi7,YangChen1,DavidvanderSpoel8,J.MarkSkehel6,AristidisMoustakas7,SimonJ.Boulton2,*,andSebastianDeindl1,9,*1DepartmentofCellandMolecularBiology,ScienceforLifeLaboratory,UppsalaUniversity,75124Uppsala,Sweden2TheFrancisCrickInstitute,1MidlandRoad,LondonNW11AT,UK3Theseauthorscontributedequally4DepartmentofBiochemistryandBiophysics,ScienceforLifeLaboratoryandStockholmUniversity,10691Stockholmand17121Solna,Sweden5Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology, 8093 Zürich,Switzerland6MRCLaboratoryofMolecularBiology,FrancisCrickAvenue,CambridgeBiomedicalCampus,CambridgeCB20QH,UK7Department of Medical Biochemistry and Microbiology, and Ludwig Institute for Cancer Research, Science for LifeLaboratory,UppsalaUniversity,75123Uppsala,Sweden8DepartmentofCellandMolecularBiology,ComputationalBiologyandBioinformatics,UppsalaUniversity,75124Uppsala,Sweden9LeadContact

HumanALC1isanoncogene-encodedchromatin-remodelingenzymerequiredforDNArepairthatpossessesapoly(ADP-ribose)(PAR)-bindingmacrodomain. ItsengagementwithPARylatedPARP1activatesALC1atsitesofDNAdamage,buttheunderlyingmechanismremainsunclear.Here,weestablishadualroleforthemacrodomaininauto-inhibitionofALC1ATPaseactivityandcouplingto nucleosome mobilization. In the absence of DNA damage, an inactive conformation of theATPase ismaintainedby juxtapositionofthemacrodomainagainstpredominantlytheC-terminalATPase lobethroughconservedelectrostatic interactions.Mutationswithinthis interfacedisplacethemacrodomain,constitutivelyactivatetheALC1ATPaseindependentofPARylatedPARP1,andalter the dynamics of ALC1 recruitment at DNA damage sites. Upon DNA damage, binding ofPARylated PARP1 by the macro domain induces a conformational change that relieves auto-inhibitory interactionswith theATPasemotor,which selectively activatesALC1 remodeling uponrecruitmenttositesofDNAdamage.

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Identification of oligodendrocyte lineage states with single-cell ATAC-seq

EneritzAgirre1,MandyMeijer1,XingqiChen2,HowardYChang2andGonçaloCastelo-Branco11LaboratoryofMolecularNeurobiology,DepartmentMedicalBiochemistryandBiophysics,KarolinskaInstitutet,Stockholm,Sweden2Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine,Stanford,CA94305,USA

Oligodendrocyteprecursorcells(OPCs)constitute5to8%ofthetotalnumberofcellsintheadultcentral nervous system (CNS) being the main population that generates oligodendrocytes (OLs)duringCNSdevelopmentandremyelinationevents[1].OLsproducemyelin,alipid-richmembranethatinsulatesneuronalaxons.TheunderstandingoftranscriptionalandepigeneticregulationoftheOLlineagehasbeenlimitedtothebulkstudyofcellpopulations.Theadventofsingle-cellgenomicsallowedagreatercellularheterogeneity.Forinstance,ourgrouphaspreviouslyshownbysingle-cellRNA-seq that OPCs and OLs are more heterogeneous at transcriptional level than previouslythought,wheredifferentsubpopulationsarerelatedtodifferentstates[2].DuringOPCproliferationtheinterplaybetweentranscriptionfactorsandepigeneticmodifiersisessentialfortheacquisitionofspecificcellstates/fates.Thedisruptionofthesecellstatesithasbeenfoundtobecharacteristicofthedecreasedabilitytorepairmyelininspecificdiseases,suchasMultipleSclerosis.

InordertocharacterizeOLlineageepigeneticstatesweperformedscATAC-seq[5],formeasuringthe chromatin accessibility at single cell level. Single cells were FACS sorted and marked withspecificmatureOLandOPCmarkers.Asaresult,werecoveredOPCs,maturedOLsandacombinedpopulation of newly formed OLs. Although scATAC-seq corresponds to a highly sparse data,preliminary results showed a high correlation between single cell and bulk ATAC-seq.Implementation of scATAC-seq showed significant chromatin accessibility variability for specifictranscription factors in the different OL lineage populations. Applying dimensionality reductionmethods, such as t-SNE, single cells from different populations were clustered based on thechromatinaccessibilityofspecificregulators.Bycombiningresultsfromchromatinaccessibilityandtranscriptomics,weplantodefinespecificstatesclueforOPCdifferentiationtolaterlinkthemtospecificdiseases,suchasMultipleSclerosis.

1. Levine JM,ReynoldsR, Fawcett JW. Theoligodendrocyteprecursor cell inhealth anddisease. TrendsNeurosci.2001;24(1):39-47.2.

2. MarquesS,ZeiselA,CodeluppiS,vanBruggenD,FalcãoAM,XiaoL,etal.Oligodendrocyteheterogeneity inthemousejuvenileandadultcentralnervoussystem.Science.2016;352(6291):1326-9.

3. Castelo-BrancoG,LiljaT,WallenborgK,FalcaoAM,MarquesSC,GraciasA,etal.Neuralstemcelldifferentiationisdictated by distinct actions of nuclear receptor corepressors and histone deacetylases. Stem Cell Reports.2014;3(3):502-15.

4. YuY,ChenY,KimB,WangH,ZhaoC,HeX,etal.Olig2TargetsChromatinRemodelersToEnhancersTo InitiateOligodendrocyteDifferentiation.Cell.2013;152(1-2):248-61.

5. BuenrostroJD,WuB,ChangHY,GreenleafWJ.ATAC-seq:AMethodforAssayingChromatinAccessibilityGenome-Wide.CurrProtocMolBiol.2015;109:2191-9.

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Protein-coding sequence exclusion by alternative transcription start site usage across the human body

Wenbo Dong2* , Berit Lilje1*, Farzaneh Shahin Varnoosfaderani2, Erik Arner3, The FANTOMconsortium,AlbinSandelin1#,AndreasLennartsson2#*Sharedfirstauthor#Sharedcorrespondingauthor1The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre (BRIC), University ofCopenhagen,OleMaaloesVej5,DK2200Copenhagen,Denmark2DepartmentofBiosciencesandNutrition,KarolinskaInstitutet,Hälsovägen7-9,SE-14183Huddinge,Sweden3RIKENCenterforLifeScienceTechnologies,DivisionofGenomicTechnologies,Yokohama,Kanagawa,230-0045Japan

Gene transcription start sites (TSSs) and associated core promoters are focal points fortranscriptional regulation. .Withina single gene, alternativeusageof TSSs can lead to truncatedRNAs excluding protein-coding exons, with functional consequences. The FANTOM5 promoterexpression atlas enables comprehensive analyses of alternative TSS usage over a wide range ofprimarycellsacrossthehumanbody.Weanalysedthefantom5data,andfoundthat fractionofusedannotatedandnovelTSSswithingenebodiesisstrikinglyuniformacrossmostcelltypes.Over1.700 annotated TSSs lead to exclusion of protein-coding exons within ~1.000 genes, includingseveral epigenetic regulators. The truncated isoforms caused by alternative TSSs usage could becanonical,anditisacommonfeatureinmostcelltypes,butespeciallyinbloodcells.WealsofoundmultiplecasesofalternativeTSSswitchingbetweencelltypesleadingtoproteindomainexclusion,andconsequentlypotentialcelltypespecificfunction.

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Nascent transcription plasticity in mouse embryonic stem cells

RuiShao1,MichaelLiedschreiber2,KatjaLiedschreiber2,PatrickCramer2,SimonElsässer11DepartmentofDepartmentofMedicalBiochemistryandBiophysics,KarolinskaInstitutet2DepartmentofBiosciencesandNutrition,KarolinskaInstitutet

Transcriptional regulation is one of the primary steps in gene expression control. It is nowappreciated that a large of the genome is transcribed, suggesting many roles of transcriptionbeyond the production of protein-coding mRNA and other functional RNAs. A recent methoddevelopedby theCramer lab for transient transcriptome sequencingTT-Seqallows sensitive andunbiased profiling of total transcriptional activity. We established the TT-Seq method in mouseembryonic stemcells tounderstand the transcriptionalplasticityofpluripotent stemcells. Inourpreliminarydata,wefound>70%nascenttranscriptsarenon-codingRNAs,inwhichnearlyhalfareintergenic RNAs. TT-Seq in combination with total RNA-Seq also allows to estimate synthesizingratesandstabilitiesofeachRNAspecies.Weaimtofurtherfunctionallyannotatenewregulatorytranscription units by intersecting transcriptomic and epigenomic data, as well as using geneticmanipulationtoperturbtranscriptiondynamics.

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Session VIII: Epitools Chair:KlevDiamanti

CommercialsponsorChromatrap®; A more efficient, sensitive & robust method of chromatin immunoprecipitation

LindsayParkes11Chromatrap,PorvairSciences,Wrexham,UK

Chromatrap® is a life science companyenabling theadvancementofepigenetic research throughit’srevolutionarysolid-statesystemforchromatinimmunoprecipitation(ChIP).Featuringauniquepatented filtration platform, Chromatrap® offers significant advantages in both handling andsensitivityoverconventionalbeadbasedChIPmethods.Chromatrap®’sadvancesinhighthroughputChIPandnextgeneration sequencingarepaving theway forglobalgeneexpressionanalysisandexamination of the epigenetic landscape. Validated on a wide range of cell types the novelChromatrap® ChIP kits eliminate the laborious use of beads, allowing researchers to investigatespecific protein-DNA interactions in a faster, easier and more sensitive platform to reveal theunderlyingmolecularmechanismsofgeneregulation.

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CommercialsponsorActive Motif, enables chromatin and gene regulation research

SarantisChlamydas11ActiveMotif

Active Motif is the industry leader in developing and delivering innovative tools to enableepigenetics and gene regulation research. We are committed to providing the highest qualityproductsalongwithsuperiorservice&supporttothelifescience,clinicalandpharmaceutical/drugdiscovery communities. Whether you are an expert in the field of epigenetics or a researcherinterested in integrating epigenetics research into your studies, our comprehensive portfolio ofexpertswillenableyoutotackleyourmostdifficultscientificchallenges.

Weprovide:

• InnovativeproductsforChromatinImmunoprecipitationandDNAMethylation• EpigeneticServices• AntibodiesforChIPandChIP-Seq• RecombinantProteinsandsubstrates• MultiplexHistonePTMQuantitationproductsandservices• LuciferaseReporterAssays

NewAdvancesinChromatinRelatedexperimentsActiveMotifhasdevelopedavarietyoftoolsandservicestoovercomemanyofcurrentchallengesin the field of Epigenetics and Transcription Regulation. Apart of our rigorously validated kits,antibodies and recombinantproteins,weareoffering a seriesof EpigeneticResearch Services tobetter studyChromatinbased interactions,HistoneModifications andDNAmethylation.A list ofhighimpactfactorpapersfromourcustomerssupportsourcapabilitiesineveryresearcharea.

Chromatin Immunoprecipitation or ChIP has provided many important insights into a variety ofbiologicalprocessesanddiseases.Ourexpertisecanprovideinsightsforchallengingsamples,suchaslowcellnumberandFormalin-FixedParaffinEmbedded(FFPE)samples,inamostaccurateandquantitativeway.

Ourlistofcapabilitiesforrareanddifficultsamplesinclude:LowCellNumberChIP-seq,FFPEChIP-Seq,ATAC-Seq,ReducedRepresentationBisulfite-Seq(RRBS),high-throughputscreeningofhistonemodification levels of clinical or compound-treated samples but also ChromatinImmunoprecipitation followed by Mass Spectrometry (RIME) to identify potential chromatinproteincomplexes.

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A novel methodology for identifying genome-wide RNA-chromatin interactions

AlessandroBonetti1andGoncaloCastelo-Branco1DepartmentofMedicalBiochemistryandBiophysics(MBB),KarolinskaInstitutet

Mammalian genomes are pervasively transcribed with the most abundant fraction beingrepresented by non-protein-coding RNAs. More recently long noncoding RNAs have gained anincreased appreciation for their functional importance. Most noncoding transcripts exhibit anuclear localization and several have shown to play a role in the regulation of gene expression.Although some methodologies to specifically identify RNA-chromatin interactions have beendeveloped, technologies to massively map the genomic binding sites of multiple transcripts arelacking.Here,toaddressthesechallenges,wehavedevelopedRNAandDNAinteractingcomplexesligatedand sequenced (RADICL-seq), anovel technology thatmaps genome-wideRNA-chromatininteractions. RADICL-seq is a proximity ligation based methodology that broadly identifies thegenomicbindingsitesofcodingandnoncodingRNAs,uncoveringanunderappreciatedcomplexityfortheRNA-DNAinteractome.

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Modeling the dynamics of epigenetic memory

LudvigLizana1andYuriB.Schwartz21DepartmentofPhysics,IntegratedScienceLab,UmeåUniversity2DepartmentofMolecularBiology,UmeåUniversity.

HerewepresentourprogresstowardsarealisticcomputationalmodelofepigeneticrepressionbyDrosophilaPolycombGroupproteins.Severalfeaturesmakethissystemattractiveformodeling.Itisevolutionaryconserved,extensivelystudiedinbothmammalsandsimplermodelorganisms,andclinicallyrelevant.

Tomakeamodel,wepartitionthegenomeintonucleosome-sized“boxes”. Inthefinalversionofthemodel theseboxeswill representeitheractivegenes,high-affinitybindingsites forPolycombcomplexes(socalledPolycombResponseElements,PREs)ortherestofthegenome.Torepresentchromatin, we will arrange the histone-sized boxes into a linear array that has the samearrangement of genes, PRE’s etc. as real Drosophila chromosomes. The epigenetic memory ofPolycombrepressionis“recorded”viamethylationofLysine27ofhistoneH3(H3K27).Torepresentall four possiblemethylation states of H3K27, themodel’s boxesmay also switch between fourstatesaccordingtocertainrates.Importantly,theseratesarenotconstant.Theydependonseveralfactors suchaspreviousmethylation states,methylation statesofneighboringnucleosomes, andconcentrationsofPolycombcomplexes.Someoftheserelationshipshavebeenmappedoutbefore,but their importance for the establishment and maintenance of the epigenetic memory onchromosomal level is not clear and is something that we explore. To visualize how changes ofparameters affect the methylation states during simulation, we employ a Java script-basedgraphicaluserinterface.

37

Listofparticipants:Firstname Familyname EmailAddress Organization/University/Company

Agota Tuzesi agota.tuzesi@gu.se SahlgrenskaCancerCenter /UniversityofGothenburg

Aida Hoshiar aida.hoshiar@igp.uu.se UppsalaUniversity

Alba Atienza-Parraga alba.atienza-parraga@igp.uu.se UppsalaUniversity

Alejandra DuqueJaramillo alduquej@gmail.com UppsalaUniversity

Alessandro Bonetti alessandro.bonetti@ki.se KarolinskaInstitutet

Alisa Alekseenko alisa.alekseenko@gmail.com KarolinskaInstitutet

Amanda Raine Amanda.Raine@medsci.uu.se UppsalaUniversity

Anders Kämpe anders.kampe@ki.se KarolinskaInstitutet

Anders Isaksson anders.isaksson@medsci.uu.se UppsalaUniversity

Andre Fontes thearkantos@hotmail.com UppsalaUniversity

Andrea Hinas andrea.hinas@icm.uu.se UppsalaUniversity

Andreas Lennartsson andreas.lennartsson@ki.se KarolinskaInstitutet

Angeliki Pournara angeliki.pournara@medsci.uu.se UppsalaUniversity

Angelo Salazar angelo.salazar@scilifelab.se KarolinskaInstitutet

Anna Wenger anna.wenger@gu.se UniversityofGothenburg

Anna PalaudeMiguel anna.palau.de.miguel@ki.se KarolinskaInstitutet

Anna-Maria Katsori anna-maria.katsori@scilifelab.se KarolinskaInstitutet

Ann-Christine Syvänen ann-christine.syvanen@medsci.uu.se UppsalaUniversity

Anne Neddermeyer anne.neddermeyer@medsci.uu.se UppsalaUniversity

Annika Scheynius annika.scheynius@ki.se KarolinskaInstitutet

Ann-Kristin ÖstlundFarrants anki.ostlund@su.se StockholmUniversity

Antoni GanezZapater toni.ganez@su.se StockholmUniversity

Antonia Kalushkova antonia.kalushkova@igp.uu.se UppsalaUniversity

Arshad NoorulAin arshad.noor.ul.ain@ki.se KarolinskaInstitutet

Asimina Zisi asimina.zisi@scilifelab.se KarolinskaInstitutet

Ayla DePaepe ayla.de.paepe@ki.se KarolinskaInstitutet

Banushree Kumar banushree.kumar@scilifelab.se KarolinskaInstitutet

Behrooz Torabi behrooz.torabi@icm.uu.se UppsalaUniversity

Benjamin Holmgren benjamin.holmgren@icm.uu.se UppsalaUniversity

Bo Segerman bo.segerman@igp.uu.se National Veterinary Institute / UppsalaUniversity

Cecilia Bergqvist Cissi@neurochem.su.se StockholmUniversity

Chandrasekhar Kanduri kanduri.chandrasekhar@gu.se UniversityofGothenburg

Charlotta Sandberg charlotta.sandberg@igp.uu.se UppsalaUniversity

Charlotte Otema co@nordicbiolabs.se NordicBiolabsAB

Charlotte Gustafsson charlotte.gustafsson@ki.se KarolinskaInstitutet

Claudia Kutter claudia.kutter@ki.se KarolinskaInstitutet

Daniel Käll daniel.kall@nordicdiagnostica.com NordicDiagnostica

Dorte Schlesinger dorte.schlesinger@scilifelab.se KarolinskaInstitutet

Eckardt Treuter eckardt.treuter@ki.se KarolinskaInstitutet

Elham Barazeghi elham.barazeghi@sugsci.uu.se UppsalaUniversity

38

Enen Guo enen.guo@su.se StockholmUniversity

Eneritz Agirre eneritz.agirre@ki.se KarolinskaInstitutet

Erik Gudmunds erik.gudmunds@hotmail.se UppsalaUniversity

Estelle SuaudLefebvre suaud@activemotif.com ActiveMotif,Europe

Eva DvorakTomastikova eva.tomastikova@slu.se SwedishUniversityofAgriculturalSciences

Eva Sverremark-Ekström eva.sverremark@su.se StockholmUniversity

Farzaneh ShahinVarnoosfaderani farzaneh.shahin.varnoosfaderani@ki.se KarolinskaInstitutet

Francesco Marabita francesco.marabita@ki.se KarolinskaInstitutet

Frida Niss frida.niss@neurochem.su.se StockholmUniversity

George Kostallas george.kostallas@bionordika.se BioNordikaSweden

Gintare Lasaviciute gintare.lasaviciute@su.se StockholmUniversity

Goncalo Castelo-Branco Goncalo.Castelo-Branco@ki.se KarolinskaInstitutet

Hani AbdulkadirAli hani.abdulkadir.ali@ki.se KarolinskaInstitutet

Helena Carén helena.caren@gu.se UniversityofGothenburg

Helena JernbergWiklund helena.jernberg_wiklund@igp.uu.se UppsalaUniversity

Helene Lindegren helene.lindegren@sial.com Merck

Henk Stunnenberg H.Stunnenberg@ncmls.ru.nl Radboud Institute for Molecular LifeSciences(RIMLS)

Hua Jiang hua.jiang@slu.se SwedishUniversityofAgriculturalSciences

HusenM. Umer husen.umer@icm.uu.se UppsalaUniversity

Huthayfa Mujahed huthayfa.mujahed@ki.se KarolinskaInstitutet

Isabel Regadas isabel.regadas@su.se StockholmUniversity

Jaclyn Quin jaclyn.quin@su.se StockholmUniversity

Jakub OrzechowskiWestholm jakub.westholm@scilifelab.se StocholmUniversity

Jan Komorowski jan.komorowski@icm.uu.se UppsalaUniversity

Jarmila Nahalkova jarmila.nahalkova@biochemworld.net private

Jason Ernst jason.ernst@ucla.edu UniversityofCalifornia,LosAngeles

Jessica Nordlund jessica.nordlund@medsci.uu.se UppsalaUniversity / SNP-SEQ TechnologyPlatform

Joaquin CustodioRojo joaquin.custodio@scilifelab.se KarolinskaInstitutet

Johan Winquist johan.winquist@beactica.com Beactica

Jordi Planells jordi.planells@su.se StockholmUniversity

JoseRamon Barcenas-Walls Joseramon.Barcenas.3611@student.uu.se UppsalaUniversity

Juan Inda Juansalvador.Inda_Diaz.4007@student.uu.se UppsalaUniversity

JuanIgnacio BarrasaLopez juan.barrasa@umu.se UmeåUniversity

Juliana Imgenberg-Kreuz juliana.imgenberg@medsci.uu.se UppsalaUniversity

Karolina Smolinska karolina.smolinska@icm.uu.se UppsalaUniversity

Katarina Lyberg katarina.lyberg@ki.se KarolinskaInstitutet

Klev Diamanti klev.diamanti@icm.uu.se UppsalaUniversity

Koji Ando koji.ando@igp.uu.se UppsalaUniversity

Kwangchol Mun kwangchol.mun@imbim.uu.se UppsalaUniversity

Kyle Kimler Kyle.kimler@scilifelab.se SciLifeLab

39

Lara Kular lara.kular@ki.se KarolinskaInstitutet

Larry Mansouri larry.mansouri@igp.uu.se UppsalaUniversity

Laura Rojas laura.rojas@icm.uu.se UppsalaUniversity

Laura Eme laura.eme@icm.uu.se UppsalaUniversity

Leif Karlsson leif.karlsson@ki.se KarolinskaInstitutet

Lejon Kralemann lejon.kralemann@slu.se SwedishUniversityofAgriculturalSciences

Li He Li.He@su.se StockholmUniversity

Lindsay Parkes l.j.parkes@swansea.ac.uk Chromatrap

Ling Shen ling.shen@ebc.uu.se UppsalaUniversity

Lluis MillanArino lluis.millan.arino@ki.se KarolinskaInstitutet

Lucia Pena-Perez lucia.pena.perez@ki.se KarolinskaInstitutet

Ludvig Lizana ludvig.lizana@umu.se UmeåUniversity

Malin Ueberschär malin.ueberschar@su.se StockholmUniversity

Marek Bartosovic marek.bartosovic@ki.se KarolinskaInstitutet

Marina Wiklander Marina.Wiklander@sial.com Merck

Marina Zelenina marinaz@kth.se KTHRoyalInstituteofTechnology

Marko Sankala marko.sankala@sial.com Merck

Mateusz Garbulowski mateusz.garbulowski@icm.uu.se UppsalaUniversity

Matilda Kjellander matilda.kjellander@ki.se KarolinskaInstitutet

Mattias Mannervik mattias.mannervik@su.se StockholmUniversity

Mattias Alenius mattias.alenius@umu.se UmeåUniversity

Melika Hajkazemian Melika.hajkazemian@su.se StockholmUniversity

Min Tang min.tang@su.se StockholmUniversity

Miyuki Nakamura miyuki.nakamura@slu.se SwedishUniversityofAgriculturalSciences

Mohsen KarimiArzenani mohsen.karimi@ki.se KarolinskaInstitutet

My Bjöklund my.bjorklund@medsci.uu.se UppsalaUniversity/

Naveed Jhamat naveed.jhamat@slu.se SwedishUniversityofAgriculturalSciences

Nicholas Baltzer nicholas.baltzer@icm.uu.se UppsalaUniversity

Ning Liang ning.liang@ki.se KarolinskaInstitutetP NavaneethKrishna Menon navaneethkmenon@gmail.com UppsalaUniversity

Panagiotis Papoutsoglou panagiotis.papoutsoglou@imbim.uu.se UppsalaUniversity

Paraskevi Heldin evi.heldin@imbim.uu.se Uppsalauniversity

Patricia Stoll stollpa@student.ethz.ch UppsalaUniversity

Patricia RomansFuertes patricia.romans@su.se StockholmUniversity

Pelin Sahlen pelinak@kth.se KTHRoyalInstituteofTechnology

Peter Svensson peter.svensson@ki.se KarolinskaInstitutet

Philippe Cronet pcr@diagenode.com Diagenode

Qi Dai qi.dai@su.se StockholmUniversity

Rita Batista rita.batista@slu.se SwedishUniversityofAgriculturalSciences

Robert Månsson robert.mansson@ki.se KarolinskaInstitutet

Rongrong Fan rongrong.fan@ki.se KarolinskaInstitutet

Roshan Vaid roshan.vaid@su.se StockholmUniversity

40

Rui Shao rui.shao@scilifelab.se KarolinskaInstitutet

Samudhra Sabari sams11star@gmail.com UppsalaUniversity

Samudyata Samudyata samudyata.samudyata@ki.se KarolinskaInstitutet

Sara Yones sara.younes@icm.uu.se UppsalaUniversity

Sarantis Chlamydas schlamydas@gmail.com ActiveMotif

Sarbashis Das sarbashis.das@icm.uu.se UppsalaUniversity

Sascha Krakovka sascha.krakovka@icm.uu.se UppsalaUniversity

Sebastian Deindl sebastian.deindl@icm.uu.se UppsalaUniversity

Sergey Belikov sergey.belikov@su.se Stockholmuniversity

Shadi Jafari shadi.jafari@liu.se LinköpingUniversity/NewYorkUniversity

Shujing Liu shujing.liu@slu.se SwedishUniversityofAgriculturalSciences

Simon Elsässer simon.elsasser@scilifelab.se KarolinskaInstitutet

Sujata Bhoi sujata.bhoi@igp.uu.se UppsalaUniversity

Susanna Larsson susanna.m.larsson@gu.se SahlgrenskaCancerCenter /UniversityofGothenburg

Susanne Kerje Susanne.Kerje@imbim.uu.se UppsalaUniversity

Sylvain Mareschal sylvain.mareschal@ki.se KarolinskaInstitutet/UppsalaUniversity

Valentina Peona valentina.peona@ebc.uu.se UppsalaUniversity

Varshni Rajagopal varshnirajagopal@yahoo.com UppsalaUniversity

Varun Maturi varun.maturi@imbim.uu.se UppsalaUniversity

VelinMarita Sequeira velin.sequeira@igp.uu.se UppsalaUniversity

Wenbo Dong wenbo.dong@ki.se KarolinskaInstitutet

Vicent Pelechano vicent.pelechano@scilifelab.se KarolinskaInstitutet

Vidhur Seshadri s.vidhur2017@gmail.com UppsalaUniversity

Xiaoyan Qian xiaoyan.qian@scilifelab.se StockholmUniversity

Xiushan Yin xiushan.yin@scilifelab.se KarolinskaInstitutet

Yanara Marincevic yanara.marincevic_zuniga@medsci.uu.se UppsalaUniversity

Yerma ParejaSanchez yerma.pareja@scilifelab.se KarolinskaInstitutet

Ying Qu ying.qu@ki.se KarolinskaInstitutet

Yuan Guo Yuan.guo@su.se StockholmUniversity

Yuri Schwartz yuri.schwartz@umu.se UmeåUniversity

Zeeshan Khaliq khaliq.zeeshan@gmail.com UppsalaUniversity

Zhiqiang Huang zhiqiang.huang@ki.se KarolinskaInstitutet

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Location map