Slides - ENCODE
Transcription
Slides - ENCODE
Players and Models of Transcription Regulation in 3D genome YijunRuan([email protected]) TheJacksonLaboratoryforGenomicMedicine DepartmentofGene=csandGenomeSciences,UConnHealthCenter at ENCODEusersmee=ng,StanfordUniversity June10,2016 Players and Models of Transcription Regulation in 3D genome Theplayers:DNA,Protein,RNA Protein-mediatedchroma@ninterac@ons RNA-mediatedchroma@ninterac@ons 3DNucleome RinnandGu3manScience2014 ChIA-PETfor3Dgenomemapping (mul@plexdatasets) Protein binding Interaction complex Self-ligation PETs Inter-ligation PETs Binding peaks Higher-order topological proximity Clusters Singletons Inclusive: High specificity and resolution: • Protein bindings, • Enriched chromatin interaction, • Non-enriched contacts (Hi-C like data) • Functional element specific, • Haplotype resolved, • Single nucleotide resolution Fullwoodetal2009Nature;Lietal2012Cell;Tangetaletal2015Cell InsituHi-C vs.CTCFChIA-PET(GM12878) Chr.7 10 PET=7190 Miseq 8 6 4 2 Chromosomescale PET=57355 Hiseq 0 PET=329 6Mb Miseq Megabasescale PET=2381 PET=66 Hiseq 0.6Mb Miseq Sub-megabasescale PET=437 PET=27 Hiseq 0.2Mb Miseq kilo-basescale Freq. PET=196 Den. Totalcontact reads=4.9Billion Raoetal2014Cell TotalPETreads:1Miseq=6.4Million;1Hiseq=30.8Million Tangetal2015Cell Hiseq Connec=ngloopstoformCTCFContactDomains(CCD) Doubleknot chr4:109556994-113054287 (3.5Mb) Freq. 1000 CTCF loops CCD CTCF motifs Den. CTCF peaks 600 Hi-C TAD in situ Hi-C loops ChromHMM 100 RNA-Seq 100 Gene Size distribution of loop and domain 2,267 3,852 Inward motifs 159 Boundaries 4,177 (97%) 166 63 56 In situ Hi-C loop CCD 0.50 0.50 Hi-C TAD 0.25 0.25 0.00 0.00 6 Outward motifs Indiv. CTCF loop 0.75 0.75 ecdf CCD Cumulative density 1.00 1.00 125 (3%) 1e+04 10kb CCD=TAD 1e+05 100kb 1e+06 1e+07 1Mb 10Mb span Genomic span 1e+08 100Mb RNAPIIassociatedchroma=ninterac=ons Extra-genic enhancer-promoter interaction (EP) Single gene complex e p g chr2:225000000-228000000 Inter-genic promoter-promoter interaction (PP) Multi-gene complex e p g p g chr2:220000000-220180000 Lietal2012Cell CCD 2Dmappingdata CTCF RNAPII RNA-Seq 3Dvisualiza=on 3Dsimula=on E 5 µm CTCF RNAPII DNA PrzemyslawSzala,DariuszPlewczynski 0.5 µm Colocalization PawelTrzaskoma,GrzegorzM.Wilczynski, Common&cell-typespecific chroma=nloopingstructures CTCF 0 2 RNAPII 4 0 2 4 4 4 878 GM12 8 GM12 2 78 0 2 0 4 4 2 2 R = 0.61 Head MCF7 HeLa K562 4e-04 4e-04 0 Head Tail 2e-04 2e-04 Tail MCF7 K562 Density Density Density 6e-04 6e-04 R = 0.42 0 1e-04 1e-04 2e-04 2e-04 0e+000 0e+000 -10000 -10000-5000 0 0 500010000 10K-5000 00 500010000 10K 10K ±2.5K Distance ±2.5K -10000 0 500010000 -10000-5000 0 0 500010000 10K-5000 0 10K 10K ±2.5K Distance ±2.5K Common&celltype-specificCCDstructure B-cell Erythroid Cervical Breast Gene=cvaria=onsalterchroma=ndomains chr6:31426075-31930740 (504 kb) GM12878 T|A All loop CCD All peak T M loop M peak A GM12878 Motifs P loop P peak Biased SNP HeLa (169|37)* T|A Loop Peak A/A Loop CCD Peak CTCFbindingmo@f MCF7 MCF7 HeLa A/A Haplotype-resolvedinterac=onslinkedtogene=cs CTCF ChIA-PET SNP rs12936231 G|C 1000 All loop All peak 1000 G 100 M loop M peak 300 P loop C D’ with low LOD D’ with high LOD 0.1 1.0 P peak CEU 300 Biased SNP Gene (270 | 4) IKZF3 GSDMB ZPBP2 GSDMA 0.5 5.0 chr17:37911048-38179492 0 0.0 ORMDL3 M:AGTTACTTACATTAGCCCCCAGATGGAGTGAAACCATCAAGTA P:AGTTACTTACATTAGCCCCCAGATGCAGTGAAACCATCAAGTA High-riskSNPsforasthmaandautoimmunediseasealter domain-widetranscrip@onofcertaingenes(Verlaan2009) SNP-basedvalida=onofCTCFbindingandlooping Individual 1 Heterozygous G G T ? T Phased Loop Peak Individual 2 Homozygous Individual 3 G G G G Homozygous T T T T 3DGenomeStructureàGenomeFunc=on 3D chromatin architecture Haplotype chromatin interaction Individual 1 Topological domains Heterozygous functional G T G T Individual 2 CTCF-mediated contact domain CTCF Homozygous functional G G G G RNAPII Individual 3 Homozygous dysfunctional T T T Open Active Closed Inactive T Topological Gene=cvaria=onsààTraits/diseases mechanism Players and Models of Transcription Regulation in 3D genome Theplayers:DNA,Protein,RNA Protein-mediatedchroma@ninterac@ons RNA-mediatedchroma@ninterac@ons 3DNucleome RinnandGu3manScience2014 Genome-wideapproachforRNA-chroma=ninterac=ons RNAInterac@onwithChroma@nbyPairedEndTagSequencing,RICh-PET RNA-chromatin contacts A RNAtags chr3R:7047557-7050982 Me18S-C1096 Me18S-A425 Psi28S-291 Me28S-G2017 (snoRNAs) RpL3 (protein-coding) Crosslinking fragmentation Linker annealing cDNA synthesis DNA ligation RNA-Seq DNA linker RNA linker RICh-PET RNA tag NNNNNN RNA linker anneal RT to make 1st cDNA DNA linker ligation NNNNNN Proximity ligation XIST target distribution in human DNAtags Chromosome Chromosome GM12878 HeLa GM12878 XIST HeLa XIST 15% 10% 2nd strand cDNA 5% 0% chr 1 PET template Amplification Sequencing 2 4 5 7 6 8 9 10 11 12 13 14 15 17 19 21 X 16 18 20 22 roX2 target distribution in Drosophila 80% Chromosome roX2 60% PET mapping 3 40% Intra-chromosome Inter-chromosome 20% 0% chr 2L 2R 3L 3R 4 X MeizhenZheng,OscarLuo MostncRNAstargetac=veopenchroma=nloci chr2L:16200000-18200000 30 RICh-PET DNA tag RICh-PET DNA peak n = 6599 DNA peak loci DHS ChromHMM 100 100 75 75 573 1656 V4 10000 RNAPII binding peak loci 3819 551 RNA-Seq 588 H3K27ac 25 25 RNAPII peak n = 5770 100 100 60 615 0 0 Supported Unsupported 3-way Not group Shared Shared DHS site n = 5573 10 H3K27me3 50 50 763 chr2L:17300000-17550000 50 RICh-PET DNA tag DNA peak loci DHS ChromHMM 10000 RNAPII binding peak loci RNA-Seq 40 Density 30 30 20 10 0 P T E O A R H HL S 60 H3K27ac Ø Enrichedinpromoter&enhancerregions 10 H3K27me3 RNAPIIChIP/RICh-PETfordetec=ng transcrip=onalRNA-chroma=ninterac=ons chr2R:14474361-14615784 ChromHMM DNase HS 15 RICh-PET DNA tag Peak call Pol2-ab 500 Rep1 DNAtag Intra-chromosome 400 Rep2 Inter-chromosome 30 coding non-coding Rep3 RNAPII/RICh-PET RNAtag RNA-Seq(RPKM) 6000 RNAPII ChIP-Seq 100 RNA-Seq 100 60 H3K27ac H3K27me3 10 RNAPIIRICh-PET(RPKM) ncRNAcontactsenrichedatTADboundaryregions chrX:11600000-13000000 (1.4 Mb) RNA-Seq Dnase HS 2000 RNAPII peak 1000 RNAPII loop 500 RNAPII RICh-PET DNA peaks 5 § roX2 § 7SK § Hrsomega 15 5 60 H3K27ac H3K27me3 15 5kb resolution 7SK roX2 Hsromega Combinatorybindingbymul=plexproteinandRNAfactors 3819ncRNAtargetsites chr3R:26198479-26310882 n=1207 n=1451 n=1023 TFChIP-Seq(modENCODE) RNA-seq DHS RNAPII RICh-PET DNA tag 7SK Hsr omega RNA factors H3K4me1 H3K4me3 RNA-Seq Protein factors (modENCODE) H3K27ac H3K27me3 snRNA:7SK Hsr omega Modulatory Cons@tu@ve Others TotesttheroleofncRNAs,… x x x x x Immuno-stain RNase A - ATAC-Seq RNase A + x x x RNAPIIChIA-PET chr2L:13196092-13314472 RNaseA+ (100µg/mL) DAPI RNA-seq Chromatin state DHS 20 Control, RNaseA- (200µg/mL) ATAC-seq RNAPII 20 100µg/mL RNaseA 20 200µg/mL RNaseA 20 (400µg/mL) 15 2 µM 3 µM RNaseAcontrol RNAPII-loop Merge 15 15 400µg/mL RNaseA PET=14 Control, RNaseA- PET=6 200µg/mL RNAseA PET=6 400µg/mL RNaseA Acknowledgements Lab members Collaborators MeizhenZheng WangPing ZhonghuiTang OscarLuo XingwangLi JianHuaCao DanjuanWang EmalyPiecuch JufenZhu GuoliangLi JAX CZZhang XiaoanRuan ZhengqingOuyang DuyguUcar MichaelS=tzel JeffChuang PaulMichalski KrishnaKaruturi KarolinaPalucka JacquesBanchereau KenPaigen CharlesLee EdLiu RouxFamily UConn BrentGraveley MarcLalande JGI Chia-LinWei NIH RafaelCasellas JohnO’Shea WarrantLeonard UniversityofWarsaw,Poland DariuszPlewczynski PrzemekSzałaj GrzegorzM.Wilczynski MNHN,Paris LaurentSachs