Reading circle of Epigenome Roadmap doi:10.1038/nature14248

Roadmap Epigenomics Consortium et. al. Integrative analysis of 111 reference human epigenomesItoshi NIKAIDO, Ph.D. <itoshi.nikaido@riken.jp> Unit Leader, Bioinformatics Research Unit RIKEN Advanced Center for Computer and Communication http://bit.accc.riken.jp/

Main figure: 9 Extended Data Figure: 12 Supplementary Figure: 13

1. Reference epigenome mapping across tissues and cell types 2. Chromatin states, DNA methylation and DNA accessibility 3. Epigenomic differences during lineage specification 4. Most variable states and distinct chromosomal domains 5. Relationships between marks and lineages 6. Imputation and completion of epigenomic data sets 7. Enhancer modules and their putative regulators 8. Impact of DNA sequence and genetic variation 9. Trait-associated variants enrich in tissue-specific marks 10. Discussion

HeadlinesIntegrative analysis of 111 reference human epigenomes

1. Histone mark combinations show distinct levels of DNA methylation and accessibility, and predict differences in RNA expression levels that are not reflected in either accessibility or methylation.

2. Megabase-scale regions with distinct epigenomic signatures show strong differences in activity, gene density and nuclear lamina associations, suggesting distinct chromosomal domains.

3. Approximately 5% of each reference epigenome shows enhancer and promoter signatures, which are twofold enriched for evolutionarily conserved non-exonic elements on average.

4. Epigenomic data sets can be imputed at high resolution from existing data, completing missing marks in additional cell types, and providing a more robust signal even for observed data sets.

5. Dynamics of epigenomic marks in their relevant chromatin states allow a data-driven approach to learn biologically meaningful relationships between cell types, tissues and lineages.

6. Enhancers with coordinated activity patterns across tissues are enriched for common gene functions and human phenotypes, suggesting that they represent coordinately regulated modules.

7. Regulatory motifs are enriched in tissue-specific enhancers, enhancer modules and DNA accessibility footprints, providing an important resource for gene-regulatory studies.

8. Genetic variants associated with diverse traits show epigenomic enrichments in trait-relevant tissues, providing an important resource for understanding the molecular basis of human disease.

Summary: 8 findingsIntegrative analysis of 111 reference human epigenomes

Pegs and guy-rope modelFigure 1Tissues and cell types profiled in the Roadmap Epigenomics

127 reference epigenome = 111 epigenome roadmap + 26 ENCODE ! 2,805 genome-wide data sets = 1,821 histone modification data sets 360 DNA accessibility data sets 277 DNA methylation data sets 166 RNA-seq !Chromatin immunoprecipitation (ChIP) DNA digestion by DNase I (DNase) Bisulfite treatment Methylated DNA immunoprecipitation (MeDIP) Methylation-sensitive restriction enzyme digestion (MRE) RNA profiling

Figure 2Data sets available for each reference epigenome.

What is chomatin states?Prediction of 51 chromatin states from epigenome data set

• 51 chromatin states •11 Promoter states

•high/mid/low expression, repressed, high/mid/low GC, … • 17 Transcribed States

•5’ proximal high/mid expression, open chromatin, TF binding, spliced exon,…

• 11 Active intergenic states • strong/weaker/distal/proximal enhancer, CTCF, H2AZ,…

• 6 Repressed states • unmappble, A/T rich, ERVL, heterochromatin…

• 6 Repetitive states • (CA)n, (TG)n, L1/LTR, Satellite repeats

http://www.nature.com/nbt/journal/v28/n8/extref/nbt.1662-S1.pdf

What is chomatin states?Prediction of 51 chromatin states from epigenome data set

Epigenome Marks (observed)

Chromatin States (Predicted)

http://www.nature.com/nbt/journal/v28/n8/fig_tab/nbt.1662_F1.html

Circles are 200 bp windows of chromatin c.

Pt-1 Pt Pt+1

Vt-1 Vt-1 Vt+1

What is chomatin states?ChromHMM: automating chromatin-state discovery and characterization

http://www.nature.com/nbt/journal/v28/n8/extref/nbt.1662-S1.pdf

http://www.nature.com/nbt/journal/v28/n8/full/nbt.1662.html#supplementary-information

Figure 3Epigenomic information across tissues and marks

Red: constitutive promoter Yellow: active enhancer

Figure 4a-eChromatin states and DNA methylation dynamics

15 states model: 5 histone modification, 127 epigenomes

1. High expression = low methylation + high accessibility 2. Low expression = high methylation + low accessibility 3. Enhancer = intermediate methylation + intermediate accessibility

Figure 4a-eChromatin states and DNA methylation dynamics

• TxFlnk, Enh, TssBiv and BivFlnk states show similar distributions of DNA accessibility but different distributions of gene expression and DNA methylation.

• Enh and PeprPC states show similar distributions of DNA methylation but different distributions of DNA accessibility

• etc…

Complex relationship: active or repressive region << chromatin states

Figure 4gChromatin states and DNA methylation dynamics

Methylation, 95 epigenomes

• TssAFlnk: unmethylated in differentiated cells and tissues • Enh: Highly methylated in ES and iPS • EnhBiv: broad distribution in ES and iPS (cell-to-cell variability) • PeprPC: varying methylation levels among cell and tissues

DNA methylation changes during ESC differentiation

Figure 5abCell-type differences in chromatin states

constitutive

Cell specific

• HSC: ↑TxWk, ↓TssA/TssBiv • ESC: ↑TssBiv, ↓PeprPCWk (restriction of

H2K27me3-establishing Polycomb at promoter) • IMR90: ↑Het/ReprPC/EhnG, ↓Quies

Variability of chromatin states Chromatin state frequency

Figure 5cdCell-type differences in chromatin states

Transition of chromatin state Chromatin states at a larger resolution (2Mb)

Figure 6Epigenome relationships

Figure 7Regulatory modules from epigenome dynamics

Figure 8Linking regulators to target tissues and cell types

Figure 9Linking regulators to target tissues and cell types

1. Reference epigenome mapping across tissues and cell types 2. Chromatin states, DNA methylation and DNA accessibility 3. Epigenomic differences during lineage specification 4. Most variable states and distinct chromosomal domains 5. Relationships between marks and lineages 6. Imputation and completion of epigenomic data sets 7. Enhancer modules and their putative regulators 8. Impact of DNA sequence and genetic variation 9. Trait-associated variants enrich in tissue-specific marks 10. Discussion

HeadlinesIntegrative analysis of 111 reference human epigenomes

1. Histone mark combinations show distinct levels of DNA methylation and accessibility, and predict differences in RNA expression levels that are not reflected in either accessibility or methylation.

2. Megabase-scale regions with distinct epigenomic signatures show strong differences in activity, gene density and nuclear lamina associations, suggesting distinct chromosomal domains.

3. Approximately 5% of each reference epigenome shows enhancer and promoter signatures, which are twofold enriched for evolutionarily conserved non-exonic elements on average.

4. Epigenomic data sets can be imputed at high resolution from existing data, completing missing marks in additional cell types, and providing a more robust signal even for observed data sets.

5. Dynamics of epigenomic marks in their relevant chromatin states allow a data-driven approach to learn biologically meaningful relationships between cell types, tissues and lineages.

6. Enhancers with coordinated activity patterns across tissues are enriched for common gene functions and human phenotypes, suggesting that they represent coordinately regulated modules.

7. Regulatory motifs are enriched in tissue-specific enhancers, enhancer modules and DNA accessibility footprints, providing an important resource for gene-regulatory studies.

8. Genetic variants associated with diverse traits show epigenomic enrichments in trait-relevant tissues, providing an important resource for understanding the molecular basis of human disease.

Summary: 8 findingsIntegrative analysis of 111 reference human epigenomes