1. Genomics 2015/16 Silvia del Burgo

2. + Same genome for all cells that arise from single fertilized egg, Identity?  Epigenomic signatures + Epigenomics: study of chemical changes in DNA and histones (without altering DNA sequence) that are inheritable and involved in regulating gene expression, development, tissue differentiation and suppression of TE. – DNA/histone Methylation – Histone Acetylation – ncRNA – Interactions between distant sections of chromatin + Epigenome is dynamic  can be altered by environmental conditions + Modification in DNA/histones  changes in chromatin structure and function: how easily DNA can be accessed by TF

3. + Promoters & Insulators: chromatin state regarding histone modification is invariant across cell types. + Enhancers: most variable class of elements between cell types. + Other cis-regulatory DNA sequences. – Distal to promoters – Strong evolutionary conservation – Marked by hystone acetylation binding of coactivator proteins or DNaseI hypersensitivity

4. + 5 important epigenetic marks: – H3K4me3: promote regions – H3K4me1: enhancer regions – H3K36me3: transcribed regions – H3K27me3: Polycomb repression – H3K9me3: heterochromatin regions + Additional epigenomic marks: – Acetylation marks H3K27ac and H3K9ac: increased activation of enhancer and promotes regions. – DNase hypersensitivity: accessible chromatin regions (associated with regulator binding) – DNA methylation: associated with repressed regulatory regions or active gene transcripts

5. + Active states – Active TSS proximal promotes states (TssA, TssAFlnk) – Transcribed state at the 5' and 3' end of genes showing both promote and enhancer signatures (TxFlnk) – Actively transcribed states (Tx, TxWk) – Enhancer states (Enh, EnhG) – State associated with Zn finger protein genes (ZNF/Rpts). + Inactive states – Constitutive heterochromatin (Het) – Bivalent regulatory states (TssBiv, BicFlnk, EnhBiv) – Represses Polycomb states (ReprPC, ReprPCWk) – Quiescent state (Quies) + Inactive states: 68% + Enhancer and promotes states: 5% and show enrichment for evolutionarily conserved non-exonic regions. – Enhancer states contain strong H3K27ac signal (EnhA1, EnhA2) show:  Higher DNA accessibility  Lower methylation  High transcription factor binding

6. + Promoter states: low DNA methylation and high accessibility. + Transcribed states: High DNA methylation and low accessibility + Enhancer states: intermediate DNA methylation and accessibility – >18.000 – 57% CpG methylation on average – Strongly enriched in genes + DNA methylation patterns are better correlated with histone methylation patterns than with the DNA sequence/ CpG density + CpGs are not distributed uniformly in the genome – High CpG density sites  unmethylated  (hypermethylation leads to heterochromatin and gene silencing) – Low CpG density sites  methylated (dynamic)

7. + Distribution of methylation levels for CpG in chromatin states across tissue and cell type: – TssFlnk (Transcribed state):  Unmethylated in differentiated cells and tissues  Methylated for pluripotent and embryonic-stem- cell-derived cells – Enh and EnhG states (Enhancer states):  Highly methylated in pluripotent cells  Intermediate methylation in differentiated cells and tissues – EnhBiv states (Bivalent regulatory states):  Unmethylated in most primary cells and tissues  Broader distribution of methylation levels in pluripotent cells. – Repressed states ReprPC: varying methylation levels among epigenomes – Het states: high levels of methylation in almost all epigenomes Common developmental origin is a primary determinant of global DNA methylation patterns rather than the tissue environment

8. + Primary DNA sequence has an impact on the epigenomic  histone modifications and DNA methylation can be predicted by DNA sequence

9. + Epigenetic: – Complex network: different elements and relationships between them – Epigenetic signatures should be studied in the context of integrated chromatin states, in relation with all DNA/histone methylation/acetyla tion, DNA accessibility and RNA transcription.

10. + Heintzman ND, Hon GC, Hawkins RD, et al (2009) Histone modifications at human enhancers reflect global cell-type- specific gene expression. Nature 459:108–112. doi: 10.1038/nature07829 + Meissner A, Mikkelsen TS, Gu H, et al (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454:766–770. doi: 10.1038/nature07107 + Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, et al (2015) Integrative analysis of 111 reference human epigenomes. Nature 518:317–330. doi: 10.1038/nature14248 + Romanoski CE, Glass CK, Stunnenberg HG, et al (2015) Epigenomics: Roadmap for regulation. Nature 518:314– 316. doi: 10.1038/518314a