Methylation of cytosines is an essential epigenetic modification in mammalian genomes, yet the rules that govern methylation patterns remain largely elusive. To gain insights into this process, we generated base-pair-resolution mouse methylomes in stem cells and neuronal progenitors. Advanced quantitative analysis identified low-methylated regions (LMRs) with an average methylation of 30%. These represent CpG-poor distal regulatory regions as evidenced by location, DNase I hypersensitivity, presence of enhancer chromatin marks and enhancer activity in reporter assays. LMRs are occupied by DNA-binding factors and their binding is necessary and sufficient to create LMRs. A comparison of neuronal and stem-cell methylomes confirms this dependency, as cell-type-specific LMRs are occupied by cell-type-specific transcription factors. This study provides methylome references for the mouse and shows that DNA-binding factors locally influence DNA methylation, enabling the identification of active regulatory regions.
At a glance
Gene Expression Omnibus
- DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6–21 (2002)
- Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447, 425–432 (2007)
- Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315–322 (2009) et al.
- Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766–770 (2008) et al.
- Generation of a defined and uniform population of CNS progenitors and neurons from mouse embryonic stem cells. Nature Protocols 2, 1034–1043 (2007) , , &
- Genomic prevalence of heterochromatic H3K9me2 and transcription do not discriminate pluripotent from terminally differentiated cells. PLoS Genet. 7, e1002090 (2011) et al.
- Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol. Cell 30, 755–766 (2008) et al.
- Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477, 289–294 (2011) et al.
- Targets and dynamics of promoter DNA methylation during early mouse development. Nature Genet. 42, 1093–1100 (2010) et al.
- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007) et al.
- Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 57, 159–197 (1988) &
- Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries. Proc. Natl Acad. Sci. USA 101, 4537–4542 (2004) et al.
- Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genet. 39, 311–318 (2007) et al.
- A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279–283 (2011) et al.
- CTCF shapes chromatin by multiple mechanisms: the impact of 20 years of CTCF research on understanding the workings of chromatin. Chromosoma 119, 351–360 (2010) , &
- Mediator and cohesin connect gene expression and chromatin architecture. Nature 467, 430–435 (2010) et al.
- Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 473, 394–397 (2011) et al.
- 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biol. 12, R54 (2011) , , , &
- Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. PLoS Genet. 7, e1002154 (2011) et al.
- TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 473, 343–348 (2011) et al.
- Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature 473, 389–393 (2011) et al.
- Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128, 1231–1245 (2007) et al.
- Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature 451, 796–801 (2008) et al.
- DNA methylation programming and reprogramming in primate embryonic stem cells. Genome Res. 19, 2193–2201 (2009) et al.
- Identification of genetic elements that autonomously determine DNA methylation states. Nature Genet. 43, 1091–1097 (2011) et al.
- Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b. Genes Cells 11, 805–814 (2006) et al.
- Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 405, 482–485 (2000) &
- CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus. Nature 405, 486–489 (2000) et al.
- Is REST required for ESC pluripotency? Nature 457, E4–E5 (2009) , , &
- CTCF mediates long-range chromatin looping and local histone modification in the β-globin locus. Genes Dev. 20, 2349–2354 (2006) et al.
- Differentiation of mouse embryonic stem cells into a defined neuronal lineage. Nature Neurosci. 7, 1003–1009 (2004) et al.
- Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006) &
- GABPα regulates Oct-3/4 expression in mouse embryonic stem cells. Biochem. Biophys. Res. Commun. 353, 686–691 (2007) et al.
- Identification of Sox17 as a transcription factor that regulates oligodendrocyte development. J. Neurosci. 26, 9722–9735 (2006) et al.
- Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106–1117 (2008) et al.
- JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res. 36, D102–D106 (2008) et al.
- CpG islands – ‘a rough guide’. FEBS Lett. 583, 1713–1720 (2009) &
- Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol. Cell 44, 17–28 (2011) et al.
- The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nature Genet. 41, 178–186 (2009) et al.
- Regulated demethylation of the myoD distal enhancer during skeletal myogenesis. Dev. Biol. 177, 490–503 (1996) , &
- Methylation changes in promoter and enhancer regions of the WT1 gene in Wilms’ tumours. Cancer Lett. 166, 165–171 (2001) et al.
- Patterns of methylation of the c-myc gene in human colorectal cancer progression. Br. J. Cancer 65, 667–672 (1992) , , &
- Dynamic reorganization of chromatin structure and selective DNA demethylation prior to stable enhancer complex formation during differentiation of primary hematopoietic cells in vitro. Blood 103, 2950–2955 (2004) et al.
- Glucocorticoid-induced DNA demethylation and gene memory during development. EMBO J. 20, 1974–1983 (2001) , , &
- Chromatin structure and de novo methylation of sperm DNA: implications for activation of the paternal genome Science. 228, 1061–1068 (1985) &
- Expanded methyl-sensitive cut counting reveals hypomethylation as an epigenetic state that highlights functional sequences of the genome. Proc. Natl Acad. Sci. USA 108, 9715–9720 (2011) et al.
- High-resolution mapping studies of chromatin and gene regulatory elements. Epigenomics 1, 319–329 (2009) &
- Europe to map the human epigenome. Nature 477, 518 (2011)
- Tackling the epigenome: challenges and opportunities for collaboration. Nature Biotechnol. 28, 1039–1044 (2010) , &
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009) , , &
- Supplementary Information (15.5M)
The file contains Supplementary Figures 1-16 with legends, Supplementary Methods and additional references. The methods in this file were replaced on 25 April 2012.
- Supplementary Table 1 (56K)
The table displays details of sequence datasets used in this study, and additional references (for external data sets only).
- Supplementary Table 2 (9.6M)
The table displays methylation segments identified in ES cells.
- Supplementary Table 3 (7M)
The table displays Methylation segments identified in NP. A short description of each column is given at the top of the table.
- Supplementary Table 4 (29K)
The table displays Genotype structure of the ES cell line used in the study.