Dataset Information

Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex.

ABSTRACT: DNA methylation (DNAm) is a key epigenetic regulator of gene expression across development. The developing prenatal brain is a highly dynamic tissue, but our understanding of key drivers of epigenetic variability across development is limited. We, therefore, assessed genomic methylation at over 39 million sites in the prenatal cortex using whole-genome bisulfite sequencing and found loci and regions in which methylation levels are dynamic across development. We saw that DNAm at these loci was associated with nearby gene expression and enriched for enhancer chromatin states in prenatal brain tissue. Additionally, these loci were enriched for genes associated with neuropsychiatric disorders and genes involved with neurogenesis. We also found autosomal differences in DNAm between the sexes during prenatal development, though these have less clear functional consequences. We lastly confirmed that the dynamic methylation at this critical period is specifically CpG methylation, with generally low levels of CpH methylation. Our findings provide detailed insight into prenatal brain development as well as clues to the pathogenesis of psychiatric traits seen later in life.

SUBMITTER: Perzel Mandell KA

PROVIDER: S-EPMC7889237 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex.

Perzel Mandell Kira A KA Price Amanda J AJ Wilton Richard R Collado-Torres Leonardo L Tao Ran R Eagles Nicholas J NJ Szalay Alexander S AS Hyde Thomas M TM Weinberger Daniel R DR Kleinman Joel E JE Jaffe Andrew E AE

Epigenetics 20200715 1

DNA methylation (DNAm) is a key epigenetic regulator of gene expression across development. The developing prenatal brain is a highly dynamic tissue, but our understanding of key drivers of epigenetic variability across development is limited. We, therefore, assessed genomic methylation at over 39 million sites in the prenatal cortex using whole-genome bisulfite sequencing and found loci and regions in which methylation levels are dynamic across development. We saw that DNAm at these loci was as ...[more]

PMID: 32602773

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Project description:DNA methylation is a defining feature of mammalian cellular identity and is essential for normal development. Most cell types, except germ cells and pre-implantation embryos, display relatively stable DNA methylation patterns, with 70-80% of all CpGs being methylated. Despite recent advances we still have a too limited understanding of when, where and how many CpGs participate in genomic regulation. Here we report the in depth analysis of 42 whole genome bisulfite sequencing (WGBS) data sets across 30 diverse human cell and tissue types. We observe dynamic regulation for only 21.8% of autosomal CpGs within a normal developmental context, a majority of which are distal to transcription start sites. These dynamic CpGs co-localize with gene regulatory elements, particularly enhancers and transcription factor binding sites (TFBS), which allow identification of key lineage specific regulators. In addition, differentially methylated regions (DMRs) often harbor SNPs associated with cell type related diseases as determined by GWAS. The results also highlight the general inefficiency of WGBS as 70-80% of the sequencing reads across these data sets provided little or no relevant information regarding CpG methylation. To further demonstrate the utility of our DMR set, we use it to classify unknown samples and identify representative signature regions that recapitulate major DNA methylation dynamics. In summary, although in theory every CpG can change its methylation state, our results confirm that only a fraction does so as part of coordinated regulatory programs. Therefore our selected DMRs can serve as a starting point to help guide novel, more effective reduced representation approaches to capture the most informative fraction of CpGs as well as further pinpoint putative regulatory elements. Analysis of 42 human WGBS libraries comprising 30 distinct primary cell lines, tissues, in vitro derived cell types and cell lines. BiSeq raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) or bsmap 2.7 (Xi et al. 2009) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010). The bed files contain all seen CpGs within the given library. The number of methylated reads/number of total reads is listed in the score column. This study includes a re-analysis of Samples from the NIH Roadmap Epigenomics Mapping Consortium (REMC; GSE16256, GSE17312), Hodges et al. 2011 (GSE31971), Molaro et al. 2011 (GSE30340), and Xi et al. 2013. WARNING: This submission is incomplete pending further deposits of raw data files from Meissner via EDACC.

Dataset Information

Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex.

Publications

Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex.

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