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.

KEYWORDS:

• DNA methylation
• brain development
• prenatal development
• whole-genome bisulfite sequencing

Acknowledgments

The authors thank the UMB Brain Bank at the Department of Pediatrics in the University of Maryland School of Medicine for the tissue provided. This project was supported by the Lieber Institute for Brain Development and by NIH grants R21MH102791, R01MH112751, and T32GM781437. Finally, we are indebted to the generosity of the families of the decedents, who donated the brain tissue used in these studies.

Authors’ contributions

KAPM, AJP, JEK, and AEJ conceptualized the project and methodology. KAPM and AEJ investigated and analyzed the data and wrote the paper. LCT, ASS, RW, and NJE provided software support. AJP, RT, TMH, and RW curated data. JEK, RT, and TMH provided resources. AJP, LCT, AEJ, and DRW reviewed and edited the paper. DRW provided supervision, and AEJ was the principal investigator and oversaw experimental design and analysis. All authors read and approved the final manuscript.

Availability of data and materials

Raw and processed nucleic acid sequencing data generated to support the findings of this study are part of the PsychENCODE Consortium and the Brainseq Consortium data releases. Specifically, WGBS data have been deposited at www.Synapse.org along with the other PsychENCODE data, under the accession code syn5842535. The homogenate RNA-seq samples were also part of a larger study of RNA-seq data from homogenate DLPFC tissue (BrainSeq Consortium Phase I) [50], which was also deposited at www.synapse.org and summarized in http://eqtl.brainseq.org/phase1. The processed, homogenate RNA-seq data for this study have additionally been deposited via Globus under the jhpce#brainepi-cellsorted collection at the following location: http://research.libd.org/globus/jhpce_brainepi-cellsorted/. NeuN-sorted RNA-seq data were originally published as part of phase II of the Brainseq Consortium (http://eqtl.brainseq.org/phase2/) and have also been deposited via Globus under the jhpce#brainepi-polyA collection at the following location: http://research.libd.org/globus/jhpce_brainepi-polyA/. Publicly available data reprocessed in support of the conclusions in this work were downloaded from the Gene Expression Omnibus under GEO accession GSE47966 and GSE74193.

Disclosure statement

The authors declare no competing interests.

Ethics approval and consent to participate

Postmortem brain tissue was obtained via a Material Transfer Agreement with the National Institute of Child Health and Human Development Brain and Tissue Bank which collected the tissue under an IRB-approved protocol and consent of the next-of-kin (https://www.medschool.umaryland.edu/btbank/).

Supplementary material

Supplemental data for this article can be accessed here.

Additional information

Funding

This project was supported by The Lieber Institute for Brain Development and by NIH grants R21MH102791, R01MH112751, and T32GM781437; National Institutes of Health [R21MH102791]; National Institutes of Health [T32GM781437]; National Institutes of Health [R01MH112751].