Characterizing 5-hydroxymethylcytosine in human prefrontal cortex at single base resolution

BMC Genomics
Jeffrey A GrossGustavo Turecki

Abstract

The recent discovery that methylated cytosines are converted to 5-hydroxymethylated cytosines (5hmC) by the family of ten-eleven translocation enzymes has sparked significant interest on the genomic location, the abundance in different tissues, the putative functions, and the stability of this epigenetic mark. 5hmC plays a key role in the brain, where it is particularly abundant and dynamic during development. Here, we comprehensively characterize 5hmC in the prefrontal cortices of 24 subjects. We show that, although there is inter-individual variability in 5hmC content among unrelated individuals, approximately 8 % of all CpGs on autosomal chromosomes contain 5hmC, while sex chromosomes contain far less. Our data also provide evidence suggesting that 5hmC has transcriptional regulatory properties, as the density of 5hmC was highest in enhancer regions and within exons. Furthermore, we link increased 5hmC density to histone modification binding sites, to the gene bodies of actively transcribed genes, and to exon-intron boundaries. Finally, we provide several genomic regions of interest that contain gender-specific 5hmC. Collectively, these results present an important reference for the growing number of studies that are interes...Continue Reading

References

Mar 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·M S PalmerP N Goodfellow
Jul 5, 2005·The American Journal of Psychiatry·Alexandre DumaisGustavo Turecki
May 29, 2007·Nucleic Acids Research·Christina BackesHans-Peter Lenhof
Apr 18, 2009·Science·Skirmantas Kriaucionis, Nathaniel Heintz
Apr 28, 2010·Proceedings of the National Academy of Sciences of the United States of America·Iris CheungSchahram Akbarian
Nov 26, 2010·Proceedings of the National Academy of Sciences of the United States of America·Menno P CreyghtonRudolf Jaenisch
May 26, 2011·The Journal of Biological Chemistry·Shannon Morey KinneySriharsa Pradhan
Jul 21, 2011·Journal of Nucleic Acids·Weiwei Li, Min Liu
Oct 4, 2011·Nature·Sanjeev ShuklaShalini Oberdoerffer
Oct 4, 2011·Nature Genetics·Florian LienertDirk Schübeler
Nov 1, 2011·Nature Neuroscience·Keith E SzulwachPeng Jin
Nov 9, 2011·Archives of General Psychiatry·Hennady P ShulhaZhiping Weng
Nov 23, 2011·Genome Research·Colm E NestorRichard R Meehan
Feb 7, 2012·American Journal of Human Genetics·Shusuke NumataBarbara K Lipska
May 11, 2012·The International Journal of Neuropsychopharmacology·Cristiana CruceanuGustavo Turecki
Sep 11, 2012·Nature Structural & Molecular Biology·Tarang KhareArturas Petronis
Dec 25, 2012·Journal of Psychiatric Research·Jeffrey A GrossGustavo Turecki
May 15, 2013·Human Molecular Genetics·Fengli WangTie-Shan Tang
Jul 6, 2013·Science·Ryan ListerJoseph R Ecker
Oct 19, 2013·Science·Maya KasowskiMichael Snyder
Oct 19, 2013·Science·Graham McVickerJonathan K Pritchard
Nov 12, 2013·Nucleic Acids Research·John P ThomsonRichard R Meehan
Jan 7, 2014·Neurobiology of Aging·Natacha CoppietersMike Dragunow

❮ Previous
Next ❯

Citations

Oct 19, 2016·Neurobiology of Disease·Ligia A PapaleReid S Alisch
May 13, 2017·Genes·Kathryn VaillancourtGustavo Turecki
Jul 12, 2017·Molecular Psychiatry·P-E LutzG Turecki
Oct 9, 2018·Nature Biotechnology·Emily K SchutskyRahul M Kohli
Sep 12, 2019·Epigenetics : Official Journal of the DNA Methylation Society·Nicholas D JohnsonKaren N Conneely
Aug 20, 2016·Environmental Epigenetics·Laura M HackNadine Provençal
Dec 3, 2016·Epigenetics : Official Journal of the DNA Methylation Society·V K Chaithanya PonnaluriMelanie Ehrlich
Apr 17, 2020·Biology of Sex Differences·Joshua B RubinJingqin Luo
Mar 16, 2019·Frontiers in Neuroscience·Laura R CortesNancy G Forger
Feb 26, 2019·Journal of Affective Disorders·Laura M HackBoadie W Dunlop
Apr 17, 2019·Chemical Research in Toxicology·Esra EmerceLode Godderis

❮ Previous
Next ❯

Methods Mentioned

BETA
AbaSI-Seq
ChIP-Seq
RNA-Seq
PCR

Software Mentioned

custom scripts
R packages
Ensembl
BEDtools
custom PERL script
GeneTrail

Related Concepts

Related Feeds

CREs: Gene & Cell Therapy

Gene and cell therapy advances have shown promising outcomes for several diseases. The role of cis-regulatory elements (CREs) is crucial in the design of gene therapy vectors. Here is the latest research on CREs in gene and cell therapy.

Alternative splicing

Alternative splicing a regulated gene expression process that allows a single genetic sequence to code for multiple proteins. Here is that latest research.