On the presence and role of human gene-body DNA methylation.

Oncotarget
Daudi JjingoI King Jordan

Abstract

DNA methylation of promoter sequences is a repressive epigenetic mark that down-regulates gene expression. However, DNA methylation is more prevalent within gene-bodies than seen for promoters, and gene-body methylation has been observed to be positively correlated with gene expression levels. This paradox remains unexplained, and accordingly the role of DNA methylation in gene-bodies is poorly understood. We addressed the presence and role of human gene-body DNA methylation using a meta-analysis of human genome-wide methylation, expression and chromatin data sets. Methylation is associated with transcribed regions as genic sequences have higher levels of methylation than intergenic or promoter sequences. We also find that the relationship between gene-body DNA methylation and expression levels is non-monotonic and bell-shaped. Mid-level expressed genes have the highest levels of gene-body methylation, whereas the most lowly and highly expressed sets of genes both have low levels of methylation. While gene-body methylation can be seen to efficiently repress the initiation of intragenic transcription, the vast majority of methylated sites within genes are not associated with intragenic promoters. In fact, highly expressed genes ...Continue Reading

References

Nov 25, 1993·Nature·E LiR Jaenisch
Jan 1, 1997·Annual Review of Genetics·E HeardP Avner
Mar 24, 1999·Trends in Genetics : TIG·P A Jones
Jan 21, 2004·Nature Reviews. Cancer·Andrew P Feinberg, Benjamin Tycko
Oct 7, 2004·Nature Structural & Molecular Biology·Matthew C LorinczMark Groudine
Oct 16, 2004·Annual Review of Genomics and Human Genetics·Yong-Hui JiangArthur L Beaudet
Oct 29, 2004·The Journal of Biological Chemistry·Giedrius VilkaitisShoji Tajima
Nov 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·Peter J SaboJohn A Stamatoyannopoulos
Apr 30, 2005·Nature Reviews. Genetics·Simon W-L ChanSteven E Jacobsen
Jun 15, 2005·Annual Review of Biochemistry·Mary Grace Goll, Timothy H Bestor
Sep 2, 2005·Nature Reviews. Genetics·Keith D Robertson
Oct 15, 2005·Nucleic Acids Research·Alexander MeissnerRudolf Jaenisch
Jan 13, 2006·Trends in Biochemical Sciences·Robert J Klose, Adrian P Bird
Jan 25, 2006·Proceedings of the National Academy of Sciences of the United States of America·Serge SaxonovDouglas L Brutlag
Feb 21, 2006·Nature Methods·Rimantas KodziusPiero Carninci
Apr 29, 2006·Nature Genetics·Piero CarninciYoshihide Hayashizaki
Feb 27, 2007·Science·Asaf Hellman, Andrew Chess
Apr 11, 2007·Genome Research·Miho M SuzukiAdrian Bird
Jun 2, 2007·Science·David S JohnsonBarbara Wold
Jun 9, 2007·Science·Stanley Fields
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Nov 8, 2008·BMC Genomics·Amandine BemmoJacek Majewski
Jan 14, 2009·Proceedings of the National Academy of Sciences of the United States of America·Tibor A RauchGerd P Pfeifer
Feb 6, 2010·Genome Research·Louise LaurentChia-Lin Wei
Apr 17, 2010·Science·Assaf ZemachDaniel Zilberman
Jul 9, 2010·Nature·Alika K MaunakeaJoseph F Costello
Sep 28, 2010·Bioinformatics·Jianrong WangI King Jordan
Nov 30, 2010·Human Molecular Genetics·Dvir AranAsaf Hellman
Apr 29, 2011·PLoS Biology·UNKNOWN ENCODE Project Consortium
May 20, 2011·Proceedings of the National Academy of Sciences of the United States of America·Carina Frauer, Heinrich Leonhardt

❮ Previous
Next ❯

Citations

Dec 18, 2012·Current Opinion in Allergy and Clinical Immunology·Wilfried KarmausJohn W Holloway
Jun 12, 2013·Epigenomics·Xiaotu MaAdi F Gazdar
Aug 27, 2013·Epigenetics : Official Journal of the DNA Methylation Society·Aniruddha ChatterjeeShinichi Nakagawa
Jul 9, 2013·Genome Biology and Evolution·Tatiana TatarinovaMatteo Pellegrini
May 29, 2014·The Journal of Clinical Investigation·Jessilyn DunnHanjoong Jo
Aug 20, 2014·British Journal of Pharmacology·David CheishviliMoshe Szyf
Jun 25, 2015·BioMed Research International·Érica S S de AraújoAna C V Krepischi
Dec 31, 2015·Molecular Biology and Evolution·Thomas E KellerSoojin V Yi
May 18, 2016·Molecular Biology and Evolution·Groves B DixonMikhail V Matz
Sep 10, 2016·BioMed Research International·Xindong ZhangLuonan Chen
Mar 28, 2017·Digestive Diseases and Sciences·Jianzhong YeLanjuan Li
Mar 28, 2017·Epigenomics·Richard Kellermayer
Jan 5, 2018·Clinical Epigenetics·Anneli C S BolundTorben Sigsgaard
Apr 13, 2018·The Tohoku Journal of Experimental Medicine·Xing-Jie BaoLi-Na Zhang
Sep 22, 2018·Genome Biology and Evolution·Hyeonsoo JeongSoojin V Yi
Jan 25, 2019·Epigenetics : Official Journal of the DNA Methylation Society·Sarah W CurtisAlicia K Smith
Jun 8, 2019·Toxicological Sciences : an Official Journal of the Society of Toxicology·Hao ChenJoshua F Robinson
Sep 12, 2019·Journal of Cachexia, Sarcopenia and Muscle·Lingxiao HeMartine Thomis
Jan 1, 2020·Journal of Diabetes and Metabolic Disorders·Thai Quoc TranFuu-Jen Tsai
Nov 18, 2019·Statistical Applications in Genetics and Molecular Biology·Tobias MadsenJakob Skou Pedersen
Apr 1, 2020·Epigenetics : Official Journal of the DNA Methylation Society·Anusha DhanasiriJorge M O Fernandes
Oct 28, 2014·Acta Physiologica·S VoisinD J Bishop

❮ Previous
Next ❯

Datasets Mentioned

BETA
GM12878
GSE19090
19966280
K562
GSE32465
17556576

Methods Mentioned

BETA
immunoprecipitation
RRBS
ChIP-seq

Software Mentioned

UCSC Genome Browser
Affymetrix ExACT
Cap Analysis of Gene Expression ( CAGE

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.