Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression.

BMC Bioinformatics
Xiaojiang XuStefan Bekiranov

Abstract

In the last decade, biochemical studies have revealed that epigenetic modifications including histone modifications, histone variants and DNA methylation form a complex network that regulate the state of chromatin and processes that depend on it including transcription and DNA replication. Currently, a large number of these epigenetic modifications are being mapped in a variety of cell lines at different stages of development using high throughput sequencing by members of the ENCODE consortium, the NIH Roadmap Epigenomics Program and the Human Epigenome Project. An extremely promising and underexplored area of research is the application of machine learning methods, which are designed to construct predictive network models, to these large-scale epigenomic data sets. Using a ChIP-Seq data set of 20 histone lysine and arginine methylations and histone variant H2A.Z in human CD4+ T-cells, we built predictive models of gene expression as a function of histone modification/variant levels using Multilinear (ML) Regression and Multivariate Adaptive Regression Splines (MARS). Along with extensive crosstalk among the 20 histone methylations, we found H4R3me2 was the most and second most globally repressive histone methylation among the ...Continue Reading

References

Jan 19, 2000·Nature·B D Strahl, C D Allis
Aug 17, 2000·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·B M Turner
Aug 11, 2001·Science·T Jenuwein, C D Allis
Apr 13, 2004·Proceedings of the National Academy of Sciences of the United States of America·Andrew I SuJohn B Hogenesch
Oct 14, 2004·Endocrine Reviews·David Y LeeMichael R Stallcup
May 4, 2005·Molecular Cell·Mark T Bedford, Stéphane Richard
Sep 9, 2005·Frontiers in Bioscience : a Journal and Virtual Library·Joanna WysockaScott Coonrod
Nov 10, 2005·Genome Biology·Michael J BuckJason D Lieb
Jan 24, 2006·Molecular and Cellular Biology·Xavier Le GuezennecHendrik G Stunnenberg
May 16, 2006·Nature Cell Biology·Katia AncelinM Azim Surani
Dec 13, 2006·Genes & Development·Michael C YuPamela A Silver
Feb 27, 2007·Cell·Bing LiJerry L Workman
Jul 3, 2007·Nature·Tarjei S MikkelsenBradley E Bernstein
Nov 7, 2007·Nature Structural & Molecular Biology·John A Latham, Sharon Y R Dent
Nov 27, 2007·Nature Reviews. Molecular Cell Biology·Alexander J RuthenburgC David Allis
Nov 18, 2008·Cell·Tamaki Suganuma, Jerry L Workman
Nov 27, 2008·Nucleic Acids Research·T J P HubbardP Flicek
Jan 20, 2009·Molecular Cell·Mark T Bedford, Steven G Clarke
Feb 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Rosa KarlićMartin Vingron

❮ Previous
Next ❯

Citations

May 13, 2014·Cell and Tissue Research·Deborah Roidl, Christine Hacker
Jul 9, 2011·Biochemistry·You FengYujun George Zheng
Jan 7, 2016·Frontiers in Neuroscience·Nikolaos MitrousisOla Hermanson
Feb 11, 2015·Cellular and Molecular Life Sciences : CMLS·Nicole StopaDavid Shechter
Jan 25, 2017·Nucleic Acids Research·Guozhen GaoMark T Bedford
Mar 25, 2017·Chemical Reviews·H Ümit KaniskanJian Jin
Jun 14, 2013·BMC Bioinformatics·Jacob BiesingerXiaohui Xie
Nov 16, 2010·FEBS Letters·Alessandra Di Lorenzo, Mark T Bedford
Nov 30, 2011·Epigenomics·Ian C Wood
Oct 8, 2011·Communicative & Integrative Biology·Ezequiel PetrilloMarcelo J Yanovsky
Feb 22, 2012·Bioinformatics·Dominik BeckJason W H Wong
Sep 3, 2013·Pediatric Nephrology : Journal of the International Pediatric Nephrology Association·Sanjeevkumar R PatelGregory R Dressler
May 20, 2017·Epigenetics : Official Journal of the DNA Methylation Society·Lawrence B HolderMichael K Skinner
Jan 28, 2017·Mediators of Inflammation·Yasuto Araki, Toshihide Mimura
Dec 18, 2019·The Journal of Clinical Investigation·Christopher L NoblesFrederic D Bushman
Aug 21, 2018·International Journal of Cancer. Journal International Du Cancer·Junhu WanLiang Ming
Sep 23, 2019·Methods : a Companion to Methods in Enzymology·Sinja RakowCaroline Bouchard
Oct 11, 2017·Toxicology and Applied Pharmacology·Baolai ZhangNengqian Ma
Jul 24, 2018·ACS Medicinal Chemistry Letters·Zahid Q BondayRobert M Campbell
Dec 22, 2015·ACS Chemical Biology·Jakob Fuhrmann, Paul R Thompson
Jun 6, 2018·Journal of Medicinal Chemistry·Yuanxiang WangYanqiu Yuan
Jul 18, 2019·ACS Medicinal Chemistry Letters·Hong LinJuan I Luengo
Sep 6, 2013·Epigenetics & Chromatin·Marcin CieślikStefan Bekiranov

❮ Previous
Next ❯

Methods Mentioned

BETA
acetylation
ChIP-chip
ChIP-Seq
gene

Software Mentioned

stepwisefit
Ensembl
MATLAB
GCRMA
MACS
SymAtlas
R
MARS

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.

Related Papers

Expert Opinion on Therapeutic Targets
Rayleen V BowmanKwun M Fong
Cell
Bradley E BernsteinEric S Lander
Nature Biotechnology
Bradley E BernsteinJames A Thomson
Current Opinion in Plant Biology
Qian Liu, Zhizhong Gong
Human Molecular Genetics
Pauline A Callinan, Andrew P Feinberg
© 2021 Meta ULC. All rights reserved