Extrapolating histone marks across developmental stages, tissues, and species: an enhancer prediction case study

BMC Genomics
John A Capra

Abstract

Dynamic activation and inactivation of gene regulatory DNA produce the expression changes that drive the differentiation of cellular lineages. Identifying regulatory regions active during developmental transitions is necessary to understand how the genome specifies complex developmental programs and how these processes are disrupted in disease. Gene regulatory dynamics are mediated by many factors, including the binding of transcription factors (TFs) and the methylation and acetylation of DNA and histones. Genome-wide maps of TF binding and DNA and histone modifications have been generated for many cellular contexts; however, given the diversity and complexity of animal development, these data cover only a small fraction of the cellular and developmental contexts of interest. Thus, there is a need for methods that use existing epigenetic and functional genomics data to analyze the thousands of contexts that remain uncharacterized. To investigate the utility of histone modification data in the analysis of cellular contexts without such data, I evaluated how well genome-wide H3K27ac and H3K4me1 data collected in different developmental stages, tissues, and species were able to predict experimentally validated heart enhancers acti...Continue Reading

References

Nov 30, 2006·Nucleic Acids Research·Axel ViselLen A Pennacchio
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Jul 16, 2010·Nature Reviews. Genetics·Roger P AlexanderMark B Gerstein
Aug 24, 2010·Nature Genetics·Matthew J BlowLen A Pennacchio
Oct 15, 2010·Nature Biotechnology·Bradley E BernsteinJames A Thomson
Nov 26, 2010·Proceedings of the National Academy of Sciences of the United States of America·Menno P CreyghtonRudolf Jaenisch
Mar 2, 2011·Nature Reviews. Genetics·Chin-Tong Ong, Victor G Corces
Oct 21, 2011·Nature·David BrawandHenrik Kaessmann
Dec 6, 2011·Nature Genetics·Dalit MayAxel Visel
Jul 31, 2012·Molecular Cell·Christoph BockAlexander Meissner
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Mar 26, 2013·PLoS Computational Biology·Nisha RajagopalBing Ren
May 8, 2013·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Chih-Hao Hsu, Ivan Ovcharenko
Aug 9, 2013·Nature·Michael J ZillerAlexander Meissner
Aug 21, 2013·Cell·Andrew B StergachisJohn A Stamatoyannopoulos
Nov 29, 2013·Proceedings of the National Academy of Sciences of the United States of America·Roberto PapaitGianluigi Condorelli
Mar 13, 2014·Nature Reviews. Genetics·Daria ShlyuevaAlexander Stark
Jun 27, 2014·PLoS Computational Biology·Genevieve D ErwinJohn A Capra
Aug 28, 2014·Bioinformatics·John A Capra, Dennis Kostka

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Citations

Jun 28, 2016·Neuroscience and Biobehavioral Reviews·Nils C GassenAnthony S Zannas
Jul 4, 2019·Nature Reviews. Molecular Cell Biology·Ashwini JambhekarYang Shi
Jul 19, 2017·BMC Genomics·Laura L ColbranJohn A Capra
May 20, 2017·Epigenetics : Official Journal of the DNA Methylation Society·Lawrence B HolderMichael K Skinner

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Methods Mentioned

BETA
acetylation
ChIP-Seq
immunoprecipitation

Software Mentioned

scipy
ENCODE
VISTA
VISTA enhancer browser
BEDtools suite
scikit
randomBed
AdaBoost
Roadmap Epigenomics
Random Forests

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