EMdeCODE: a novel algorithm capable of reading words of epigenetic code to predict enhancers and retroviral integration sites and to identify H3R2me1 as a distinctive mark of coding versus non-coding genes

Details

Serval ID
serval:BIB_8C0E255D3C1D
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
EMdeCODE: a novel algorithm capable of reading words of epigenetic code to predict enhancers and retroviral integration sites and to identify H3R2me1 as a distinctive mark of coding versus non-coding genes
Journal
Nucleic Acids Res
Author(s)
Santoni F. A.
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Publication state
Published
Issued date
2013
Volume
41
Number
3
Pages
e48
Language
english
Notes
Santoni, Federico Andrea
eng
249968/European Research Council/International
Research Support, Non-U.S. Gov't
England
Nucleic Acids Res. 2013 Feb 1;41(3):e48. doi: 10.1093/nar/gks1214. Epub 2012 Dec 11.
Abstract
Existence of some extra-genetic (epigenetic) codes has been postulated since the discovery of the primary genetic code. Evident effects of histone post-translational modifications or DNA methylation over the efficiency and the regulation of DNA processes are supporting this postulation. EMdeCODE is an original algorithm that approximate the genomic distribution of given DNA features (e.g. promoter, enhancer, viral integration) by identifying relevant ChIPSeq profiles of post-translational histone marks or DNA binding proteins and combining them in a supermark. EMdeCODE kernel is essentially a two-step procedure: (i) an expectation-maximization process calculates the mixture of epigenetic factors that maximize the Sensitivity (recall) of the association with the feature under study; (ii) the approximated density is then recursively trimmed with respect to a control dataset to increase the precision by reducing the number of false positives. EMdeCODE densities improve significantly the prediction of enhancer loci and retroviral integration sites with respect to previous methods. Importantly, it can also be used to extract distinctive factors between two arbitrary conditions. Indeed EMdeCODE identifies unexpected epigenetic profiles specific for coding versus non-coding RNA, pointing towards a new role for H3R2me1 in coding regions.
Keywords
*Algorithms, Chromatin Immunoprecipitation, *Enhancer Elements, Genetic, *Epigenesis, Genetic, Genes, High-Throughput Nucleotide Sequencing, Histones/*analysis, RNA, Long Noncoding/genetics, Retroviridae/*genetics, *Virus Integration
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20/05/2019 13:52
Last modification date
02/10/2019 6:26
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