Modeling circRNA expression pattern with integrated sequence and epigenetic features demonstrates the potential involvement of H3K79me2 in circRNA expression.

Bioinformatics
Jia-Bin ChenTie-Lin Yang

Abstract

CircRNAs are an abundant class of non-coding RNAs with widespread, cell-/tissue-specific patterns. Previous work suggested that epigenetic features might be related to circRNA expression. However, the contribution of epigenetic changes to circRNA expression has not been investigated systematically. Here, we built a machine learning framework named CIRCScan, to predict circRNA expression in various cell lines based on the sequence and epigenetic features. The predicted accuracy of the expression status models was high with area under the curve of receiver operating characteristic (ROC) values of 0.89-0.92 and the false-positive rates of 0.17-0.25. Predicted expressed circRNAs were further validated by RNA-seq data. The performance of expression-level prediction models was also good with normalized root-mean-square errors of 0.28-0.30 and Pearson's correlation coefficient r over 0.4 in all cell lines, along with Spearman's correlation coefficient ρ of 0.33-0.46. Noteworthy, H3K79me2 was highly ranked in modeling both circRNA expression status and levels across different cells. Further analysis in additional nine cell lines demonstrated a significant enrichment of H3K79me2 in circRNA flanking intron regions, supporting the potenti...Continue Reading

References

Aug 30, 2000·Proceedings of the National Academy of Sciences of the United States of America·O AlterD Botstein
May 2, 2003·The Journal of Biological Chemistry·Yutaka Kondo, Jean-Pierre J Issa
May 5, 2004·Proceedings of the National Academy of Sciences of the United States of America·Yutaka KondoJean-Pierre J Issa
Feb 16, 2008·Structure·Jordanka Zlatanova, Amit Thakar
Jul 16, 2008·BMC Bioinformatics·Carolin StroblAchim Zeileis
Aug 19, 2009·Genome Research·Robin AnderssonJan Komorowski
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Feb 6, 2010·Science·Reini F LucoTom Misteli
Feb 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Rosa KarlićMartin Vingron
Mar 6, 2012·Nature·Tamer T OnderGeorge Q Daley
Sep 7, 2012·Genome Biology·Xianjun DongZhiping Weng
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Dec 20, 2012·RNA·William R JeckNorman E Sharpless
Mar 1, 2013·Nature·Thomas B HansenJørgen Kjems
Mar 1, 2013·Nature·Sebastian MemczakNikolaus Rajewsky
Jun 26, 2013·Nature Genetics·Tim R MercerJohn A Stamatoyannopoulos
Sep 10, 2013·Cancer Research·Thomas B HansenChristian K Damgaard
Sep 17, 2013·PLoS Genetics·Julia SalzmanPatrick O Brown
Apr 8, 2014·Cell Reports·Ming SuJing-Dong J Han
May 7, 2014·Nucleic Acids Research·Fidel RamírezThomas Manke
Jun 6, 2014·PLoS Computational Biology·Ondrej PodlahaFranziska Michor
Sep 23, 2014·RNA·Petar GlažarNikolaus Rajewsky
Sep 23, 2014·Cell·Xiao-Ou ZhangLi Yang
Sep 27, 2014·Cell·Quentin Vicens, Eric Westhof
Dec 3, 2014·Genes & Development·Nova FongDavid L Bentley
Dec 30, 2014·Cell Reports·Stefan StarkeAlbrecht Bindereif
Jan 6, 2015·Cell Reports·Andranik IvanovNikolaus Rajewsky
Apr 30, 2015·Molecular Cell·Agnieszka Rybak-WolfNikolaus Rajewsky
Jun 4, 2015·Annual Review of Biochemistry·Shiran NaftelbergAlberto R Kornblihtt
Jun 9, 2015·Cancer Letters·Shibin QuHaimin Li
Nov 19, 2015·Proceedings of the National Academy of Sciences of the United States of America·Silvia Jimeno-GonzálezJosé C Reyes
Dec 15, 2015·Nucleic Acids Research·Thomas B HansenJørgen Kjems
Jun 2, 2016·Development·Steven P Barrett, Julia Salzman
Jul 23, 2016·Trends in Neurosciences·Wei Chen, Erin Schuman
Aug 19, 2016·Genome Medicine·Juan L TrincadoE Eyras
Apr 28, 2017·Genes & Development·Kelly E NissenChristine Guthrie
Jun 9, 2017·PLoS Computational Biology·Xiangxiang ZengQuan Zou
Jul 31, 2018·Molecular Cell·Xiang LiLing-Ling Chen
Feb 9, 2019·Cell·Josh N VoArul M Chinnaiyan

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