Genome-wide DNA methylome analysis reveals epigenetically dysregulated non-coding RNAs in human breast cancer

Scientific Reports
Yongsheng LiXia Li

Abstract

Despite growing appreciation of the importance of epigenetics in breast cancer, our understanding of epigenetic alterations of non-coding RNAs (ncRNAs) in breast cancer remains limited. Here, we explored the epigenetic patterns of ncRNAs in breast cancers using published sequencing-based methylome data, primarily focusing on the two most commonly studied ncRNA biotypes, long ncRNAs and miRNAs. We observed widely aberrant methylation in the promoters of ncRNAs, and this abnormal methylation was more frequent than that in protein-coding genes. Specifically, intergenic ncRNAs were observed to comprise a majority (51.45% of the lncRNAs and 51.57% of the miRNAs) of the aberrantly methylated ncRNA promoters. Moreover, we summarized five patterns of aberrant ncRNA promoter methylation in the context of genomic CpG islands (CGIs), in which aberrant methylation occurred not only on CGIs, but also in regions flanking CGI and in CGI-lacking promoters. Integration with transcriptional datasets enabled us to determine that the ncRNA promoter methylation events were associated with transcriptional changes. Furthermore, a panel of ncRNAs were identified as biomarkers that discriminated between disease phenotypes. Finally, the potential functi...Continue Reading

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Citations

Aug 19, 2015·Frontiers in Genetics·Prashanth SuravajhalaHaja N Kadarmideen
May 5, 2016·Molecular Nutrition & Food Research·Donato F RomagnoloOrnella I Selmin
Dec 5, 2017·Journal of Alzheimer's Disease : JAD·Paulami ChatterjeeNitin Rathi
Jan 10, 2018·Frontiers in Microbiology·Daniel Frías-Lasserre, Cristian A Villagra
Oct 24, 2018·International Journal of Cancer. Journal International Du Cancer·Steffen DietzHolger Sültmann
Nov 30, 2018·Medicinal Chemistry·Abbasali EmamjomehGhasem Mahdevar
May 10, 2016·Nature Structural & Molecular Biology·Viviane LabrieArturas Petronis
Dec 10, 2015·Genes, Chromosomes & Cancer·Musaffe TunaGeorge A Calin
Oct 5, 2019·International Journal of Molecular Sciences·Chiara VillaRomina Combi
Nov 28, 2019·Nature·Yang LiuKarolin Luger
May 26, 2018·Carcinogenesis·Matteo GiuliettiFrancesco Piva
Apr 23, 2020·International Journal of Molecular Medicine·Jianghuai JiDongguo Li
Jul 19, 2017·Scientific Reports·Tzu-Kang LinKwang-Huei Lin

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Methods Mentioned

BETA
immunoprecipitation
MBDCap-seq
RNA-seq

Software Mentioned

Cuffdiff
UCSC browser
GENCODE
LiftOver
TopHat
MedCalc

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