Analysis of H3K4me3-ChIP-Seq and RNA-Seq data to understand the putative role of miRNAs and their target genes in breast cancer cell lines

• DOI: 10.5808/gi.21020
• Publication Date: 2021-06-30T07:47:12Z
• Authors: Aneesh Kotipalli; Ruma Banerjee; Sunitha Manjari K...; Rajendra Joshi
• Keywords: H3K4me3; Chromatin immunoprecipitation; RNA-Seq

Breast cancer is one of the leading causes in women all over world and accounts for ~25% newly observed cancers women. Epigenetic modifications influence differential expression genes through non-coding RNA play a crucial role regulation. In present study, epigenetic regulation gene by in-silico analysis histone using chromatin immunoprecipitation sequencing (ChIP-Seq) has been carried out. Histone modification data H3K4me3 from normal-like four breast cell lines were used to predict miRNA at promoter level. Predicted promoters (based on ChIP-Seq) as probe identify targets. Five triple-negative (TNBC)‒specific miRNAs (miR153-1, miR4767, miR4487, miR6720, miR-LET7I) identified corresponding 13 targets predicted. Eight peaks predicted be differentially expressed least three (miR4512, miR6791, miR330, miR3180-3, miR6080, miR5787, miR6733, miR3613). A total 44 based 3′-untranslated regions downregulated mRNA that contain putative binding these eight miRNAs. These include 17 15 luminal-A type TNBC respectively, have reported associated with Of remaining 12 genes, seven (A4GALT, C2ORF74, HRCT1, ZC4H2, ZNF512, ZNF655, ZNF608) show similar relative profiles large patient samples other thereby giving insight into mediated via miRNA-mRNA axis. Keywords: neoplasms, ChIP-Seq, luminal-A/triple-negative, miRNA, RNA-Seq