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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
Breast cancer is one of the leading causes of cancer in women all over the world and accounts for ~25% of newly observed cancers in women. Epigenetic modifications influence differential expression of genes through non-coding RNA and play a crucial role in cancer regulation. In the present study, ep...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Korea Genome Organization
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8261273/ https://www.ncbi.nlm.nih.gov/pubmed/34261302 http://dx.doi.org/10.5808/gi.21020 |
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author | Kotipalli, Aneesh Banerjee, Ruma Kasibhatla, Sunitha Manjari Joshi, Rajendra |
author_facet | Kotipalli, Aneesh Banerjee, Ruma Kasibhatla, Sunitha Manjari Joshi, Rajendra |
author_sort | Kotipalli, Aneesh |
collection | PubMed |
description | Breast cancer is one of the leading causes of cancer in women all over the world and accounts for ~25% of newly observed cancers in women. Epigenetic modifications influence differential expression of genes through non-coding RNA and play a crucial role in cancer regulation. In the present study, epigenetic regulation of gene expression by in-silico analysis of histone modifications using chromatin immunoprecipitation sequencing (ChIP-Seq) has been carried out. Histone modification data of H3K4me3 from one normal-like and four breast cancer cell lines were used to predict miRNA expression at the promoter level. Predicted miRNA promoters (based on ChIP-Seq) were used as a probe to identify gene targets. Five triple-negative breast cancer (TNBC)‒specific miRNAs (miR153-1, miR4767, miR4487, miR6720, and miR-LET7I) were identified and corresponding 13 gene targets were predicted. Eight miRNA promoter peaks were predicted to be differentially expressed in at least three breast cancer cell lines (miR4512, miR6791, miR330, miR3180-3, miR6080, miR5787, miR6733, and miR3613). A total of 44 gene targets were identified based on the 3′-untranslated regions of downregulated mRNA genes that contain putative binding targets to these eight miRNAs. These include 17 and 15 genes in luminal-A type and TNBC respectively, that have been reported to be associated with breast cancer regulation. Of the remaining 12 genes, seven (A4GALT, C2ORF74, HRCT1, ZC4H2, ZNF512, ZNF655, and ZNF608) show similar relative expression profiles in large patient samples and other breast cancer cell lines thereby giving insight into predicted role of H3K4me3 mediated gene regulation via the miRNA-mRNA axis. |
format | Online Article Text |
id | pubmed-8261273 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Korea Genome Organization |
record_format | MEDLINE/PubMed |
spelling | pubmed-82612732021-07-16 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 Kotipalli, Aneesh Banerjee, Ruma Kasibhatla, Sunitha Manjari Joshi, Rajendra Genomics Inform Original Article Breast cancer is one of the leading causes of cancer in women all over the world and accounts for ~25% of newly observed cancers in women. Epigenetic modifications influence differential expression of genes through non-coding RNA and play a crucial role in cancer regulation. In the present study, epigenetic regulation of gene expression by in-silico analysis of histone modifications using chromatin immunoprecipitation sequencing (ChIP-Seq) has been carried out. Histone modification data of H3K4me3 from one normal-like and four breast cancer cell lines were used to predict miRNA expression at the promoter level. Predicted miRNA promoters (based on ChIP-Seq) were used as a probe to identify gene targets. Five triple-negative breast cancer (TNBC)‒specific miRNAs (miR153-1, miR4767, miR4487, miR6720, and miR-LET7I) were identified and corresponding 13 gene targets were predicted. Eight miRNA promoter peaks were predicted to be differentially expressed in at least three breast cancer cell lines (miR4512, miR6791, miR330, miR3180-3, miR6080, miR5787, miR6733, and miR3613). A total of 44 gene targets were identified based on the 3′-untranslated regions of downregulated mRNA genes that contain putative binding targets to these eight miRNAs. These include 17 and 15 genes in luminal-A type and TNBC respectively, that have been reported to be associated with breast cancer regulation. Of the remaining 12 genes, seven (A4GALT, C2ORF74, HRCT1, ZC4H2, ZNF512, ZNF655, and ZNF608) show similar relative expression profiles in large patient samples and other breast cancer cell lines thereby giving insight into predicted role of H3K4me3 mediated gene regulation via the miRNA-mRNA axis. Korea Genome Organization 2021-06-30 /pmc/articles/PMC8261273/ /pubmed/34261302 http://dx.doi.org/10.5808/gi.21020 Text en (c) 2021, Korea Genome Organization https://creativecommons.org/licenses/by/4.0/(CC) This is an open-access article distributed under the terms of the Creative Commons Attribution license(https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Article Kotipalli, Aneesh Banerjee, Ruma Kasibhatla, Sunitha Manjari Joshi, Rajendra 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 |
title | 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 |
title_full | 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 |
title_fullStr | 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 |
title_full_unstemmed | 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 |
title_short | 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 |
title_sort | 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 |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8261273/ https://www.ncbi.nlm.nih.gov/pubmed/34261302 http://dx.doi.org/10.5808/gi.21020 |
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