Finding commonality between the pattern of histone modifications across normal and cancer cell types dictated by DNA sequence features
Introduction: Histone modification, a covalent post-translational modification of histone proteins, influences gene expression by altering chromatin structure giving rise to key characteristics to various cell types. While interaction of histone proteins with DNA is not known to be dependent on DNA...
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doaj-a7107bd7b85948a9b62110864bb156552020-11-25T00:22:28ZengScience Planet Inc.Canadian Journal of Biotechnology2560-83042017-10-011Special Issue434310.24870/cjb.2017-a30Finding commonality between the pattern of histone modifications across normal and cancer cell types dictated by DNA sequence featuresSubhamoy Datta0Manthan Patel1Divyesh Patel2Umashankar Singh3Department of Biological Engineering, Indian Institute of Technology, Gandhinagar, Gujarat, INDIADepartment of Biological Engineering, Indian Institute of Technology, Gandhinagar, Gujarat, INDIADepartment of Biological Engineering, Indian Institute of Technology, Gandhinagar, Gujarat, INDIADepartment of Biological Engineering, Indian Institute of Technology, Gandhinagar, Gujarat, INDIAIntroduction: Histone modification, a covalent post-translational modification of histone proteins, influences gene expression by altering chromatin structure giving rise to key characteristics to various cell types. While interaction of histone proteins with DNA is not known to be dependent on DNA sequence features, histone modifications are highly regulated in certain genomic regions. This specificity is required in normal cells to prevent genome instability, chromosome segregation defects and to maintain cellular homeostasis and is altered in cancer. Identifying [1] if specific sequence features are associated with certain histone modifications and [2] if these associations are consistently disrupted in transformed cells, will establish links between the genotype and epigenotype giving us valuable predictability about histone code. In this study, we have analyzed ChIP-seq data of different histone modifications in human across primary and immortalized cell lines from ENCODE database. Experiments and key results findings: We have identified unique as well as common genomic regions that carry histone marks commonly in primary and immortal cell lines. Additionally, motif finding analysis indeed shows certain modifications are associated with crucial genes required for cell survival and function; some uniquely in transformed cell lines. The regions with consistently different histone marks are currently being studied to check whether they are associated with certain cytosine methylation profile too. Our results suggest a genotypic predisposition for epigenotype.https://www.canadianjbiotech.com/CAN_J_BIOTECH/Archives/v1/Special Issue/cjb.2017-a30.pdf |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Subhamoy Datta Manthan Patel Divyesh Patel Umashankar Singh |
spellingShingle |
Subhamoy Datta Manthan Patel Divyesh Patel Umashankar Singh Finding commonality between the pattern of histone modifications across normal and cancer cell types dictated by DNA sequence features Canadian Journal of Biotechnology |
author_facet |
Subhamoy Datta Manthan Patel Divyesh Patel Umashankar Singh |
author_sort |
Subhamoy Datta |
title |
Finding commonality between the pattern of histone modifications across normal and cancer cell types dictated by DNA sequence features |
title_short |
Finding commonality between the pattern of histone modifications across normal and cancer cell types dictated by DNA sequence features |
title_full |
Finding commonality between the pattern of histone modifications across normal and cancer cell types dictated by DNA sequence features |
title_fullStr |
Finding commonality between the pattern of histone modifications across normal and cancer cell types dictated by DNA sequence features |
title_full_unstemmed |
Finding commonality between the pattern of histone modifications across normal and cancer cell types dictated by DNA sequence features |
title_sort |
finding commonality between the pattern of histone modifications across normal and cancer cell types dictated by dna sequence features |
publisher |
Science Planet Inc. |
series |
Canadian Journal of Biotechnology |
issn |
2560-8304 |
publishDate |
2017-10-01 |
description |
Introduction: Histone modification, a covalent post-translational modification of histone proteins, influences gene expression by altering chromatin structure giving rise to key characteristics to various cell types. While interaction of histone proteins with DNA is not known to be dependent on DNA sequence features, histone modifications are highly regulated in certain genomic regions. This specificity is required in normal cells to prevent genome instability, chromosome segregation defects and to maintain cellular homeostasis and is altered in cancer. Identifying [1] if specific sequence features are associated with certain histone modifications and [2] if these associations are consistently disrupted in transformed cells, will establish links between the genotype and epigenotype giving us valuable predictability about histone code. In this study, we have analyzed ChIP-seq data of different histone modifications in human across primary and immortalized cell lines from ENCODE database.
Experiments and key results findings: We have identified unique as well as common genomic regions that carry histone marks commonly in primary and immortal cell lines. Additionally, motif finding analysis indeed shows certain modifications are associated with crucial genes required for cell survival and function; some uniquely in transformed cell lines. The regions with consistently different histone marks are currently being studied to check whether they are associated with certain cytosine methylation profile too. Our results suggest a genotypic predisposition for epigenotype. |
url |
https://www.canadianjbiotech.com/CAN_J_BIOTECH/Archives/v1/Special Issue/cjb.2017-a30.pdf |
work_keys_str_mv |
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