Cargando…
Epigenetic regulation of gene expression in cancer: techniques, resources and analysis
Cancer is a complex disease, driven by aberrant activity in numerous signaling pathways in even individual malignant cells. Epigenetic changes are critical mediators of these functional changes that drive and maintain the malignant phenotype. Changes in DNA methylation, histone acetylation and methy...
Autores principales: | , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860551/ https://www.ncbi.nlm.nih.gov/pubmed/28968850 http://dx.doi.org/10.1093/bfgp/elx018 |
_version_ | 1783307978778083328 |
---|---|
author | Kagohara, Luciane T Stein-O’Brien, Genevieve L Kelley, Dylan Flam, Emily Wick, Heather C Danilova, Ludmila V Easwaran, Hariharan Favorov, Alexander V Qian, Jiang Gaykalova, Daria A Fertig, Elana J |
author_facet | Kagohara, Luciane T Stein-O’Brien, Genevieve L Kelley, Dylan Flam, Emily Wick, Heather C Danilova, Ludmila V Easwaran, Hariharan Favorov, Alexander V Qian, Jiang Gaykalova, Daria A Fertig, Elana J |
author_sort | Kagohara, Luciane T |
collection | PubMed |
description | Cancer is a complex disease, driven by aberrant activity in numerous signaling pathways in even individual malignant cells. Epigenetic changes are critical mediators of these functional changes that drive and maintain the malignant phenotype. Changes in DNA methylation, histone acetylation and methylation, noncoding RNAs, posttranslational modifications are all epigenetic drivers in cancer, independent of changes in the DNA sequence. These epigenetic alterations were once thought to be crucial only for the malignant phenotype maintenance. Now, epigenetic alterations are also recognized as critical for disrupting essential pathways that protect the cells from uncontrolled growth, longer survival and establishment in distant sites from the original tissue. In this review, we focus on DNA methylation and chromatin structure in cancer. The precise functional role of these alterations is an area of active research using emerging high-throughput approaches and bioinformatics analysis tools. Therefore, this review also describes these high-throughput measurement technologies, public domain databases for high-throughput epigenetic data in tumors and model systems and bioinformatics algorithms for their analysis. Advances in bioinformatics data that combine these epigenetic data with genomics data are essential to infer the function of specific epigenetic alterations in cancer. These integrative algorithms are also a focus of this review. Future studies using these emerging technologies will elucidate how alterations in the cancer epigenome cooperate with genetic aberrations during tumor initiation and progression. This deeper understanding is essential to future studies with epigenetics biomarkers and precision medicine using emerging epigenetic therapies. |
format | Online Article Text |
id | pubmed-5860551 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-58605512018-03-28 Epigenetic regulation of gene expression in cancer: techniques, resources and analysis Kagohara, Luciane T Stein-O’Brien, Genevieve L Kelley, Dylan Flam, Emily Wick, Heather C Danilova, Ludmila V Easwaran, Hariharan Favorov, Alexander V Qian, Jiang Gaykalova, Daria A Fertig, Elana J Brief Funct Genomics Review Papers Cancer is a complex disease, driven by aberrant activity in numerous signaling pathways in even individual malignant cells. Epigenetic changes are critical mediators of these functional changes that drive and maintain the malignant phenotype. Changes in DNA methylation, histone acetylation and methylation, noncoding RNAs, posttranslational modifications are all epigenetic drivers in cancer, independent of changes in the DNA sequence. These epigenetic alterations were once thought to be crucial only for the malignant phenotype maintenance. Now, epigenetic alterations are also recognized as critical for disrupting essential pathways that protect the cells from uncontrolled growth, longer survival and establishment in distant sites from the original tissue. In this review, we focus on DNA methylation and chromatin structure in cancer. The precise functional role of these alterations is an area of active research using emerging high-throughput approaches and bioinformatics analysis tools. Therefore, this review also describes these high-throughput measurement technologies, public domain databases for high-throughput epigenetic data in tumors and model systems and bioinformatics algorithms for their analysis. Advances in bioinformatics data that combine these epigenetic data with genomics data are essential to infer the function of specific epigenetic alterations in cancer. These integrative algorithms are also a focus of this review. Future studies using these emerging technologies will elucidate how alterations in the cancer epigenome cooperate with genetic aberrations during tumor initiation and progression. This deeper understanding is essential to future studies with epigenetics biomarkers and precision medicine using emerging epigenetic therapies. Oxford University Press 2017-08-11 /pmc/articles/PMC5860551/ /pubmed/28968850 http://dx.doi.org/10.1093/bfgp/elx018 Text en © The Author 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Review Papers Kagohara, Luciane T Stein-O’Brien, Genevieve L Kelley, Dylan Flam, Emily Wick, Heather C Danilova, Ludmila V Easwaran, Hariharan Favorov, Alexander V Qian, Jiang Gaykalova, Daria A Fertig, Elana J Epigenetic regulation of gene expression in cancer: techniques, resources and analysis |
title | Epigenetic regulation of gene expression in cancer: techniques, resources and analysis |
title_full | Epigenetic regulation of gene expression in cancer: techniques, resources and analysis |
title_fullStr | Epigenetic regulation of gene expression in cancer: techniques, resources and analysis |
title_full_unstemmed | Epigenetic regulation of gene expression in cancer: techniques, resources and analysis |
title_short | Epigenetic regulation of gene expression in cancer: techniques, resources and analysis |
title_sort | epigenetic regulation of gene expression in cancer: techniques, resources and analysis |
topic | Review Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860551/ https://www.ncbi.nlm.nih.gov/pubmed/28968850 http://dx.doi.org/10.1093/bfgp/elx018 |
work_keys_str_mv | AT kagoharalucianet epigeneticregulationofgeneexpressionincancertechniquesresourcesandanalysis AT steinobriengenevievel epigeneticregulationofgeneexpressionincancertechniquesresourcesandanalysis AT kelleydylan epigeneticregulationofgeneexpressionincancertechniquesresourcesandanalysis AT flamemily epigeneticregulationofgeneexpressionincancertechniquesresourcesandanalysis AT wickheatherc epigeneticregulationofgeneexpressionincancertechniquesresourcesandanalysis AT danilovaludmilav epigeneticregulationofgeneexpressionincancertechniquesresourcesandanalysis AT easwaranhariharan epigeneticregulationofgeneexpressionincancertechniquesresourcesandanalysis AT favorovalexanderv epigeneticregulationofgeneexpressionincancertechniquesresourcesandanalysis AT qianjiang epigeneticregulationofgeneexpressionincancertechniquesresourcesandanalysis AT gaykalovadariaa epigeneticregulationofgeneexpressionincancertechniquesresourcesandanalysis AT fertigelanaj epigeneticregulationofgeneexpressionincancertechniquesresourcesandanalysis |