Document Detail

Methods for cancer epigenome analysis.
MedLine Citation:
PMID:  22956508     Owner:  NLM     Status:  MEDLINE    
Accurate detection of epimutations in tumor cells is crucial for -understanding the molecular pathogenesis of cancer. Alterations in DNA methylation in cancer are functionally important and clinically relevant, but even this well-studied area is continually re-evaluated in light of unanticipated results, such as the strong association between aberrant DNA methylation in adult tumors and polycomb group profiles in embryonic stem cells, cancer-associated genetic mutations in epigenetic regulators such as DNMT3A and TET family genes, and the discovery of altered 5-hydroxymethylcytosine, a product of TET proteins acting on 5-methylcytosine, in human tumors with TET mutations. The abundance and distribution of covalent histone modifications in primary cancer tissues relative to normal cells is an important but largely uncharted area, although there is good evidence for a mechanistic role of cancer-specific alterations in histone modifications in tumor etiology, drug response, and tumor progression. Meanwhile, the discovery of new epigenetic marks continues, and there are many useful methods for epigenome analysis applicable to primary tumor samples, in addition to cancer cell lines. For DNA methylation and hydroxymethylation, next-generation sequencing allows increasingly inexpensive and quantitative whole-genome profiling. Similarly, the refinement and maturation of chromatin immunoprecipitation with next-generation sequencing (ChIP-seq) has made possible genome-wide mapping of histone modifications, open chromatin, and transcription factor binding sites. Computational tools have been developed apace with these epigenome methods to better enable accurate interpretation of the profiling data.
Raman P Nagarajan; Shaun D Fouse; Robert J A Bell; Joseph F Costello
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Publication Detail:
Type:  Journal Article; Review    
Journal Detail:
Title:  Advances in experimental medicine and biology     Volume:  754     ISSN:  0065-2598     ISO Abbreviation:  Adv. Exp. Med. Biol.     Publication Date:  2013  
Date Detail:
Created Date:  2012-09-07     Completed Date:  2012-12-11     Revised Date:  2014-08-06    
Medline Journal Info:
Nlm Unique ID:  0121103     Medline TA:  Adv Exp Med Biol     Country:  United States    
Other Details:
Languages:  eng     Pagination:  313-38     Citation Subset:  IM    
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MeSH Terms
Epigenesis, Genetic / genetics*
Epigenomics / methods*
Gene Expression Regulation, Neoplastic*
Neoplasms / genetics*
Tumor Markers, Biological / genetics*
Grant Support
Reg. No./Substance:
0/Tumor Markers, Biological

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