Epigenome

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An Epigenome consists of a record of the chemical changes to the DNA and histone proteins of an organism; these changes can be passed down to an organism's offspring. Changes to the epigenome can result in changes to the structure of chromatin and changes to the function of the genome.[1]

The epigenome is involved in regulating gene expression, development, tissue differentiation, and suppression of transposable elements. Unlike the underlying genome which is largely static within an individual, the epigenome can be dynamically altered by environmental conditions.

Epigenetics is one of the currently active topics in cancer research. Human tumors undergo a major disruption of DNA methylation and histone modification patterns. The aberrant epigenetic landscape of the cancer cell is characterized by a global genomic hypomethylation, CpG island promoter hypermethylation of tumor suppressor genes, an altered histone code for critical genes and a global loss of monoacetylated and trimethylated histone H4.

Much of the subject matter is not yet fully understood. Some people have suggested a Human Epigenome Project.[2] As a prelude to a full-scale Human Epigenome Project, the Human Epigenome Pilot Project aims to identify and catalogue Methylation Variable Positions (MVPs) in the human genome.[3] Advances in sequencing technology now allow for assaying genome-wide epigenomic states by a variety of molecular methodologies.[4] A variety of micro- and nanoscale devices have been constructed or proposed to investigate the epigenome.[5]

One goal of the NIH Roadmap Epigenomics Project is to generate human reference epigenomes from normal, healthy individuals across a large variety of cell lines, primary cells and primary tissues. Data produced by the Roadmap Epigenomics Project, which can be browsed and downloaded from the Human Epigenome Atlas, fall into five types that assay different aspects of the epigenome and outcomes of epigenomic states (such as gene expression):

  1. Histone Modifications - Chromatin Immunoprecipitation Sequencing (ChIP-Seq) identifies genome wide patterns of histone modifications using antibodies against the modifications.[6]
  2. DNA Methylation - Whole Genome Bisulfite-Seq, Reduced Representation Bisulfite-Seq (RRBS), Methylated DNA Immunoprecipitation Sequencing (MeDIP-Seq), and Methylation-sensitive Restriction Enzyme Sequencing (MRE-Seq) identify DNA methylation across portions of the genome at varying levels of resolution down to basepair level.[7]
  3. Chromatin Accessibility - DNase I hypersensitive sites Sequencing (DNase-Seq) identifies regions of open chromatin.
  4. Gene Expression - RNA-Seq and expression arrays identify expression levels or protein coding genes.
  5. Small RNA Expression - smRNA-Seq identifies expression of small noncoding RNA, primarily miRNAs.

Reference epigenomes for healthy individuals will enable the second goal of the Roadmap Epigenomics Project which is to examine epigenomic differences that occur in disease states such as Alzheimer's disease.

An international effort to assay reference epigenomes has recently commenced in the form of the International Human Epigenome Consortium.

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References[edit]

  1. ^ Bernstein, Bradley E.; Meissner, Alexander; Lander,Eric S. (February 2007). "The Mammalian Epigenome". Cell 128 (4): 669–681. doi:10.1016/j.cell.2007.01.033. PMID 17320505. Retrieved 19 December 2011. 
  2. ^ Jones, Peter A.; Martienssen, Robert (December 15, 2005). "A Blueprint for a Human Epigenome Project: The AACR Human Epigenome Workshop". Cancer Research 65 (24): 11241–6. doi:10.1158/0008-5472.CAN-05-3865. PMID 16357125. Retrieved 19 December 2011. 
  3. ^ Human Epigenome Project
  4. ^ Milosavljevic, Aleksandar (June 2011). "Emerging patterns of epigenomic variation". Trends in Genetics 27: 242–250. doi:10.1016/j.tig.2011.03.001. 
  5. ^ Aguilar, Carlos; Craighead, Harold (October 4, 2013). "Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics". Nature Nanotechnology 8 (10): 709–718. doi:10.1038/nnano.2013.195. 
  6. ^ Zhu, J., et al.. (2013). "Genome-wide chromatin state transitions associated with developmental and environmental cues". Cell 152 (3): 642–654. doi:10.1016/j.cell.2012.12.033. PMID 23333102. 
  7. ^ Harris, R. Alan; et al.; (September 19, 2010). "Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications". Nature Biotechnology 28 (10): 1097–1105. doi:10.1038/nbt.1682. 

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