Epigenome

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Epigenome is a term from the scientific field of epigenetics and is used to describe the entirety of epigenetic states. An epigenome is a set of chemical changes in an organism's DNA and histone proteins. These changes can be passed on to the offspring of an organism via transgenerational epigenetic inheritance. Changes in the epigenome can lead to changes in the structure of the chromatin and changes in the function of the genome.

The epigenome is involved in the regulation of gene expression, development, tissue differentiation and the suppression of transposable elements. In contrast to the underlying genome, which is largely static in an individual, the epigenome can be changed dynamically by environmental conditions.

Epigenome research projects

As a prelude to a potential human epigenome project , the Human Epigenome Pilot Project aims to identify and catalog variable methylation positions (MVPs) in the human genome. Advances in sequencing technology now allow the investigation of genome-wide epigenomic states by multiple molecular methods. Instruments at the micro and nano levels have been designed or proposed to study the epigenome. An international effort to study epigenomes began in 2010 in the form of the International Human Epigenome Consortium (IHEC). The IHEC members aim to generate at least 1,000 reference epigenomes from various normal and disease-associated human cell types.

Roadmap Epigenomics Project

One goal of the NIH Epigenomics Project roadmap is to generate reference human epigenomes from normal, healthy individuals across a wide variety of cell lines, primary cells, and primary tissues. The data generated by the project and available through the Human Epigenome Atlas are classified into five types that shed light on different aspects of the epigenome of its states (such as gene expression):

  1. Histone Modifications - Chromatin Immunoprecipitation Sequencing (ChIP-Seq) identifies genome-wide patterns of histone modifications by antibodies against the modifications.
  2. DNA methylation - bisulfite-Seq over the whole genome, reduced representation bisulfite-Seq (RRBS), immunoprecipitation sequencing of methylated DNA (MeDIP-Seq) and methylation-sensitive restriction enzyme sequencing (MRE-Seq) determine the DNA methylation of genome areas with different Resolution down to the single base pair.
  3. Chromatin Accessibility - The DNase I hypersensitive sites sequencing (DNase-Seq) uses the DNase-I enzyme to find open or accessible areas in the genome.
  4. Gene Expression - RNA Seq and Expression Arrays determine the level of expression of protein-coding genes.
  5. Small RNA Expression - smRNA-Seq identifies the expression of small, non-coding RNAs, primarily miRNAs.

Reference epigenomes for healthy people will enable the second goal of the Roadmap Epigenomics project, namely to investigate the epigenomic differences that occur in disease states such as Alzheimer's disease.

research results

In the large intestine of mice fiber digesting bacteria , the epigenome influenced: to fatty acids degraded polysaccharides (complex sugars) affected the gene activity and the metabolism of the mice; the short-chain fatty acids formed changed z. B. the structure of histones , proteins that hold the long DNA threads in cell nuclei together.

cancer

Epigenetics is a hot topic in cancer research. Human tumors are subject to extensive disruption of DNA methylation and histone modification patterns. The anomalous epigenetic landscape of cancer cells is characterized by global genomic hypomethylation, hypermethylation of the CpG island promoters of tumor suppressor genes, an altered histone code for critical genes, and a global loss of monoacetylated and trimethylated histone H4.

warning

The surgical oncologist David Gorski and geneticist Adam Rutherford warned of the presentation and dissemination of false and pseudo-scientific conclusions by New Age -Autoren as Deepak Chopra and Bruce Lipton . Such conclusions are owed to the early stages of epigenetics as a science and the showmanship that surrounds it.

Individual evidence

  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 .
  2. ^ Conley, AB, King Jordan, I. (2012). Endogenous Retroviruses and the Epigenome. In: Witzany, G. (ed). Viruses: Essential Agents of Life , Springer, Dordrecht, pp. 309-323. eBook ISBN 978-94-007-4899-6 .
  3. ↑ Human Epigenome Project, epigenome.org ( Memento of the original from July 16, 2011 in the Internet Archive ) Info: The archive link was inserted automatically and has not yet been checked. Please check the original and archive link according to the instructions and then remove this notice. @1@ 2Template: Webachiv / IABot / www.epigenome.org
  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. ^ Editorial Time for the epigenome . Nature 463, 587 (February 4, 2010), doi : 10.1038 / 463587a .
  7. ↑ Alison Abbott. Project set to map marks on genomes. Nature 463,596-597 (2010) doi : 10.1038 / 463596b .
  8. ↑ Jae-Bum Bae. Perspectives of International Human Epigenome Consortium. Genomics Inform. 2013 Mar; 11 (1): 7-14. doi : 10.5808 / GI.2013.11.1.7 .
  9. ↑ Charlie McDermott. Human Epigenome project launched . Bionews 2015-02-15.
  10. ^ "France: Human epigenome consortium takes first steps". 5 March 2010. No longer available ( Memento of the original from July 8, 2015 in the Internet Archive ) Info: The archive link was automatically inserted and has not yet been checked. Please check the original and archive link according to the instructions and then remove this notice. @1@ 2Template: Webachiv / IABot / www.european-biotechnology-news.com
  11. ↑ Eurice GmbH. About IHEC .
  12. ^ "Frontiers | Multilayer-omics analyzes of human cancers: exploration of biomarkers and drug targets based on the activities of the International Human Epigenome Consortium | Epigenomics and Epigenetics". Frontiers. doi : 10.3389 / fgene.2014.00024 .
  13. ↑ 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 .
  14. ↑ Harris, R Alan; Wang, Ting; Coarfa, Cristian; Nagarajan, Raman P; Hong, Chibo; Downey, Sara L; 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 / Fnbt.1682 .
  15. ↑ deutschlandfunk.de, Forschungs aktuell , November 24, 2016: Effects of dietary fiber: "Eat vegetables!" (December 27, 2016)
  16. ↑ theguardian.com , July 15, 2015, Adam Rutherfort, Beware the pseudo gene genies
  17. ↑ David Gorski, February 4, 2013, sciencebasedmedicine.org: Epigenetics: It doesn't mean what quacks think it means