Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution
| العنوان: | Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution |
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| المؤلفون: | Noboru J. Sakabe, Marcelo A. Nobrega |
| المصدر: | Philosophical Transactions of the Royal Society B: Biological Sciences. 368:20130022 |
| بيانات النشر: | The Royal Society, 2013. |
| سنة النشر: | 2013 |
| مصطلحات موضوعية: | Epigenomics, Genetics, Regulation of gene expression, Chromatin Immunoprecipitation, Genomics, Enhancer RNAs, Articles, Computational biology, Biology, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, Enhancer Elements, Genetic, Gene Expression Regulation, Databases, Genetic, General Agricultural and Biological Sciences, Enhancer, Chromatin immunoprecipitation, Gene, ChIA-PET, Transcription Factors |
| الوصف: | The complex expression patterns observed for many genes are often regulated by distal transcription enhancers. Changes in the nucleotide sequences of enhancers may therefore lead to changes in gene expression, representing a central mechanism by which organisms evolve. With the development of the experimental technique of chromatin immunoprecipitation (ChIP), in which discrete regions of the genome bound by specific proteins can be identified, it is now possible to identify transcription factor binding events (putative cis -regulatory elements) in entire genomes. Comparing protein–DNA binding maps allows us, for the first time, to attempt to identify regulatory differences and infer global patterns of change in gene expression across species. Here, we review studies that used genome-wide ChIP to study the evolution of enhancers. The trend is one of high divergence of cis -regulatory elements between species, possibly compensated by extensive creation and loss of regulatory elements and rewiring of their target genes. We speculate on the meaning of the differences observed and discuss that although ChIP experiments identify the biochemical event of protein–DNA interaction, it cannot determine whether the event results in a biological function, and therefore more studies are required to establish the effect of divergence of binding events on species-specific gene expression. |
| تدمد: | 1471-2970 0962-8436 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::86f2c73f487dc9f0ad4ef725a3ea4f4fTest https://doi.org/10.1098/rstb.2013.0022Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....86f2c73f487dc9f0ad4ef725a3ea4f4f |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 14712970 09628436 |
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