Long Conserved Fragments Upstream of Mammalian Polyadenylation Sites
| Autor: | Samuel I. Gunderson, Eric S. Ho |
|---|---|
| Rok vydání: | 2011 |
| Předmět: |
RNA
Untranslated Polyadenylation conserved fragments Biology Conserved sequence Evolution Molecular Mice 03 medical and health sciences chemistry.chemical_compound 0302 clinical medicine Transcription (biology) RNA polymerase Databases Genetic RNA Precursors Genetics Animals Deoxyribonuclease I Humans Selection Genetic Platypus Conserved Sequence Research Articles Ecology Evolution Behavior and Systematics 030304 developmental biology Expressed Sequence Tags Regulation of gene expression 0303 health sciences Computational Biology RNA bioinformatics Chromatin Rats Gene Expression Regulation chemistry cis-regulatory elements RNA splicing Cattle 030217 neurology & neurosurgery |
| Zdroj: | Genome Biology and Evolution |
| ISSN: | 1759-6653 |
| Popis: | Polyadenylation is a cotranscriptional nuclear RNA processing event involving endonucleolytic cleavage of the nascent, emerging pre-messenger RNA (pre-mRNA) from the RNA polymerase, immediately followed by the polymerization of adenine ribonucleotides, called the poly(A) tail, to the cleaved 3′ end of the polyadenylation site (PAS). This apparently simple molecular processing step has been discovered to be connected to transcription and splicing therefore increasing its potential for regulation of gene expression. Here, through a bioinformatic analysis of cis-PAS–regulatory elements in mammals that includes taking advantage of multiple evolutionary time scales, we find unexpected selection pressure much further upstream, up to 200 nt, from the PAS than previously thought. Strikingly, close to 3,000 long (30–500 nt) noncoding conserved fragments (CFs) were discovered in the PAS flanking region of three remotely related mammalian species, human, mouse, and cow. When an even more remote transitional mammal, platypus, was included, still over a thousand CFs were found in the proximity of the PAS. Even though the biological function of these CFs remains unknown, their considerable sizes makes them unlikely to serve as protein recognition sites, which are typically ≤15 nt. By harnessing genome wide DNaseI hypersensitivity data, we have discovered that the presence of CFs correlates with chromatin accessibility. Our study is important in highlighting novel experimental targets, which may provide new understanding about the regulatory aspects of polyadenylation. |
| Databáze: | OpenAIRE |
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