Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters.
The recruitment of RNA-Pol-II to the transcription start site (TSS) is an important step in gene regulation in all organisms. Core promoter elements (CPE) are conserved sequence motifs that guide Pol-II to the TSS by interacting with specific transcription factors (TFs). However, only a minority of...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2016-10-01
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| Series: | PLoS Computational Biology |
| Online Access: | http://europepmc.org/articles/PMC5055345?pdf=render |
| _version_ | 1818527556689723392 |
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| author | René Dreos Giovanna Ambrosini Philipp Bucher |
| author_facet | René Dreos Giovanna Ambrosini Philipp Bucher |
| author_sort | René Dreos |
| collection | DOAJ |
| description | The recruitment of RNA-Pol-II to the transcription start site (TSS) is an important step in gene regulation in all organisms. Core promoter elements (CPE) are conserved sequence motifs that guide Pol-II to the TSS by interacting with specific transcription factors (TFs). However, only a minority of animal promoters contains CPEs. It is still unknown how Pol-II selects the TSS in their absence. Here we present a comparative analysis of promoters' sequence composition and chromatin architecture in five eukaryotic model organisms, which shows the presence of common and unique DNA-encoded features used to organize chromatin. Analysis of Pol-II initiation patterns uncovers that, in the absence of certain CPEs, there is a strong correlation between the spread of initiation and the intensity of the 10 bp periodic signal in the nearest downstream nucleosome. Moreover, promoters' primary and secondary initiation sites show a characteristic 10 bp periodicity in the absence of CPEs. We also show that DNA natural variants in the region immediately downstream the TSS are able to affect both the nucleosome-DNA affinity and Pol-II initiation pattern. These findings support the notion that, in addition to CPEs mediated selection, sequence-induced nucleosome positioning could be a common and conserved mechanism of TSS selection in animals. |
| first_indexed | 2024-12-11T06:37:39Z |
| format | Article |
| id | doaj.art-3d5774fc3e2242db942a67a5a03a8fbc |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-11T06:37:39Z |
| publishDate | 2016-10-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-3d5774fc3e2242db942a67a5a03a8fbc2022-12-22T01:17:20ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582016-10-011210e100514410.1371/journal.pcbi.1005144Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters.René DreosGiovanna AmbrosiniPhilipp BucherThe recruitment of RNA-Pol-II to the transcription start site (TSS) is an important step in gene regulation in all organisms. Core promoter elements (CPE) are conserved sequence motifs that guide Pol-II to the TSS by interacting with specific transcription factors (TFs). However, only a minority of animal promoters contains CPEs. It is still unknown how Pol-II selects the TSS in their absence. Here we present a comparative analysis of promoters' sequence composition and chromatin architecture in five eukaryotic model organisms, which shows the presence of common and unique DNA-encoded features used to organize chromatin. Analysis of Pol-II initiation patterns uncovers that, in the absence of certain CPEs, there is a strong correlation between the spread of initiation and the intensity of the 10 bp periodic signal in the nearest downstream nucleosome. Moreover, promoters' primary and secondary initiation sites show a characteristic 10 bp periodicity in the absence of CPEs. We also show that DNA natural variants in the region immediately downstream the TSS are able to affect both the nucleosome-DNA affinity and Pol-II initiation pattern. These findings support the notion that, in addition to CPEs mediated selection, sequence-induced nucleosome positioning could be a common and conserved mechanism of TSS selection in animals.http://europepmc.org/articles/PMC5055345?pdf=render |
| spellingShingle | René Dreos Giovanna Ambrosini Philipp Bucher Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters. PLoS Computational Biology |
| title | Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters. |
| title_full | Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters. |
| title_fullStr | Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters. |
| title_full_unstemmed | Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters. |
| title_short | Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters. |
| title_sort | influence of rotational nucleosome positioning on transcription start site selection in animal promoters |
| url | http://europepmc.org/articles/PMC5055345?pdf=render |
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