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Ssl2/TFIIH function in transcription start site scanning by RNA polymerase II in Saccharomyces cerevisiae
In Saccharomyces cerevisiae, RNA polymerase II (Pol II) selects transcription start sites (TSSs) by a unidirectional scanning process. During scanning, a preinitiation complex (PIC) assembled at an upstream core promoter initiates at select positions within a window ~40–120 bp downstream. Several li...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
eLife Sciences Publications, Ltd
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8589449/ https://www.ncbi.nlm.nih.gov/pubmed/34652274 http://dx.doi.org/10.7554/eLife.71013 |
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author | Zhao, Tingting Vvedenskaya, Irina O Lai, William KM Basu, Shrabani Pugh, B Franklin Nickels, Bryce E Kaplan, Craig D |
author_facet | Zhao, Tingting Vvedenskaya, Irina O Lai, William KM Basu, Shrabani Pugh, B Franklin Nickels, Bryce E Kaplan, Craig D |
author_sort | Zhao, Tingting |
collection | PubMed |
description | In Saccharomyces cerevisiae, RNA polymerase II (Pol II) selects transcription start sites (TSSs) by a unidirectional scanning process. During scanning, a preinitiation complex (PIC) assembled at an upstream core promoter initiates at select positions within a window ~40–120 bp downstream. Several lines of evidence indicate that Ssl2, the yeast homolog of XPB and an essential and conserved subunit of the general transcription factor (GTF) TFIIH, drives scanning through its DNA-dependent ATPase activity, therefore potentially controlling both scanning rate and scanning extent (processivity). To address questions of how Ssl2 functions in promoter scanning and interacts with other initiation activities, we leveraged distinct initiation-sensitive reporters to identify novel ssl2 alleles. These ssl2 alleles, many of which alter residues conserved from yeast to human, confer either upstream or downstream TSS shifts at the model promoter ADH1 and genome-wide. Specifically, tested ssl2 alleles alter TSS selection by increasing or narrowing the distribution of TSSs used at individual promoters. Genetic interactions of ssl2 alleles with other initiation factors are consistent with ssl2 allele classes functioning through increasing or decreasing scanning processivity but not necessarily scanning rate. These alleles underpin a residue interaction network that likely modulates Ssl2 activity and TFIIH function in promoter scanning. We propose that the outcome of promoter scanning is determined by two functional networks, the first being Pol II activity and factors that modulate it to determine initiation efficiency within a scanning window, and the second being Ssl2/TFIIH and factors that modulate scanning processivity to determine the width of the scanning widow. |
format | Online Article Text |
id | pubmed-8589449 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | eLife Sciences Publications, Ltd |
record_format | MEDLINE/PubMed |
spelling | pubmed-85894492021-11-15 Ssl2/TFIIH function in transcription start site scanning by RNA polymerase II in Saccharomyces cerevisiae Zhao, Tingting Vvedenskaya, Irina O Lai, William KM Basu, Shrabani Pugh, B Franklin Nickels, Bryce E Kaplan, Craig D eLife Genetics and Genomics In Saccharomyces cerevisiae, RNA polymerase II (Pol II) selects transcription start sites (TSSs) by a unidirectional scanning process. During scanning, a preinitiation complex (PIC) assembled at an upstream core promoter initiates at select positions within a window ~40–120 bp downstream. Several lines of evidence indicate that Ssl2, the yeast homolog of XPB and an essential and conserved subunit of the general transcription factor (GTF) TFIIH, drives scanning through its DNA-dependent ATPase activity, therefore potentially controlling both scanning rate and scanning extent (processivity). To address questions of how Ssl2 functions in promoter scanning and interacts with other initiation activities, we leveraged distinct initiation-sensitive reporters to identify novel ssl2 alleles. These ssl2 alleles, many of which alter residues conserved from yeast to human, confer either upstream or downstream TSS shifts at the model promoter ADH1 and genome-wide. Specifically, tested ssl2 alleles alter TSS selection by increasing or narrowing the distribution of TSSs used at individual promoters. Genetic interactions of ssl2 alleles with other initiation factors are consistent with ssl2 allele classes functioning through increasing or decreasing scanning processivity but not necessarily scanning rate. These alleles underpin a residue interaction network that likely modulates Ssl2 activity and TFIIH function in promoter scanning. We propose that the outcome of promoter scanning is determined by two functional networks, the first being Pol II activity and factors that modulate it to determine initiation efficiency within a scanning window, and the second being Ssl2/TFIIH and factors that modulate scanning processivity to determine the width of the scanning widow. eLife Sciences Publications, Ltd 2021-10-15 /pmc/articles/PMC8589449/ /pubmed/34652274 http://dx.doi.org/10.7554/eLife.71013 Text en © 2021, Zhao et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited. |
spellingShingle | Genetics and Genomics Zhao, Tingting Vvedenskaya, Irina O Lai, William KM Basu, Shrabani Pugh, B Franklin Nickels, Bryce E Kaplan, Craig D Ssl2/TFIIH function in transcription start site scanning by RNA polymerase II in Saccharomyces cerevisiae |
title | Ssl2/TFIIH function in transcription start site scanning by RNA polymerase II in Saccharomyces cerevisiae |
title_full | Ssl2/TFIIH function in transcription start site scanning by RNA polymerase II in Saccharomyces cerevisiae |
title_fullStr | Ssl2/TFIIH function in transcription start site scanning by RNA polymerase II in Saccharomyces cerevisiae |
title_full_unstemmed | Ssl2/TFIIH function in transcription start site scanning by RNA polymerase II in Saccharomyces cerevisiae |
title_short | Ssl2/TFIIH function in transcription start site scanning by RNA polymerase II in Saccharomyces cerevisiae |
title_sort | ssl2/tfiih function in transcription start site scanning by rna polymerase ii in saccharomyces cerevisiae |
topic | Genetics and Genomics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8589449/ https://www.ncbi.nlm.nih.gov/pubmed/34652274 http://dx.doi.org/10.7554/eLife.71013 |
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