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A cell-based splicing reporter system to identify regulators of cis-splicing between adjacent genes
Chimeric RNAs generated by cis-splicing between adjacent genes (cis-SAGe) are increasingly recognized as a widespread phenomenon. These chimeric messenger RNAs are present in normal human cells, and are also detected in various cancers. The mechanisms for how this group of chimeras is formed are not...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393300/ https://www.ncbi.nlm.nih.gov/pubmed/30590765 http://dx.doi.org/10.1093/nar/gky1288 |
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author | Chwalenia, Katarzyna Qin, Fujun Singh, Sandeep Li, Hui |
author_facet | Chwalenia, Katarzyna Qin, Fujun Singh, Sandeep Li, Hui |
author_sort | Chwalenia, Katarzyna |
collection | PubMed |
description | Chimeric RNAs generated by cis-splicing between adjacent genes (cis-SAGe) are increasingly recognized as a widespread phenomenon. These chimeric messenger RNAs are present in normal human cells, and are also detected in various cancers. The mechanisms for how this group of chimeras is formed are not yet clear, in part due to the lack of a tractable system for their experimental investigation. Here we developed a fast, easy and versatile cell-based reporter system to identify regulators of cis-SAGe. The reporter, consisting of four main cassettes, simultaneously measures the effects of a candidate regulator on cis-SAGe and canonical splicing. Using this cell-based assay, we screened 102 candidate factors involved in RNA pol II cleavage and termination, elongation, splicing, alternative splicing and R-loop formation. We discovered that two factors, SRRM1 and SF3B1, affect not only cis-SAGe chimeras, but also other types of chimeric RNAs in a genome-wide fashion. This system can be used for studying trans-acting factors and cis-acting sequence elements and factors, as well as for screening small molecule inhibitors. |
format | Online Article Text |
id | pubmed-6393300 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-63933002019-03-05 A cell-based splicing reporter system to identify regulators of cis-splicing between adjacent genes Chwalenia, Katarzyna Qin, Fujun Singh, Sandeep Li, Hui Nucleic Acids Res Methods Online Chimeric RNAs generated by cis-splicing between adjacent genes (cis-SAGe) are increasingly recognized as a widespread phenomenon. These chimeric messenger RNAs are present in normal human cells, and are also detected in various cancers. The mechanisms for how this group of chimeras is formed are not yet clear, in part due to the lack of a tractable system for their experimental investigation. Here we developed a fast, easy and versatile cell-based reporter system to identify regulators of cis-SAGe. The reporter, consisting of four main cassettes, simultaneously measures the effects of a candidate regulator on cis-SAGe and canonical splicing. Using this cell-based assay, we screened 102 candidate factors involved in RNA pol II cleavage and termination, elongation, splicing, alternative splicing and R-loop formation. We discovered that two factors, SRRM1 and SF3B1, affect not only cis-SAGe chimeras, but also other types of chimeric RNAs in a genome-wide fashion. This system can be used for studying trans-acting factors and cis-acting sequence elements and factors, as well as for screening small molecule inhibitors. Oxford University Press 2019-02-28 2018-12-21 /pmc/articles/PMC6393300/ /pubmed/30590765 http://dx.doi.org/10.1093/nar/gky1288 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Methods Online Chwalenia, Katarzyna Qin, Fujun Singh, Sandeep Li, Hui A cell-based splicing reporter system to identify regulators of cis-splicing between adjacent genes |
title | A cell-based splicing reporter system to identify regulators of cis-splicing between adjacent genes |
title_full | A cell-based splicing reporter system to identify regulators of cis-splicing between adjacent genes |
title_fullStr | A cell-based splicing reporter system to identify regulators of cis-splicing between adjacent genes |
title_full_unstemmed | A cell-based splicing reporter system to identify regulators of cis-splicing between adjacent genes |
title_short | A cell-based splicing reporter system to identify regulators of cis-splicing between adjacent genes |
title_sort | cell-based splicing reporter system to identify regulators of cis-splicing between adjacent genes |
topic | Methods Online |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393300/ https://www.ncbi.nlm.nih.gov/pubmed/30590765 http://dx.doi.org/10.1093/nar/gky1288 |
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