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Article

CAPTURE of the Human U2 snRNA Genes Expands the Repertoire of Associated Factors

1
Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
2
Advanced Proteomics Facility, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editors: Donald Cameron and Jürg Bähler
Biomolecules 2022, 12(5), 704; https://doi.org/10.3390/biom12050704
Received: 2 March 2022 / Revised: 29 April 2022 / Accepted: 12 May 2022 / Published: 14 May 2022
(This article belongs to the Collection Feature Papers in Molecular Genetics)
In order to identify factors involved in transcription of human snRNA genes and 3′ end processing of the transcripts, we have carried out CRISPR affinity purification in situ of regulatory elements (CAPTURE), which is deadCas9-mediated pull-down, of the tandemly repeated U2 snRNA genes in human cells. CAPTURE enriched many factors expected to be associated with these human snRNA genes including RNA polymerase II (pol II), Cyclin-Dependent Kinase 7 (CDK7), Negative Elongation Factor (NELF), Suppressor of Ty 5 (SPT5), Mediator 23 (MED23) and several subunits of the Integrator Complex. Suppressor of Ty 6 (SPT6); Cyclin K, the partner of Cyclin-Dependent Kinase 12 (CDK12) and Cyclin-Dependent Kinase 13 (CDK13); and SWI/SNF chromatin remodelling complex-associated SWI/SNF-related, Matrix-associated, Regulator of Chromatin (SMRC) factors were also enriched. Several polyadenylation factors, including Cleavage and Polyadenylation Specificity Factor 1 (CPSF1), Cleavage Stimulation Factors 1 and 2 (CSTF1,and CSTF2) were enriched by U2 gene CAPTURE. We have already shown by chromatin immunoprecipitation (ChIP) that CSTF2—and Pcf11 and Ssu72, which are also polyadenylation factors—are associated with the human U1 and U2 genes. ChIP-seq and ChIP-qPCR confirm the association of SPT6, Cyclin K, and CDK12 with the U2 genes. In addition, knockdown of SPT6 causes loss of subunit 3 of the Integrator Complex (INTS3) from the U2 genes, indicating a functional role in snRNA gene expression. CAPTURE has therefore expanded the repertoire of transcription and RNA processing factors associated with these genes and helped to identify a functional role for SPT6. View Full-Text
Keywords: CAPTURE; U2 snRNA gene; transcription; SPT6; CDK12; RNA processing; polyadenylation CAPTURE; U2 snRNA gene; transcription; SPT6; CDK12; RNA processing; polyadenylation
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MDPI and ACS Style

Guiro, J.; Fagbemi, M.; Tellier, M.; Zaborowska, J.; Barker, S.; Fournier, M.; Murphy, S. CAPTURE of the Human U2 snRNA Genes Expands the Repertoire of Associated Factors. Biomolecules 2022, 12, 704. https://doi.org/10.3390/biom12050704

AMA Style

Guiro J, Fagbemi M, Tellier M, Zaborowska J, Barker S, Fournier M, Murphy S. CAPTURE of the Human U2 snRNA Genes Expands the Repertoire of Associated Factors. Biomolecules. 2022; 12(5):704. https://doi.org/10.3390/biom12050704

Chicago/Turabian Style

Guiro, Joana, Mathias Fagbemi, Michael Tellier, Justyna Zaborowska, Stephanie Barker, Marjorie Fournier, and Shona Murphy. 2022. "CAPTURE of the Human U2 snRNA Genes Expands the Repertoire of Associated Factors" Biomolecules 12, no. 5: 704. https://doi.org/10.3390/biom12050704

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