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Gómez-Orte E, Sáenz-Narciso B, Zheleva A, Ezcurra B, de Toro M, López R, Gastaca I, Nilsen H, Sacristán MP, Schnabel R, Cabello J. Disruption of the Caenorhabditis elegans Integrator complex triggers a non-conventional transcriptional mechanism beyond snRNA genes. PLoS Genet 2019; 15:e1007981. [PMID: 30807579 PMCID: PMC6390993 DOI: 10.1371/journal.pgen.1007981] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 01/22/2019] [Indexed: 01/09/2023] Open
Abstract
Gene expression is generally regulated by recruitment of transcription factors and RNA polymerase II (RNAP II) to specific sequences in the gene promoter region. The Integrator complex mediates processing of small nuclear RNAs (snRNAs) as well as the initiation and release of paused RNAP II at specific genes in response to growth factors. Here we show that in C. elegans, disruption of the Integrator complex leads to transcription of genes located downstream of the snRNA loci via a non-conventional transcription mechanism based on the lack of processing of the snRNAs. RNAP II read-through generates long chimeric RNAs containing snRNA, the intergenic region and the mature mRNA of the downstream gene located in sense. These chimeric sn-mRNAs remain as untranslated long non-coding RNAs, in the case of U1- and U2-derived sn-mRNAs, but can be translated to proteins in the case of SL-derived sn-mRNAs. The transcriptional effect caused by disruption of the Integrator complex is not restricted to genes located downstream of the snRNA loci but also affects key regulators of signal transduction such as kinases and phosphatases. Our findings highlight that these transcriptional alterations may be behind the correlation between mutations in the Integrator complex and tumor transformation.
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Affiliation(s)
- Eva Gómez-Orte
- Oncology Area, CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Beatriz Sáenz-Narciso
- Oncology Area, CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Angelina Zheleva
- Oncology Area, CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Begoña Ezcurra
- Oncology Area, CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - María de Toro
- Oncology Area, CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Rosario López
- Scientific Computing Group (GRUCACI), University of La Rioja, Logroño, La Rioja, Spain
| | - Irene Gastaca
- Oncology Area, CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - María P. Sacristán
- Instituto de Biología Molecular y Celular del Cáncer, Centro de Investigación del Cáncer, CSIC-Universidad de Salamanca, Salamanca, Spain
| | - Ralf Schnabel
- Department of Developmental Genetics, Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Juan Cabello
- Oncology Area, CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
- * E-mail:
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