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Sabath K, Nabih A, Arnold C, Moussa R, Domjan D, Zaugg JB, Jonas S. Basis of gene-specific transcription regulation by the Integrator complex. Mol Cell 2024:S1097-2765(24)00474-X. [PMID: 38906142 DOI: 10.1016/j.molcel.2024.05.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 03/04/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
The Integrator complex attenuates gene expression via the premature termination of RNA polymerase II (RNAP2) at promoter-proximal pausing sites. It is required for stimulus response, cell differentiation, and neurodevelopment, but how gene-specific and adaptive regulation by Integrator is achieved remains unclear. Here, we identify two sites on human Integrator subunits 13/14 that serve as binding hubs for sequence-specific transcription factors (TFs) and other transcription effector complexes. When Integrator is attached to paused RNAP2, these hubs are positioned upstream of the transcription bubble, consistent with simultaneous TF-promoter tethering. The TFs co-localize with Integrator genome-wide, increase Integrator abundance on target genes, and co-regulate responsive transcriptional programs. For instance, sensory cilia formation induced by glucose starvation depends on Integrator-TF contacts. Our data suggest TF-mediated promoter recruitment of Integrator as a widespread mechanism for targeted transcription regulation.
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Affiliation(s)
- Kevin Sabath
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.
| | - Amena Nabih
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Christian Arnold
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Rim Moussa
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - David Domjan
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Judith B Zaugg
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Stefanie Jonas
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.
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2
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Dokaneheifard S, Gomes Dos Santos H, Guiselle Valencia M, Arigela H, Edupuganti RR, Shiekhattar R. Neuronal differentiation requires BRAT1 complex to remove REST from chromatin. Proc Natl Acad Sci U S A 2024; 121:e2318740121. [PMID: 38805275 PMCID: PMC11161795 DOI: 10.1073/pnas.2318740121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/17/2024] [Indexed: 05/30/2024] Open
Abstract
Repressor element-1 silencing transcription factor (REST) is required for the formation of mature neurons. REST dysregulation underlies a key mechanism of neurodegeneration associated with neurological disorders. However, the mechanisms leading to alterations of REST-mediated silencing of key neurogenesis genes are not known. Here, we show that BRCA1 Associated ATM Activator 1 (BRAT1), a gene linked to neurodegenerative diseases, is required for the activation of REST-responsive genes during neuronal differentiation. We find that INTS11 and INTS9 subunits of Integrator complex interact with BRAT1 as a distinct trimeric complex to activate critical neuronal genes during differentiation. BRAT1 depletion results in persistence of REST residence on critical neuronal genes disrupting the differentiation of NT2 cells into astrocytes and neuronal cells. We identified BRAT1 and INTS11 co-occupying the promoter region of these genes and pinpoint a role for BRAT1 in recruiting INTS11 to their promoters. Disease-causing mutations in BRAT1 diminish its association with INTS11/INTS9, linking the manifestation of disease phenotypes with a defect in transcriptional activation of key neuronal genes by BRAT1/INTS11/INTS9 complex. Finally, loss of Brat1 in mouse embryonic stem cells leads to a defect in neuronal differentiation assay. Importantly, while reconstitution with wild-type BRAT1 restores neuronal differentiation, the addition of a BRAT1 mutant is unable to associate with INTS11/INTS9 and fails to rescue the neuronal phenotype. Taken together, our study highlights the importance of BRAT1 association with INTS11 and INTS9 in the development of the nervous system.
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Affiliation(s)
- Sadat Dokaneheifard
- Department of Human Genetics, University of Miami, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL33136
| | - Helena Gomes Dos Santos
- Department of Human Genetics, University of Miami, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL33136
| | - Monica Guiselle Valencia
- Department of Human Genetics, University of Miami, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL33136
| | - Harikumar Arigela
- Department of Human Genetics, University of Miami, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL33136
| | - Raghu Ram Edupuganti
- Department of Human Genetics, University of Miami, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL33136
| | - Ramin Shiekhattar
- Department of Human Genetics, University of Miami, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL33136
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3
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Razew M, Fraudeau A, Pfleiderer MM, Linares R, Galej WP. Structural basis of the Integrator complex assembly and association with transcription factors. Mol Cell 2024:S1097-2765(24)00431-3. [PMID: 38823386 DOI: 10.1016/j.molcel.2024.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 03/18/2024] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
Integrator is a multi-subunit protein complex responsible for premature transcription termination of coding and non-coding RNAs. This is achieved via two enzymatic activities, RNA endonuclease and protein phosphatase, acting on the promoter-proximally paused RNA polymerase Ⅱ (RNAPⅡ). Yet, it remains unclear how Integrator assembly and recruitment are regulated and what the functions of many of its core subunits are. Here, we report the structures of two human Integrator sub-complexes: INTS10/13/14/15 and INTS5/8/10/15, and an integrative model of the fully assembled Integrator bound to the RNAPⅡ paused elongating complex (PEC). An in silico protein-protein interaction screen of over 1,500 human transcription factors (TFs) identified ZNF655 as a direct interacting partner of INTS13 within the fully assembled Integrator. We propose a model wherein INTS13 acts as a platform for the recruitment of TFs that could modulate the stability of the Integrator's association at specific loci and regulate transcription attenuation of the target genes.
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Affiliation(s)
- Michal Razew
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Angelique Fraudeau
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Moritz M Pfleiderer
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Romain Linares
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Wojciech P Galej
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38042 Grenoble, France.
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4
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Willsey HR, Seaby EG, Godwin A, Ennis S, Guille M, Grainger RM. Modelling human genetic disorders in Xenopus tropicalis. Dis Model Mech 2024; 17:dmm050754. [PMID: 38832520 PMCID: PMC11179720 DOI: 10.1242/dmm.050754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024] Open
Abstract
Recent progress in human disease genetics is leading to rapid advances in understanding pathobiological mechanisms. However, the sheer number of risk-conveying genetic variants being identified demands in vivo model systems that are amenable to functional analyses at scale. Here we provide a practical guide for using the diploid frog species Xenopus tropicalis to study many genes and variants to uncover conserved mechanisms of pathobiology relevant to human disease. We discuss key considerations in modelling human genetic disorders: genetic architecture, conservation, phenotyping strategy and rigour, as well as more complex topics, such as penetrance, expressivity, sex differences and current challenges in the field. As the patient-driven gene discovery field expands significantly, the cost-effective, rapid and higher throughput nature of Xenopus make it an essential member of the model organism armamentarium for understanding gene function in development and in relation to disease.
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Affiliation(s)
- Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA 94518, USA
| | - Eleanor G Seaby
- Genomic Informatics Group, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Annie Godwin
- European Xenopus Resource Centre (EXRC), School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Sarah Ennis
- Genomic Informatics Group, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Matthew Guille
- European Xenopus Resource Centre (EXRC), School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Robert M Grainger
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
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5
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Fianu I, Ochmann M, Walshe JL, Dybkov O, Cruz JN, Urlaub H, Cramer P. Structural basis of Integrator-dependent RNA polymerase II termination. Nature 2024; 629:219-227. [PMID: 38570683 PMCID: PMC11062913 DOI: 10.1038/s41586-024-07269-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024]
Abstract
The Integrator complex can terminate RNA polymerase II (Pol II) in the promoter-proximal region of genes. Previous work has shed light on how Integrator binds to the paused elongation complex consisting of Pol II, the DRB sensitivity-inducing factor (DSIF) and the negative elongation factor (NELF) and how it cleaves the nascent RNA transcript1, but has not explained how Integrator removes Pol II from the DNA template. Here we present three cryo-electron microscopy structures of the complete Integrator-PP2A complex in different functional states. The structure of the pre-termination complex reveals a previously unresolved, scorpion-tail-shaped INTS10-INTS13-INTS14-INTS15 module that may use its 'sting' to open the DSIF DNA clamp and facilitate termination. The structure of the post-termination complex shows that the previously unresolved subunit INTS3 and associated sensor of single-stranded DNA complex (SOSS) factors prevent Pol II rebinding to Integrator after termination. The structure of the free Integrator-PP2A complex in an inactive closed conformation2 reveals that INTS6 blocks the PP2A phosphatase active site. These results lead to a model for how Integrator terminates Pol II transcription in three steps that involve major rearrangements.
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Affiliation(s)
- Isaac Fianu
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Moritz Ochmann
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - James L Walshe
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Olexandr Dybkov
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Joseph Neos Cruz
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, Bioanalytics Group, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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Hannes L, Atzori M, Goldenberg A, Argente J, Attie-Bitach T, Amiel J, Attanasio C, Braslavsky DG, Bruel AL, Castanet M, Dubourg C, Jacobs A, Lyonnet S, Martinez-Mayer J, Pérez Millán MI, Pezzella N, Pelgrims E, Aerden M, Bauters M, Rochtus A, Scaglia P, Swillen A, Sifrim A, Tammaro R, Mau-Them FT, Odent S, Thauvin-Robinet C, Franco B, Breckpot J. Differential alternative splicing analysis links variation in ZRSR2 to a novel type of oral-facial-digital syndrome. Genet Med 2024; 26:101059. [PMID: 38158857 DOI: 10.1016/j.gim.2023.101059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024] Open
Abstract
PURPOSE Oral-facial-digital (OFD) syndromes are genetically heterogeneous developmental disorders, caused by pathogenic variants in genes involved in primary cilia formation and function. We identified a previously undescribed type of OFD with brain anomalies, ranging from alobar holoprosencephaly to pituitary anomalies, in 6 unrelated families. METHODS Exome sequencing of affected probands was supplemented with alternative splicing analysis in patient and control lymphoblastoid and fibroblast cell lines, and primary cilia structure analysis in patient fibroblasts. RESULTS In 1 family with 2 affected males, we identified a germline variant in the last exon of ZRSR2, NM_005089.4:c.1211_1212del NP_005080.1:p.(Gly404GlufsTer23), whereas 7 affected males from 5 unrelated families were hemizygous for the ZRSR2 variant NM_005089.4:c.1207_1208del NP_005080.1:p.(Arg403GlyfsTer24), either occurring de novo or inherited in an X-linked recessive pattern. ZRSR2, located on chromosome Xp22.2, encodes a splicing factor of the minor spliceosome complex, which recognizes minor introns, representing 0.35% of human introns. Patient samples showed significant enrichment of minor intron retention. Among differentially spliced targets are ciliopathy-related genes, such as TMEM107 and CIBAR1. Primary fibroblasts containing the NM_005089.4:c.1207_1208del ZRSR2 variant had abnormally elongated cilia, confirming an association between defective U12-type intron splicing, OFD and abnormal primary cilia formation. CONCLUSION We introduce a novel type of OFD associated with elongated cilia and differential splicing of minor intron-containing genes due to germline variation in ZRSR2.
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Affiliation(s)
- Laurens Hannes
- Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Marta Atzori
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Alice Goldenberg
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, CHU Rouen, Rouen, France
| | - Jesús Argente
- Department of Pediatrics & Pediatric Endocrinology, Hospital Infantil Universitario Niño Jesús, Madrid, Spain; Department of Pediatrics, Universidad Autónoma de Madrid, Madrid, Spain; CIBEROBN de fisiopatología de la obesidad y nutrición, Instituto de Salud Carlos III, Madrid, Spain; IMDEA Food Institute, Madrid, Spain
| | - Tania Attie-Bitach
- Université Paris Cité, INSERM, IHU Imagine - Institut des maladies génétiques, Paris, France; Service de médecine génomique des maladies rares, Hôpital Universitaire Necker-Enfants Malades, AP-HP, Institut Imagine, Paris, France
| | - Jeanne Amiel
- Université Paris Cité, INSERM, IHU Imagine - Institut des maladies génétiques, Paris, France; Service de médecine génomique des maladies rares, Hôpital Universitaire Necker-Enfants Malades, AP-HP, Institut Imagine, Paris, France
| | | | - Débora G Braslavsky
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE) CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez. Buenos Aires, Argentina
| | - Ange-Line Bruel
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France; UF Innovation diagnostique des maladies rares, FHU TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Mireille Castanet
- Normandie Univ, UNIROUEN, Inserm U1239, CHU Rouen, Department of Pediatrics, Rouen, France
| | - Christèle Dubourg
- Department of Molecular Genetics and Genomics, Rennes University Hospital, Rennes, France; Univ Rennes, CNRS, INSERM, IGDR, UMR 6290, ERL U1305, Rennes, France
| | - An Jacobs
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Stanislas Lyonnet
- Université Paris Cité, INSERM, IHU Imagine - Institut des maladies génétiques, Paris, France; Service de médecine génomique des maladies rares, Hôpital Universitaire Necker-Enfants Malades, AP-HP, Institut Imagine, Paris, France
| | - Julian Martinez-Mayer
- Instituto de Biociencias, Biotecnología y Biología Traslacional (IB3), Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - María Inés Pérez Millán
- Instituto de Biociencias, Biotecnología y Biología Traslacional (IB3), Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Nunziana Pezzella
- Telethon Institute of Genetics and Medicine-TIGEM, Naples, Italy; Scuola Superiore Meridionale, School for Advanced Studies, Genomics and Experimental Medicine program, Naples, Italy
| | - Elise Pelgrims
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Mio Aerden
- Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Marijke Bauters
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Anne Rochtus
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Paula Scaglia
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE) CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez. Buenos Aires, Argentina
| | - Ann Swillen
- Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | - Roberta Tammaro
- Telethon Institute of Genetics and Medicine-TIGEM, Naples, Italy
| | - Frederic Tran Mau-Them
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France; UF Innovation diagnostique des maladies rares, FHU TRANSLAD, CHU Dijon Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France
| | - Sylvie Odent
- Department of Molecular Genetics and Genomics, Rennes University Hospital, Rennes, France; Univ Rennes, CNRS, INSERM, IGDR, UMR 6290, ERL U1305, Rennes, France; Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Ouest, ERN ITHACA, FHU GenOmedS, Centre Hospitalier Universitaire Rennes, Rennes, France
| | - Christel Thauvin-Robinet
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France; UF Innovation diagnostique des maladies rares, FHU TRANSLAD, CHU Dijon Bourgogne, Dijon, France; Centre de Référence Anomalies du Développement de l'Est, Centre de Génétique, Centre Hospitalier Universitaire Dijon Bourgogne, Dijon, France
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine-TIGEM, Naples, Italy; Scuola Superiore Meridionale, School for Advanced Studies, Genomics and Experimental Medicine program, Naples, Italy; Department of Translational Medicine, Medical Genetics Federico II University of Naples, Naples, Italy
| | - Jeroen Breckpot
- Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium.
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7
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Kuang H, Li Y, Wang Y, Shi M, Duan R, Xiao Q, She H, Liu Y, Liang Q, Teng Y, Zhou M, Liang D, Li Z, Wu L. A homozygous variant in INTS11 links mitosis and neurogenesis defects to a severe neurodevelopmental disorder. Cell Rep 2023; 42:113445. [PMID: 37980560 DOI: 10.1016/j.celrep.2023.113445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/15/2023] [Accepted: 10/31/2023] [Indexed: 11/21/2023] Open
Abstract
The INTS11 endonuclease is crucial in modulating gene expression and has only recently been linked to human neurodevelopmental disorders (NDDs). However, how INTS11 participates in human development and disease remains unclear. Here, we identify a homozygous INTS11 variant in two siblings with a severe NDD. The variant impairs INTS11 catalytic activity, supported by its substrate's accumulation, and causes G2/M arrest in patient cells with length-dependent dysregulation of genes involved in mitosis and neural development, including the NDD gene CDKL5. The mutant knockin (KI) in induced pluripotent stem cells (iPSCs) disturbs their mitotic spindle organization and thus leads to slow proliferation and increased apoptosis, possibly through the decreased neurally functional CDKL5-induced extracellular signal-regulated kinase (ERK) pathway inhibition. The generation of neural progenitor cells (NPCs) from the mutant iPSCs is also delayed, with long transcript loss concerning neurogenesis. Our work reveals a mechanism underlying INTS11 dysfunction-caused human NDD and provides an iPSC model for this disease.
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Affiliation(s)
- Hanzhe Kuang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China
| | - Yunlong Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China
| | - Yixuan Wang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China
| | - Meizhen Shi
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China; Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Ranhui Duan
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China
| | - Qiao Xiao
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China
| | - Haoyuan She
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China
| | - Yingdi Liu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China
| | - Qiaowei Liang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China; Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha 410000, China
| | - Yanling Teng
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China
| | - Miaojin Zhou
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China
| | - Desheng Liang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China; Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha 410000, China.
| | - Zhuo Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China.
| | - Lingqian Wu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha 410000, China; Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha 410000, China.
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8
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Fujiwara R, Zhai SN, Liang D, Shah AP, Tracey M, Ma XK, Fields CJ, Mendoza-Figueroa MS, Meline MC, Tatomer DC, Yang L, Wilusz JE. IntS6 and the Integrator phosphatase module tune the efficiency of select premature transcription termination events. Mol Cell 2023; 83:4445-4460.e7. [PMID: 37995689 PMCID: PMC10841813 DOI: 10.1016/j.molcel.2023.10.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 10/12/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023]
Abstract
The metazoan-specific Integrator complex catalyzes 3' end processing of small nuclear RNAs (snRNAs) and premature termination that attenuates the transcription of many protein-coding genes. Integrator has RNA endonuclease and protein phosphatase activities, but it remains unclear if both are required for complex function. Here, we show IntS6 (Integrator subunit 6) over-expression blocks Integrator function at a subset of Drosophila protein-coding genes, although having no effect on snRNAs or attenuation of other loci. Over-expressed IntS6 titrates protein phosphatase 2A (PP2A) subunits, thereby only affecting gene loci where phosphatase activity is necessary for Integrator function. IntS6 functions analogous to a PP2A regulatory B subunit as over-expression of canonical B subunits, which do not bind Integrator, is also sufficient to inhibit Integrator activity. These results show that the phosphatase module is critical at only a subset of Integrator-regulated genes and point to PP2A recruitment as a tunable step that modulates transcription termination efficiency.
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Affiliation(s)
- Rina Fujiwara
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Si-Nan Zhai
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Dongming Liang
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Aayushi P Shah
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew Tracey
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Xu-Kai Ma
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Christopher J Fields
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - María Saraí Mendoza-Figueroa
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Michele C Meline
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Deirdre C Tatomer
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA.
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9
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Aoi Y, Shilatifard A. Transcriptional elongation control in developmental gene expression, aging, and disease. Mol Cell 2023; 83:3972-3999. [PMID: 37922911 DOI: 10.1016/j.molcel.2023.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/23/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
The elongation stage of transcription by RNA polymerase II (RNA Pol II) is central to the regulation of gene expression in response to developmental and environmental cues in metazoan. Dysregulated transcriptional elongation has been associated with developmental defects as well as disease and aging processes. Decades of genetic and biochemical studies have painstakingly identified and characterized an ensemble of factors that regulate RNA Pol II elongation. This review summarizes recent findings taking advantage of genetic engineering techniques that probe functions of elongation factors in vivo. We propose a revised model of elongation control in this accelerating field by reconciling contradictory results from the earlier biochemical evidence and the recent in vivo studies. We discuss how elongation factors regulate promoter-proximal RNA Pol II pause release, transcriptional elongation rate and processivity, RNA Pol II stability and RNA processing, and how perturbation of these processes is associated with developmental disorders, neurodegenerative disease, cancer, and aging.
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Affiliation(s)
- Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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10
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Bruel AL, Ganga AK, Nosková L, Valenzuela I, Martinovic J, Duffourd Y, Zikánová M, Majer F, Kmoch S, Mohler M, Sun J, Sweeney LK, Martínez-Gil N, Thauvin-Robinet C, Breslow DK. Pathogenic RAB34 variants impair primary cilium assembly and cause a novel oral-facial-digital syndrome. Hum Mol Genet 2023; 32:2822-2831. [PMID: 37384395 PMCID: PMC10481091 DOI: 10.1093/hmg/ddad109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/12/2023] [Accepted: 06/17/2023] [Indexed: 07/01/2023] Open
Abstract
Oral-facial-digital syndromes (OFDS) are a group of clinically and genetically heterogeneous disorders characterized by defects in the development of the face and oral cavity along with digit anomalies. Pathogenic variants in over 20 genes encoding ciliary proteins have been found to cause OFDS through deleterious structural or functional impacts on primary cilia. We identified by exome sequencing bi-allelic missense variants in a novel disease-causing ciliary gene RAB34 in four individuals from three unrelated families. Affected individuals presented a novel form of OFDS (OFDS-RAB34) accompanied by cardiac, cerebral, skeletal and anorectal defects. RAB34 encodes a member of the Rab GTPase superfamily and was recently identified as a key mediator of ciliary membrane formation. Unlike many genes required for cilium assembly, RAB34 acts selectively in cell types that use the intracellular ciliogenesis pathway, in which nascent cilia begin to form in the cytoplasm. We find that the protein products of these pathogenic variants, which are clustered near the RAB34 C-terminus, exhibit a strong loss of function. Although some variants retain the ability to be recruited to the mother centriole, cells expressing mutant RAB34 exhibit a significant defect in cilium assembly. While many Rab proteins have been previously linked to ciliogenesis, our studies establish RAB34 as the first small GTPase involved in OFDS and reveal the distinct clinical manifestations caused by impairment of intracellular ciliogenesis.
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Affiliation(s)
- Ange-Line Bruel
- INSERM U1231 Génétique des Anomalies du Développement (GAD), University Bourgogne Franche-Comté, 21070 Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU-TRANSLAD), Centre Hospitalo-Universitaire (CHU) Dijon Bourgogne, 21079 Dijon, France
| | - Anil Kumar Ganga
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Lenka Nosková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 128 08, Czech Republic
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
- Medical Genetics Group, Vall d'Hebron Research Institute,08035 Barcelona, Spain
| | - Jelena Martinovic
- Unit of Embryo-Fetal Pathology, AP-HP, Antoine Béclère Hospital, Paris Saclay University, 92141 Clamart, France
| | - Yannis Duffourd
- INSERM U1231 Génétique des Anomalies du Développement (GAD), University Bourgogne Franche-Comté, 21070 Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU-TRANSLAD), Centre Hospitalo-Universitaire (CHU) Dijon Bourgogne, 21079 Dijon, France
| | - Marie Zikánová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 128 08, Czech Republic
| | - Filip Majer
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 128 08, Czech Republic
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 128 08, Czech Republic
| | - Markéta Mohler
- Institute of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Ostrava 708 52, Czech Republic
| | - Jingbo Sun
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Lauren K Sweeney
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Núria Martínez-Gil
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
- Medical Genetics Group, Vall d'Hebron Research Institute,08035 Barcelona, Spain
| | - Christel Thauvin-Robinet
- INSERM U1231 Génétique des Anomalies du Développement (GAD), University Bourgogne Franche-Comté, 21070 Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU-TRANSLAD), Centre Hospitalo-Universitaire (CHU) Dijon Bourgogne, 21079 Dijon, France
- Centre de Génétique et Centre de référence maladies rares ‘Anomalies du Développement et Syndromes Malformatifs’, FHU-TRANSLAD, Hôpital d'Enfants, CHU Dijon Bourgogne, 21079 Dijon, France
| | - David K Breslow
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
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11
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Tepe B, Macke EL, Niceta M, Weisz Hubshman M, Kanca O, Schultz-Rogers L, Zarate YA, Schaefer GB, Granadillo De Luque JL, Wegner DJ, Cogne B, Gilbert-Dussardier B, Le Guillou X, Wagner EJ, Pais LS, Neil JE, Mochida GH, Walsh CA, Magal N, Drasinover V, Shohat M, Schwab T, Schmitz C, Clark K, Fine A, Lanpher B, Gavrilova R, Blanc P, Burglen L, Afenjar A, Steel D, Kurian MA, Prabhakar P, Gößwein S, Di Donato N, Bertini ES, Wangler MF, Yamamoto S, Tartaglia M, Klee EW, Bellen HJ. Bi-allelic variants in INTS11 are associated with a complex neurological disorder. Am J Hum Genet 2023; 110:774-789. [PMID: 37054711 PMCID: PMC10183469 DOI: 10.1016/j.ajhg.2023.03.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/18/2023] [Indexed: 04/15/2023] Open
Abstract
The Integrator complex is a multi-subunit protein complex that regulates the processing of nascent RNAs transcribed by RNA polymerase II (RNAPII), including small nuclear RNAs, enhancer RNAs, telomeric RNAs, viral RNAs, and protein-coding mRNAs. Integrator subunit 11 (INTS11) is the catalytic subunit that cleaves nascent RNAs, but, to date, mutations in this subunit have not been linked to human disease. Here, we describe 15 individuals from 10 unrelated families with bi-allelic variants in INTS11 who present with global developmental and language delay, intellectual disability, impaired motor development, and brain atrophy. Consistent with human observations, we find that the fly ortholog of INTS11, dIntS11, is essential and expressed in the central nervous systems in a subset of neurons and most glia in larval and adult stages. Using Drosophila as a model, we investigated the effect of seven variants. We found that two (p.Arg17Leu and p.His414Tyr) fail to rescue the lethality of null mutants, indicating that they are strong loss-of-function variants. Furthermore, we found that five variants (p.Gly55Ser, p.Leu138Phe, p.Lys396Glu, p.Val517Met, and p.Ile553Glu) rescue lethality but cause a shortened lifespan and bang sensitivity and affect locomotor activity, indicating that they are partial loss-of-function variants. Altogether, our results provide compelling evidence that integrity of the Integrator RNA endonuclease is critical for brain development.
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Affiliation(s)
- Burak Tepe
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Erica L Macke
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Marcello Niceta
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Monika Weisz Hubshman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | | | - Yuri A Zarate
- Division of Genetics and Metabolism, University of Kentucky, Lexington, KY, USA
| | - G Bradley Schaefer
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jorge Luis Granadillo De Luque
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel J Wegner
- Edward Mallinckrodt Department of Pediatrics, Washington University in St. Louis School of Medicine and St. Louis Children's Hospital, St. Louis, Missouri, USA
| | - Benjamin Cogne
- Laboratory of Molecular Genetics, CHU de Nantes, Nantes, France
| | | | | | - Eric J Wagner
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY 14642, USA
| | - Lynn S Pais
- Division of Genetics and Genomics, and Howard Hughes Medical Institute, Boston Children's Hospital, and Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jennifer E Neil
- Division of Genetics and Genomics, and Howard Hughes Medical Institute, Boston Children's Hospital, and Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Ganeshwaran H Mochida
- Division of Genetics and Genomics, and Howard Hughes Medical Institute, Boston Children's Hospital, and Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, and Howard Hughes Medical Institute, Boston Children's Hospital, and Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Nurit Magal
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petach Tikva, Israel
| | - Valerie Drasinover
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petach Tikva, Israel
| | - Mordechai Shohat
- Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, Israel; Medical Genetics Institute of Maccabi HMO, Rechovot, Israel
| | - Tanya Schwab
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Chris Schmitz
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Karl Clark
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Anthony Fine
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Brendan Lanpher
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Ralitza Gavrilova
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Pierre Blanc
- APHP, Département de génétique, Sorbonne Université, GRC n°19, ConCer-LD, Centre de Référence déficiences intellectuelles de causes rares, Hôpital Armand Trousseau, 75012 Paris, France
| | - Lydie Burglen
- APHP, Département de génétique, Sorbonne Université, GRC n°19, ConCer-LD, Centre de Référence déficiences intellectuelles de causes rares, Hôpital Armand Trousseau, 75012 Paris, France
| | - Alexandra Afenjar
- APHP. SU, Centre de Référence Malformations et maladies congénitales du cervelet, département de génétique et embryologie médicale, Hôpital Trousseau, 75012 Paris, France
| | - Dora Steel
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Neurology, Great Ormond Street Hospital for Children, London, UK
| | - Manju A Kurian
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Neurology, Great Ormond Street Hospital for Children, London, UK
| | - Prab Prabhakar
- Department of Neurology, Great Ormond Street Hospital for Children, London, UK
| | - Sophie Gößwein
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Nataliya Di Donato
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Enrico S Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
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12
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Wagner EJ, Tong L, Adelman K. Integrator is a global promoter-proximal termination complex. Mol Cell 2023; 83:416-427. [PMID: 36634676 PMCID: PMC10866050 DOI: 10.1016/j.molcel.2022.11.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 01/13/2023]
Abstract
Integrator is a metazoan-specific protein complex capable of inducing termination at all RNAPII-transcribed loci. Integrator recognizes paused, promoter-proximal RNAPII and drives premature termination using dual enzymatic activities: an endonuclease that cleaves nascent RNA and a protein phosphatase that removes stimulatory phosphorylation associated with RNAPII pause release and productive elongation. Recent breakthroughs in structural biology have revealed the overall architecture of Integrator and provided insights into how multiple Integrator modules are coordinated to elicit termination effectively. Furthermore, functional genomics and biochemical studies have unraveled how Integrator-mediated termination impacts protein-coding and noncoding loci. Here, we review the current knowledge about the assembly and activity of Integrator and describe the role of Integrator in gene regulation, highlighting the importance of this complex for human health.
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Affiliation(s)
- Eric J Wagner
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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