1
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Grzechnik P, Mischo HE. Fateful Decisions of Where to Cut the Line: Pathology Associated with Aberrant 3' End Processing and Transcription Termination. J Mol Biol 2024:168802. [PMID: 39321865 DOI: 10.1016/j.jmb.2024.168802] [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: 07/31/2024] [Revised: 09/17/2024] [Accepted: 09/19/2024] [Indexed: 09/27/2024]
Abstract
Aberrant gene expression lies at the heart of many pathologies. This review will point out how 3' end processing, the final mRNA-maturation step in the transcription cycle, is surprisingly prone to regulated as well as stochastic variations with a wide range of consequences. Whereas smaller variations contribute to the plasticity of gene expression, larger alternations to 3' end processing and coupled transcription termination can lead to pathological consequences. These can be caused by the local mutation of one gene or affect larger numbers of genes systematically, if aspects of the mechanisms of 3' end processing and transcription termination are altered.
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Affiliation(s)
- Pawel Grzechnik
- Division of Molecular and Cellular Function, School of Biological Sciences, University of Manchester, United Kingdom
| | - Hannah E Mischo
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, United Kingdom.
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2
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Lin MH, Jensen MK, Elrod ND, Chu HF, Haseley M, Beam AC, Huang KL, Chiang W, Russell WK, Williams K, Pröschel C, Wagner EJ, Tong L. Cytoplasmic binding partners of the Integrator endonuclease INTS11 and its paralog CPSF73 are required for their nuclear function. Mol Cell 2024; 84:2900-2917.e10. [PMID: 39032490 PMCID: PMC11316654 DOI: 10.1016/j.molcel.2024.06.017] [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: 11/08/2023] [Revised: 06/04/2024] [Accepted: 06/18/2024] [Indexed: 07/23/2024]
Abstract
INTS11 and CPSF73 are metal-dependent endonucleases for Integrator and pre-mRNA 3'-end processing, respectively. Here, we show that the INTS11 binding partner BRAT1/CG7044, a factor important for neuronal fitness, stabilizes INTS11 in the cytoplasm and is required for Integrator function in the nucleus. Loss of BRAT1 in neural organoids leads to transcriptomic disruption and precocious expression of neurogenesis-driving transcription factors. The structures of the human INTS9-INTS11-BRAT1 and Drosophila dIntS11-CG7044 complexes reveal that the conserved C terminus of BRAT1/CG7044 is captured in the active site of INTS11, with a cysteine residue directly coordinating the metal ions. Inspired by these observations, we find that UBE3D is a binding partner for CPSF73, and UBE3D likely also uses a conserved cysteine residue to directly coordinate the active site metal ions. Our studies have revealed binding partners for INTS11 and CPSF73 that behave like cytoplasmic chaperones with a conserved impact on the nuclear functions of these enzymes.
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Affiliation(s)
- Min-Han Lin
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Madeline K Jensen
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA; Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Nathan D Elrod
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Hsu-Feng Chu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - MaryClaire Haseley
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Alissa C Beam
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Kai-Lieh Huang
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA; Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Wesley Chiang
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Kelsey Williams
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA; Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Christoph Pröschel
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA; Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Eric J Wagner
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA; Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77550, USA.
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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3
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Sabath K, Qiu C, Jonas S. Assembly mechanism of Integrator's RNA cleavage module. Mol Cell 2024; 84:2882-2899.e10. [PMID: 39032489 DOI: 10.1016/j.molcel.2024.06.032] [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: 11/06/2023] [Revised: 05/17/2024] [Accepted: 06/26/2024] [Indexed: 07/23/2024]
Abstract
The modular Integrator complex is a transcription regulator that is essential for embryonic development. It attenuates coding gene expression via premature transcription termination and performs 3'-processing of non-coding RNAs. For both activities, Integrator requires endonuclease activity that is harbored by an RNA cleavage module consisting of INTS4-9-11. How correct assembly of Integrator modules is achieved remains unknown. Here, we show that BRAT1 and WDR73 are critical biogenesis factors for the human cleavage module. They maintain INTS9-11 inactive during maturation by physically blocking the endonuclease active site and prevent premature INTS4 association. Furthermore, BRAT1 facilitates import of INTS9-11 into the nucleus, where it is joined by INTS4. Final BRAT1 release requires locking of the mature cleavage module conformation by inositol hexaphosphate (IP6). Our data explain several neurodevelopmental disorders caused by BRAT1, WDR73, and INTS11 mutations as Integrator assembly defects and reveal that IP6 is an essential co-factor for cleavage module maturation.
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Affiliation(s)
- Kevin Sabath
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Chunhong Qiu
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Stefanie Jonas
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
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4
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Confino S, Wexler Y, Medvetzky A, Elazary Y, Ben-Moshe Z, Reiter J, Dor T, Edvardson S, Prag G, Harel T, Gothilf Y. A deleterious variant of INTS1 leads to disrupted sleep-wake cycles. Dis Model Mech 2024; 17:dmm050746. [PMID: 39189071 PMCID: PMC11381918 DOI: 10.1242/dmm.050746] [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: 02/05/2024] [Accepted: 06/25/2024] [Indexed: 08/28/2024] Open
Abstract
Sleep disturbances are common among children with neurodevelopmental disorders. Here, we report a syndrome characterized by prenatal microcephaly, intellectual disability and severe disruption of sleep-wake cycles in a consanguineous family. Exome sequencing revealed homozygous variants (c.5224G>A and c.6506G>T) leading to the missense mutations E1742K and G2169V in integrator complex subunit 1 (INTS1), the core subunit of the Integrator complex. Conservation and structural analyses suggest that G2169V has a minor impact on the structure and function of the complex, while E1742K significantly alters a negatively charged conserved patch on the surface of the protein. The severe sleep-wake cycles disruption in human carriers highlights a new aspect of Integrator complex impairment. To further study INTS1 pathogenicity, we generated Ints1-deficient zebrafish lines. Mutant zebrafish larvae displayed abnormal circadian rhythms of locomotor activity and sleep, as is the case with the affected humans. Furthermore, Ints1-deficent larvae exhibited elevated levels of dopamine β-hydroxylase (dbh) mRNA in the locus coeruleus, a wakefulness-inducing brainstem center. Altogether, these findings suggest a significant, likely indirect, effect of INTS1 and the Integrator complex on maintaining circadian rhythms of locomotor activity and sleep homeostasis across vertebrates.
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Affiliation(s)
- Shir Confino
- School of Neurobiology, Biochemistry and Biophysics, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Yair Wexler
- School of Neurobiology, Biochemistry and Biophysics, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Adar Medvetzky
- School of Neurobiology, Biochemistry and Biophysics, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Yotam Elazary
- School of Neurobiology, Biochemistry and Biophysics, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Zohar Ben-Moshe
- School of Neurobiology, Biochemistry and Biophysics, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Joel Reiter
- Pediatric Pulmonary & Sleep Unit, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Talya Dor
- ALYN - Children and Adolescent Rehabilitation Center, Jerusalem 9109002, Israel
| | - Simon Edvardson
- ALYN - Children and Adolescent Rehabilitation Center, Jerusalem 9109002, Israel
| | - Gali Prag
- School of Neurobiology, Biochemistry and Biophysics, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
- Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Tamar Harel
- Department of Genetics, Hadassah Medical Center, Jerusalem 91120, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yoav Gothilf
- School of Neurobiology, Biochemistry and Biophysics, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
- Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv 6997801, Israel
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5
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Jiang L, Wang Y, Zhang W, Zhang X, Gao F, Yuan Z. INTS11-related neurodevelopmental disorder: a case report and literature review. J Hum Genet 2024:10.1038/s10038-024-01276-z. [PMID: 39030370 DOI: 10.1038/s10038-024-01276-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 07/01/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND INTS11 is a critical catalytic component of the Integrator complex that regulates RNA polymerase II termination and modulates gene expression. Until recently, INTS11 mutations were associated with human neurodevelopmental disorders, characterized by global developmental and language delays, generalized hypotonia, and progressive brain atrophy. CASE We report the case of a 2-year-old Chinese girl who presented with global developmental delay, generalized hypotonia, refractory epilepsy, craniofacial dysmorphism, and progressive brain atrophy. Novel variants were identified in exon 2 of INTS11 gene c.588_589del (p. Trp197AspfsTer2) and c.457_459del (p. Glu153del). CONCLUSION We identified a compound heterozygous mutation in INTS11, a clinical feature consistent with two previous reports of the variants in human INTS11, but her recurrent seizures were more pronounced and refractory to most antiepileptic drugs and ketogenic diets.
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Affiliation(s)
- Lihua Jiang
- Department of Neurology, The Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Yilong Wang
- Department of Neurology, The Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Weiqin Zhang
- Department of Neurology, The Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Xin Zhang
- Department of Neurology, The Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Feng Gao
- Department of Neurology, The Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Zhefeng Yuan
- Department of Neurology, The Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China.
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6
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Pang T, Ding N, Zhao Y, Zhao J, Yang L, Chang S. Novel genetic loci of inhibitory control in ADHD and healthy children and genetic correlations with ADHD. Prog Neuropsychopharmacol Biol Psychiatry 2024; 132:110988. [PMID: 38430954 DOI: 10.1016/j.pnpbp.2024.110988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/26/2023] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Cumulative evidence has showed the deficits of inhibitory control in patients with attention deficit hyperactivity disorder (ADHD), which is considered as an endophenotype of ADHD. Genetic study of inhibitory control could advance gene discovery and further facilitate the understanding of ADHD genetic basis, but the studies were limited in both the general population and ADHD patients. To reveal genetic risk variants of inhibitory control and its potential genetic relationship with ADHD, we conducted genome-wide association studies (GWAS) on inhibitory control using three datasets, which included 783 and 957 ADHD patients and 1350 healthy children. Subsequently, we employed polygenic risk scores (PRS) to explore the association of inhibitory control with ADHD and related psychiatric disorders. Firstly, we identified three significant loci for inhibitory control in the healthy dataset, two loci in the case dataset, and one locus in the meta-analysis of three datasets. Besides, we found more risk genes and variants by applying transcriptome-wide association study (TWAS) and conditional FDR method. Then, we constructed a network by connecting the genes identified in our study, leading to the identification of several vital genes. Lastly, we identified a potential relationship between inhibitory control and ADHD and autism by PRS analysis and found the direct and mediated contribution of the identified genetic loci on ADHD symptoms by mediation analysis. In conclusion, we revealed some genetic risk variants associated with inhibitory control and elucidated the benefit of inhibitory control as an endophenotype, providing valuable insights into the mechanisms underlying ADHD.
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Affiliation(s)
- Tao Pang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing 100191, China
| | - Ning Ding
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China
| | - Yilu Zhao
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing 100191, China
| | - Jingjing Zhao
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Xi'an, China.
| | - Li Yang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing 100191, China.
| | - Suhua Chang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing 100191, China; Research Unit of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences, Peking University, Beijing 100191, China.
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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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Jung JH, Jeon S, Kim H, Jung SH. Generation of ints14 Knockout Zebrafish using CRISPR/Cas9 for the Study of Development and Disease Mechanisms. Dev Reprod 2023; 27:205-211. [PMID: 38292235 PMCID: PMC10824568 DOI: 10.12717/dr.2023.27.4.205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/17/2023] [Accepted: 11/25/2023] [Indexed: 02/01/2024]
Abstract
INTS14/VWA9, a component of the integrator complex subunits, plays a pivotal role in regulating the fate of numerous nascent RNAs transcribed by RNA polymerase II, particularly in the biogenesis of small nuclear RNAs and enhancer RNAs. Despite its significance, a comprehensive mutation model for developmental research has been lacking. To address this gap, we aimed to investigate the expression patterns of INTS14 during zebrafish embryonic development. We generated ints14 mutant strains using the CRISPR/Cas9 system. We validated the gRNA activity by co-injecting Cas9 protein and a single guide RNA into fertilized zebrafish eggs, subsequently confirming the presence of a 6- or 9-bp deletion in the ints14 gene. In addition, we examined the two mutant alleles through PCR analysis, T7E1 assay, TA-cloning, and sequencing. For the first time, we used the CRISPR/Cas9 system to create a model in which some sequences of the ints14 gene were removed. This breakthrough opens new avenues for in-depth exploration of the role of ints14 in animal diseases. The mutant strains generated in this study can provide a valuable resource for further investigations into the specific consequences of ints14 gene deletion during zebrafish development. This research establishes a foundation for future studies exploring the molecular mechanisms underlying the functions of ints14, its interactions with other genes or proteins, and its broader implications for biological processes.
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Affiliation(s)
- Ji Hye Jung
- Department of Genetic Resources, 75 National Marine
Biodiversity Institute of Korea, Seocheon 33662,
Korea
| | - Sanghoon Jeon
- Department of Genetic Resources, 75 National Marine
Biodiversity Institute of Korea, Seocheon 33662,
Korea
| | - Heabin Kim
- Department of Genetic Resources, 75 National Marine
Biodiversity Institute of Korea, Seocheon 33662,
Korea
| | - Seung-Hyun Jung
- Department of Genetic Resources, 75 National Marine
Biodiversity Institute of Korea, Seocheon 33662,
Korea
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9
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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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10
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Welsh SA, Gardini A. Genomic regulation of transcription and RNA processing by the multitasking Integrator complex. Nat Rev Mol Cell Biol 2023; 24:204-220. [PMID: 36180603 PMCID: PMC9974566 DOI: 10.1038/s41580-022-00534-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2022] [Indexed: 11/09/2022]
Abstract
In higher eukaryotes, fine-tuned activation of protein-coding genes and many non-coding RNAs pivots around the regulated activity of RNA polymerase II (Pol II). The Integrator complex is the only Pol II-associated large multiprotein complex that is metazoan specific, and has therefore been understudied for years. Integrator comprises at least 14 subunits, which are grouped into distinct functional modules. The phosphodiesterase activity of the core catalytic module is co-transcriptionally directed against several RNA species, including long non-coding RNAs (lncRNAs), U small nuclear RNAs (U snRNAs), PIWI-interacting RNAs (piRNAs), enhancer RNAs and nascent pre-mRNAs. Processing of non-coding RNAs by Integrator is essential for their biogenesis, and at protein-coding genes, Integrator is a key modulator of Pol II promoter-proximal pausing and transcript elongation. Recent studies have identified an Integrator-specific serine/threonine-protein phosphatase 2A (PP2A) module, which targets Pol II and other components of the basal transcription machinery. In this Review, we discuss how the activity of Integrator regulates transcription, RNA processing, chromatin landscape and DNA repair. We also discuss the diverse roles of Integrator in development and tumorigenesis.
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11
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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: 41] [Impact Index Per Article: 41.0] [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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12
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Sabath K, Jonas S. Take a break: Transcription regulation and RNA processing by the Integrator complex. Curr Opin Struct Biol 2022; 77:102443. [PMID: 36088798 DOI: 10.1016/j.sbi.2022.102443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/16/2022] [Accepted: 07/19/2022] [Indexed: 12/14/2022]
Abstract
The metazoan-specific Integrator complex is a >1.5 MDa machinery that interacts with RNA polymerase II (RNAP2) to attenuate coding gene transcription by early termination close to transcription start sites. Using a highly related mechanism, Integrator also performs the initial 3'-end processing step for many non-coding RNAs. Its transcription regulation functions are essential for cell differentiation and response to external stimuli. Recent studies revealed that the complex incorporates phosphatase PP2A to counteract phosphorylation reactions that are required for transcription elongation. Structures of Integrator bound to RNAP2 explain the basis for its recruitment to promoter proximal RNAP2 by recognition of its paused state. Furthermore, several studies indicate that Integrator's cleavage activity is regulated at multiple levels through activators, modifications, and small molecules.
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Affiliation(s)
- Kevin Sabath
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Switzerland
| | - Stefanie Jonas
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Switzerland.
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13
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Lin MH, Jensen MK, Elrod ND, Huang KL, Welle KA, Wagner EJ, Tong L. Inositol hexakisphosphate is required for Integrator function. Nat Commun 2022; 13:5742. [PMID: 36180473 PMCID: PMC9525679 DOI: 10.1038/s41467-022-33506-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/20/2022] [Indexed: 11/09/2022] Open
Abstract
Integrator is a multi-subunit protein complex associated with RNA polymerase II (Pol II), with critical roles in noncoding RNA 3'-end processing and transcription attenuation of a broad collection of mRNAs. IntS11 is the endonuclease for RNA cleavage, as a part of the IntS4-IntS9-IntS11 Integrator cleavage module (ICM). Here we report a cryo-EM structure of the Drosophila ICM, at 2.74 Å resolution, revealing stable association of an inositol hexakisphosphate (IP6) molecule. The IP6 binding site is located in a highly electropositive pocket at an interface among all three subunits of ICM, 55 Å away from the IntS11 active site and generally conserved in other ICMs. We also confirmed IP6 association with the same site in human ICM. IP6 binding is not detected in ICM samples harboring mutations in this binding site. Such mutations or disruption of IP6 biosynthesis significantly reduced Integrator function in snRNA 3'-end processing and mRNA transcription attenuation. Our structural and functional studies reveal that IP6 is required for Integrator function in Drosophila, humans, and likely other organisms.
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Affiliation(s)
- Min-Han Lin
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Madeline K Jensen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, 77550, USA
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Nathan D Elrod
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, 77550, USA
| | - Kai-Lieh Huang
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, 77550, USA
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Kevin A Welle
- Center for Advanced Research Technologies, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, 77550, USA.
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA.
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
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14
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BRAT1 links Integrator and defective RNA processing with neurodegeneration. Nat Commun 2022; 13:5026. [PMID: 36028512 PMCID: PMC9418311 DOI: 10.1038/s41467-022-32763-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 08/15/2022] [Indexed: 11/19/2022] Open
Abstract
Mutations in BRAT1, encoding BRCA1-associated ATM activator 1, have been associated with neurodevelopmental and neurodegenerative disorders characterized by heterogeneous phenotypes with varying levels of clinical severity. However, the underlying molecular mechanisms of disease pathology remain poorly understood. Here, we show that BRAT1 tightly interacts with INTS9/INTS11 subunits of the Integrator complex that processes 3' ends of various noncoding RNAs and pre-mRNAs. We find that Integrator functions are disrupted by BRAT1 deletion. In particular, defects in BRAT1 impede proper 3' end processing of UsnRNAs and snoRNAs, replication-dependent histone pre-mRNA processing, and alter the expression of protein-coding genes. Importantly, impairments in Integrator function are also evident in patient-derived cells from BRAT1 related neurological disease. Collectively, our data suggest that defects in BRAT1 interfere with proper Integrator functions, leading to incorrect expression of RNAs and proteins, resulting in neurodegeneration.
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15
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Eigenhuis KN, Somsen HB, van den Berg DLC. Transcription Pause and Escape in Neurodevelopmental Disorders. Front Neurosci 2022; 16:846272. [PMID: 35615272 PMCID: PMC9125161 DOI: 10.3389/fnins.2022.846272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Transcription pause-release is an important, highly regulated step in the control of gene expression. Modulated by various factors, it enables signal integration and fine-tuning of transcriptional responses. Mutations in regulators of pause-release have been identified in a range of neurodevelopmental disorders that have several common features affecting multiple organ systems. This review summarizes current knowledge on this novel subclass of disorders, including an overview of clinical features, mechanistic details, and insight into the relevant neurodevelopmental processes.
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16
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Wheater ENW, Galdi P, McCartney DL, Blesa M, Sullivan G, Stoye DQ, Lamb G, Sparrow S, Murphy L, Wrobel N, Quigley AJ, Semple S, Thrippleton MJ, Wardlaw JM, Bastin ME, Marioni RE, Cox SR, Boardman JP. DNA methylation in relation to gestational age and brain dysmaturation in preterm infants. Brain Commun 2022; 4:fcac056. [PMID: 35402911 PMCID: PMC8984700 DOI: 10.1093/braincomms/fcac056] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 12/10/2021] [Accepted: 03/04/2022] [Indexed: 11/14/2022] Open
Abstract
Preterm birth is associated with dysconnectivity of structural brain networks and is a leading cause of neurocognitive impairment in childhood. Variation in DNA methylation is associated with early exposure to extrauterine life but there has been little research exploring its relationship with brain development. Using genome-wide DNA methylation data from the saliva of 258 neonates, we investigated the impact of gestational age on the methylome and performed functional analysis to identify enriched gene sets from probes that contributed to differentially methylated probes or regions. We tested the hypothesis that variation in DNA methylation could underpin the association between low gestational age at birth and atypical brain development by linking differentially methylated probes with measures of white matter connectivity derived from diffusion MRI metrics: peak width skeletonized mean diffusivity, peak width skeletonized fractional anisotropy and peak width skeletonized neurite density index. Gestational age at birth was associated with widespread differential methylation at term equivalent age, with genome-wide significant associations observed for 8870 CpG probes (P < 3.6 × 10-8) and 1767 differentially methylated regions. Functional analysis identified 14 enriched gene ontology terms pertaining to cell-cell contacts and cell-extracellular matrix contacts. Principal component analysis of probes with genome-wide significance revealed a first principal component that explained 23.5% of the variance in DNA methylation, and this was negatively associated with gestational age at birth. The first principal component was associated with peak width of skeletonized mean diffusivity (β = 0.349, P = 8.37 × 10-10) and peak width skeletonized neurite density index (β = 0.364, P = 4.15 × 10-5), but not with peak width skeletonized fraction anisotropy (β = -0.035, P = 0.510); these relationships mirrored the imaging metrics' associations with gestational age at birth. Low gestational age at birth has a profound and widely distributed effect on the neonatal saliva methylome that is apparent at term equivalent age. Enriched gene ontology terms related to cell-cell contacts reveal pathways that could mediate the effect of early life environmental exposures on development. Finally, associations between differential DNA methylation and image markers of white matter tract microstructure suggest that variation in DNA methylation may provide a link between preterm birth and the dysconnectivity of developing brain networks that characterizes atypical brain development in preterm infants.
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Affiliation(s)
- Emily N. W. Wheater
- MRC Centre for Reproductive Health, The University of Edinburgh, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Paola Galdi
- MRC Centre for Reproductive Health, The University of Edinburgh, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Daniel L. McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Manuel Blesa
- MRC Centre for Reproductive Health, The University of Edinburgh, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Gemma Sullivan
- MRC Centre for Reproductive Health, The University of Edinburgh, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - David Q. Stoye
- MRC Centre for Reproductive Health, The University of Edinburgh, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Gillian Lamb
- MRC Centre for Reproductive Health, The University of Edinburgh, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Sarah Sparrow
- MRC Centre for Reproductive Health, The University of Edinburgh, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Lee Murphy
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Nicola Wrobel
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Alan J. Quigley
- Department of Paediatric Radiology, Royal Hospital for Sick Children, NHS Lothian, Edinburgh, UK
| | - Scott Semple
- Edinburgh Imaging, University of Edinburgh, EH16 4SB Edinburgh, UK
- Centre for Cardiovascular Science, The University of Edinburgh, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Michael J. Thrippleton
- Edinburgh Imaging, University of Edinburgh, EH16 4SB Edinburgh, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Joanna M. Wardlaw
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Mark E. Bastin
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Simon R. Cox
- Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - James P. Boardman
- MRC Centre for Reproductive Health, The University of Edinburgh, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
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17
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Mancini GMS, Smits DJ, Dekker J, Schot R, de Wit MCY, Lequin MH, Dremmen M, Brooks AS, van Ham T, Verheijen FW, Fornerod M, Dobyns WB, Wilke M. Multidisciplinary interaction and MCD gene discovery. The perspective of the clinical geneticist. Eur J Paediatr Neurol 2021; 35:27-34. [PMID: 34592643 DOI: 10.1016/j.ejpn.2021.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/18/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]
Abstract
The increasing pace of gene discovery in the last decade has brought a major change in the way the genetic causes of brain malformations are being diagnosed. Unbiased genomic screening has gained the first place in the diagnostic protocol of a child with congenital (brain) anomalies and the detected variants are matched with the phenotypic presentation afterwards. This process is defined as "reverse phenotyping". Screening of DNA, through copy number variant analysis of microarrays and analysis of exome data on different platforms, obtained from the index patient and both parents has become a routine approach in many centers worldwide. Clinicians are used to multidisciplinary team interaction in patient care and disease management and this explains why the majority of research that has led to the discovery of new genetic disorders nowadays proceeds from clinical observations to genomic analysis and to data exchange facilitated by open access sharing databases. However, the relevance of multidisciplinary team interaction has not been object of systematic research in the field of brain malformations. This review will illustrate some examples of how diagnostically driven questions through multidisciplinary interaction, among clinical and preclinical disciplines, can be successful in the discovery of new genes related to brain malformations. The first example illustrates the setting of interaction among neurologists, geneticists and neuro-radiologists. The second illustrates the importance of interaction among clinical dysmorphologists for pattern recognition of syndromes with multiple congenital anomalies. The third example shows how fruitful it can be to step out of the "clinical comfort zone", and interact with basic scientists in applying emerging technologies to solve the diagnostic puzzles.
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Affiliation(s)
- Grazia M S Mancini
- Department of Clinical Genetics, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands; ENCORE Expertise Center for Genetic Neurocognitive Developmental Disorders, Erasmus, MC, Rotterdam.
| | - Daphne J Smits
- Department of Clinical Genetics, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Jordy Dekker
- Department of Clinical Genetics, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Rachel Schot
- Department of Clinical Genetics, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands; ENCORE Expertise Center for Genetic Neurocognitive Developmental Disorders, Erasmus, MC, Rotterdam
| | - Marie Claire Y de Wit
- Department of Child Neurology, Sophia Children's Hospital, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, Rotterdam, NL, the Netherlands; ENCORE Expertise Center for Genetic Neurocognitive Developmental Disorders, Erasmus, MC, Rotterdam
| | - Maarten H Lequin
- Department of Radiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Marjolein Dremmen
- Department of Radiology, Sophia Children's Hospital, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands; ENCORE Expertise Center for Genetic Neurocognitive Developmental Disorders, Erasmus, MC, Rotterdam
| | - Alice S Brooks
- Department of Clinical Genetics, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Tjakko van Ham
- Department of Clinical Genetics, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Frans W Verheijen
- Department of Clinical Genetics, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands; ENCORE Expertise Center for Genetic Neurocognitive Developmental Disorders, Erasmus, MC, Rotterdam
| | - Maarten Fornerod
- Department of Cell Biology, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - William B Dobyns
- Department of Pediatrics (Genetics), University of Minnesota, 420 Delaware Street SE, MMC75, Minneapolis, MN, 55454, USA
| | - Martina Wilke
- Department of Clinical Genetics, ErasmusMC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands; ENCORE Expertise Center for Genetic Neurocognitive Developmental Disorders, Erasmus, MC, Rotterdam
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18
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Pfleiderer MM, Galej WP. Emerging insights into the function and structure of the Integrator complex. Transcription 2021; 12:251-265. [PMID: 35311473 PMCID: PMC9006982 DOI: 10.1080/21541264.2022.2047583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/03/2022] Open
Abstract
The Integrator was originally discovered as a specialized 3'-end processing endonuclease complex required for maturation of RNA polymerase II (RNAPII)-dependent small nuclear RNAs (snRNAs). Since its discovery, Integrator's spectrum of substrates was significantly expanded to include non-polyadenylated long noncoding RNAs (lncRNA), enhancer RNAs (eRNAs), telomerase RNA (tertRNA), several Herpesvirus transcripts, and messenger RNAs (mRNAs). Recently emerging transcriptome-wide studies reveled an important role of the Integrator in protein-coding genes, where it contributes to gene expression regulation through promoter-proximal transcription attenuation. These new functional data are complemented by several structures of Integrator modules and higher-order complexes, providing mechanistic insights into Integrator-mediated processing events. In this work, we summarize recent progress in our understanding of the structure and function of the Integrator complex.
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19
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Slavotinek A, Misceo D, Htun S, Mathisen L, Frengen E, Foreman M, Hurtig JE, Enyenihi L, Sterrett MC, Leung SW, Schneidman-Duhovny D, Estrada-Veras J, Duncan JL, Haaxma CA, Kamsteeg EJ, Xia V, Beleford D, Si Y, Douglas G, Treidene HE, van Hoof A, Fasken MB, Corbett AH. Biallelic variants in the RNA exosome gene EXOSC5 are associated with developmental delays, short stature, cerebellar hypoplasia and motor weakness. Hum Mol Genet 2021; 29:2218-2239. [PMID: 32504085 DOI: 10.1093/hmg/ddaa108] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/10/2020] [Accepted: 05/28/2020] [Indexed: 12/15/2022] Open
Abstract
The RNA exosome is an essential ribonuclease complex required for processing and/or degradation of both coding and non-coding RNAs. We identified five patients with biallelic variants in EXOSC5, which encodes a structural subunit of the RNA exosome. The clinical features of these patients include failure to thrive, short stature, feeding difficulties, developmental delays that affect motor skills, hypotonia and esotropia. Brain MRI revealed cerebellar hypoplasia and ventriculomegaly. While we ascertained five patients, three patients with distinct variants of EXOSC5 were studied in detail. The first patient had a deletion involving exons 5-6 of EXOSC5 and a missense variant, p.Thr114Ile, that were inherited in trans, the second patient was homozygous for p.Leu206His and the third patient had paternal isodisomy for chromosome 19 and was homozygous for p.Met148Thr. The additional two patients ascertained are siblings who had an early frameshift mutation in EXOSC5 and the p.Thr114Ile missense variant that were inherited in trans. We employed three complementary approaches to explore the requirement for EXOSC5 in brain development and assess consequences of pathogenic EXOSC5 variants. Loss of function for exosc5 in zebrafish results in shortened and curved tails/bodies, reduced eye/head size and edema. We modeled pathogenic EXOSC5 variants in both budding yeast and mammalian cells. Some of these variants cause defects in RNA exosome function as well as altered interactions with other RNA exosome subunits. These findings expand the number of genes encoding RNA exosome subunits linked to human disease while also suggesting that disease mechanism varies depending on the specific pathogenic variant.
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Affiliation(s)
- Anne Slavotinek
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Doriana Misceo
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo 0450, Norway
| | - Stephanie Htun
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Linda Mathisen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo 0450, Norway
| | - Eirik Frengen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo 0450, Norway
| | - Michelle Foreman
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
| | - Jennifer E Hurtig
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
| | - Liz Enyenihi
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | | | - Sara W Leung
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering and the Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Juvianee Estrada-Veras
- Department of Pediatrics-Medical Genetics and Metabolism, Uniformed Services University/Walter Reed NMMC Bethesda, MD 20889, USA
| | - Jacque L Duncan
- Department of Ophthalmology, University of California, San Francisco, CA 94143, USA
| | - Charlotte A Haaxma
- Department of Pediatric Neurology, Amalia Children's Hospital and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands
| | - Vivian Xia
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Daniah Beleford
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Yue Si
- GeneDx Inc., MD 20877, USA
| | | | - Hans Einar Treidene
- Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo 0450, Norway
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
| | - Milo B Fasken
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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20
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Kour S, Rajan DS, Fortuna TR, Anderson EN, Ward C, Lee Y, Lee S, Shin YB, Chae JH, Choi M, Siquier K, Cantagrel V, Amiel J, Stolerman ES, Barnett SS, Cousin MA, Castro D, McDonald K, Kirmse B, Nemeth AH, Rajasundaram D, Innes AM, Lynch D, Frosk P, Collins A, Gibbons M, Yang M, Desguerre I, Boddaert N, Gitiaux C, Rydning SL, Selmer KK, Urreizti R, Garcia-Oguiza A, Osorio AN, Verdura E, Pujol A, McCurry HR, Landers JE, Agnihotri S, Andriescu EC, Moody SB, Phornphutkul C, Sacoto MJG, Begtrup A, Houlden H, Kirschner J, Schorling D, Rudnik-Schöneborn S, Strom TM, Leiz S, Juliette K, Richardson R, Yang Y, Zhang Y, Wang M, Wang J, Wang X, Platzer K, Donkervoort S, Bönnemann CG, Wagner M, Issa MY, Elbendary HM, Stanley V, Maroofian R, Gleeson JG, Zaki MS, Senderek J, Pandey UB. Loss of function mutations in GEMIN5 cause a neurodevelopmental disorder. Nat Commun 2021; 12:2558. [PMID: 33963192 PMCID: PMC8105379 DOI: 10.1038/s41467-021-22627-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/19/2021] [Indexed: 02/01/2023] Open
Abstract
GEMIN5, an RNA-binding protein is essential for assembly of the survival motor neuron (SMN) protein complex and facilitates the formation of small nuclear ribonucleoproteins (snRNPs), the building blocks of spliceosomes. Here, we have identified 30 affected individuals from 22 unrelated families presenting with developmental delay, hypotonia, and cerebellar ataxia harboring biallelic variants in the GEMIN5 gene. Mutations in GEMIN5 perturb the subcellular distribution, stability, and expression of GEMIN5 protein and its interacting partners in patient iPSC-derived neurons, suggesting a potential loss-of-function mechanism. GEMIN5 mutations result in disruption of snRNP complex assembly formation in patient iPSC neurons. Furthermore, knock down of rigor mortis, the fly homolog of human GEMIN5, leads to developmental defects, motor dysfunction, and a reduced lifespan. Interestingly, we observed that GEMIN5 variants disrupt a distinct set of transcripts and pathways as compared to SMA patient neurons, suggesting different molecular pathomechanisms. These findings collectively provide evidence that pathogenic variants in GEMIN5 perturb physiological functions and result in a neurodevelopmental delay and ataxia syndrome.
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Affiliation(s)
- Sukhleen Kour
- Department of Pediatrics, Childrens Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Deepa S Rajan
- Department of Pediatrics, Childrens Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Tyler R Fortuna
- Department of Pediatrics, Childrens Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Eric N Anderson
- Department of Pediatrics, Childrens Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Caroline Ward
- Department of Pediatrics, Childrens Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Youngha Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sangmoon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yong Beom Shin
- Department of Rehabilitative Medicine, Pusan National University School of Medicine, Pusan, Republic of Korea
| | - Jong-Hee Chae
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Karine Siquier
- Developmental Brain Disorders Laboratory, Paris University, Imagine Institute, INSERM UMR, Paris, France
| | - Vincent Cantagrel
- Developmental Brain Disorders Laboratory, Paris University, Imagine Institute, INSERM UMR, Paris, France
| | - Jeanne Amiel
- Department of Genetics, AP-HP, Necker Enfants Malades Hospital, Paris University, Imagine Institute, Paris, France
| | | | - Sarah S Barnett
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Diana Castro
- Department of Pediatrics and Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Brian Kirmse
- Division of Genetics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Andrea H Nemeth
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals National Health Service Foundation Trust, Oxford, UK
| | - Dhivyaa Rajasundaram
- Department of Pediatrics, Division of Health Informatics, Childrens Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - A Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Danielle Lynch
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Patrick Frosk
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Abigail Collins
- Department of Pediatrics and Neurology, Children's Hospital of Colorado, University of Colorado School of Medicine, Aurora, CO, USA
| | - Melissa Gibbons
- Department of Pediatrics and Neurology, Children's Hospital of Colorado, University of Colorado School of Medicine, Aurora, CO, USA
| | - Michele Yang
- Department of Pediatrics and Neurology, Children's Hospital of Colorado, University of Colorado School of Medicine, Aurora, CO, USA
| | - Isabelle Desguerre
- Department of Pediatric Neurology, AP-HP, Necker Enfants Malades Hospital, Paris University Imagine Institute, Paris, France
| | - Nathalie Boddaert
- Department of Pediatric Radiology, AP-HP, Necker Enfants Malades Hospital, Paris University Imagine Institute, Paris, France
| | - Cyril Gitiaux
- Department of Pediatric Neurophysiology AP-HP, Necker Enfants Malades Hospital, Paris University, Paris, France
| | | | - Kaja K Selmer
- Department of Research and Development, Division of Neuroscience, Oslo University Hospital and the University of Oslo, Oslo, Norway
| | - Roser Urreizti
- Department of Clinical Biochemistry, Institut de Recerca Sant Joan de Déu and CIBERER, Barcelona, Spain
| | | | | | - Edgard Verdura
- Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Aurora Pujol
- Centre for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Hannah R McCurry
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sameer Agnihotri
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - E Corina Andriescu
- Department of Pediatrics, University of Texas Health Science Center, Houston, TX, USA
| | - Shade B Moody
- Department of Pediatrics, University of Texas Health Science Center, Houston, TX, USA
| | - Chanika Phornphutkul
- Department of Pediatrics, Division of Human Genetics, Rhode Island Hospital and Warren Alpert Medical School of Brown University, Providence, RI, USA
| | | | | | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Janbernd Kirschner
- Department of Neuropediatrics and Muscle Disorders, Medical Center,, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - David Schorling
- Department of Neuropediatrics and Muscle Disorders, Medical Center,, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Tim M Strom
- Institute of Human Genetics, Faculty of Medicine, Technical University Munich, Munich, Germany
| | - Steffen Leiz
- Clinic for Children and Adolescents Dritter Orden, Divison of Neuropediatrics, Munchen, Germany
| | - Kali Juliette
- Department of Neurology, Gillette Children's Specialty Healthcare, St Paul, MN, USA
| | - Randal Richardson
- Department of Neurology, Gillette Children's Specialty Healthcare, St Paul, MN, USA
| | - Ying Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yuehua Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Minghui Wang
- The First People's Hospital of Changde City, Hunan, China
| | | | | | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der IsarTechnical, University of Munich, Munich, Germany
| | - Mahmoud Y Issa
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Hasnaa M Elbendary
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Valentina Stanley
- Departments of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Joseph G Gleeson
- Departments of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Jan Senderek
- Department of Neurology, Friedrich-Baur-Institute, University Hospital, LMU Munich, Munich, Germany
| | - Udai Bhan Pandey
- Department of Pediatrics, Childrens Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
- Children's Neuroscience Institute, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
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21
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Pfleiderer MM, Galej WP. Structure of the catalytic core of the Integrator complex. Mol Cell 2021; 81:1246-1259.e8. [PMID: 33548203 PMCID: PMC7980224 DOI: 10.1016/j.molcel.2021.01.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/29/2020] [Accepted: 01/05/2021] [Indexed: 12/17/2022]
Abstract
The Integrator is a specialized 3' end-processing complex involved in cleavage and transcription termination of a subset of nascent RNA polymerase II transcripts, including small nuclear RNAs (snRNAs). We provide evidence of the modular nature of the Integrator complex by biochemically characterizing its two subcomplexes, INTS5/8 and INTS10/13/14. Using cryoelectron microscopy (cryo-EM), we determined a 3.5-Å-resolution structure of the INTS4/9/11 ternary complex, which constitutes Integrator's catalytic core. Our structure reveals the spatial organization of the catalytic nuclease INTS11, bound to its catalytically impaired homolog INTS9 via several interdependent interfaces. INTS4, a helical repeat protein, plays a key role in stabilizing nuclease domains and other components. In this assembly, all three proteins form a composite electropositive groove, suggesting a putative RNA binding path within the complex. Comparison with other 3' end-processing machineries points to distinct features and a unique architecture of the Integrator's catalytic module.
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Affiliation(s)
- Moritz M Pfleiderer
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Wojciech P Galej
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France.
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22
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Kirstein N, Gomes Dos Santos H, Blumenthal E, Shiekhattar R. The Integrator complex at the crossroad of coding and noncoding RNA. Curr Opin Cell Biol 2020; 70:37-43. [PMID: 33340967 DOI: 10.1016/j.ceb.2020.11.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/10/2020] [Accepted: 11/17/2020] [Indexed: 12/31/2022]
Abstract
Genomic transcription is fundamental to all organisms. In metazoans, the Integrator complex is required for endonucleolytic processing of noncoding RNAs, regulation of RNA polymerase II pause-release, and premature transcription attenuation at coding genes. Recent insights into the structural composition and evolution of Integrator subunits have informed our understanding of its biochemical functionality. Moreover, studies in multiple model organisms point to an essential function of Integrator in signaling response and cellular development, highlighting a key role in neuronal differentiation. Indeed, alterations in Integrator complex subunits have been identified in patients with neurodevelopmental diseases and cancer. Taken together, we propose that Integrator is a central regulator of transcriptional processes and that its evolution reflects genomic complexity in regulatory elements and chromatin architecture.
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Affiliation(s)
- Nina Kirstein
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Department of Human Genetics, Biomedical Research Building, Room 719, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Helena Gomes Dos Santos
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Department of Human Genetics, Biomedical Research Building, Room 719, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Ezra Blumenthal
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Department of Human Genetics, Biomedical Research Building, Room 719, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Ramin Shiekhattar
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Department of Human Genetics, Biomedical Research Building, Room 719, 1501 NW 10th Avenue, Miami, FL 33136, USA.
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23
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Mendoza-Figueroa MS, Tatomer DC, Wilusz JE. The Integrator Complex in Transcription and Development. Trends Biochem Sci 2020; 45:923-934. [PMID: 32800671 DOI: 10.1016/j.tibs.2020.07.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/03/2020] [Accepted: 07/17/2020] [Indexed: 12/15/2022]
Abstract
The Integrator complex is conserved across metazoans and controls the fate of many nascent RNAs transcribed by RNA polymerase II (RNAPII). Among the 14 subunits of Integrator is an RNA endonuclease that is crucial for the biogenesis of small nuclear RNAs and enhancer RNAs. Integrator is further employed to trigger premature transcription termination at many protein-coding genes, thereby attenuating gene expression. Integrator thus helps to shape the transcriptome and ensure that genes can be robustly induced when needed. The molecular functions of Integrator subunits beyond the RNA endonuclease remain poorly understood, but some can act independently of the multisubunit complex. We highlight recent molecular insights into Integrator and propose how misregulation of this complex may lead to developmental defects and disease.
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Affiliation(s)
- María Saraí Mendoza-Figueroa
- 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
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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24
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Zhang X, Wang Y, Yang F, Tang J, Xu X, Yang L, Yang XA, Wu D. Biallelic INTS1 Mutations Cause a Rare Neurodevelopmental Disorder in Two Chinese Siblings. J Mol Neurosci 2019; 70:1-8. [PMID: 31428919 DOI: 10.1007/s12031-019-01393-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/29/2019] [Indexed: 01/08/2023]
Abstract
This study presents two Chinese siblings with a rare neurodevelopmental disorder (NDD) caused by biallelic INTS1 mutations and investigates the clinical features of this disease by means of in silico analysis. Two siblings, an 11-year-old brother and a 5-year-old sister, visited our hospital due to physical retardation and profound intellectual disability. Whole-exome sequencing (WES) was performed for the girl, and Sanger sequencing was used to validate the identified variants. Phenotype correlation analysis and in silico genetic interaction network analysis were performed to investigate genes that could lead to diseases similar to the rare disease in the patients. Growth retardation, distinct intellectual disability, hypertelorism, mild cataract, uneven teeth, abnormal palmar and plantar creases, and dubious genitalia were noted in the sister. No neurological features related to neuropathy were found. The brother showed features and growth delay similar to his sister. Heterozygous novel variants of c.1645A>G,p.Met549Val and c.5881C>T,p.Gln1961* in INTS1 were considered a candidate etiology. Sanger sequencing demonstrated that the variants were inherited from the grandfather and (maternal) grandmother. Phenotype correlation analysis revealed that CTDP1 mutation-induced congenital cataracts-facial dysmorphism-neuropathy (CCFDN) mostly overlapped with the performance of our patients. In silico analysis of the genetic interaction network showed that INTS1 is highly associated with INTS8 and CTDP1. Our study further validated that biallelic INTS1 mutations could bring about the onset of a novel neurodevelopmental disorder.
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Affiliation(s)
- Xuemin Zhang
- The Children's Neurorehabilitation Center, Pediatric Department, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, People's Republic of China
| | - Yajian Wang
- Beijing Chigene Translational Medicine Research Center Co., Ltd., Beijing, 100875, People's Republic of China
| | - Fang Yang
- School of Basic Medical Science, Chengde Medical University, Anyuan Road, Chengde, 067000, People's Republic of China
| | - Jiulai Tang
- The Children's Neurorehabilitation Center, Pediatric Department, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, People's Republic of China
| | - Xiaoyan Xu
- The Children's Neurorehabilitation Center, Pediatric Department, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, People's Republic of China
| | - Li Yang
- The Children's Neurorehabilitation Center, Pediatric Department, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, People's Republic of China
| | - Xiu-An Yang
- School of Basic Medical Science, Chengde Medical University, Anyuan Road, Chengde, 067000, People's Republic of China.
| | - De Wu
- The Children's Neurorehabilitation Center, Pediatric Department, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Hefei, 230022, People's Republic of China.
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