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Skerrett-Byrne DA, Stanger SJ, Trigg NA, Anderson AL, Sipilä P, Bernstein IR, Lord T, Schjenken JE, Murray HC, Verrills NM, Dun MD, Pang TY, Nixon B. Phosphoproteomic analysis of the adaption of epididymal epithelial cells to corticosterone challenge. Andrology 2024; 12:1038-1057. [PMID: 38576152 DOI: 10.1111/andr.13636] [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: 08/16/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND The epididymis has long been of interest owing to its role in promoting the functional maturation of the male germline. More recent evidence has also implicated the epididymis as an important sensory tissue responsible for remodeling of the sperm epigenome, both under physiological conditions and in response to diverse forms of environmental stress. Despite this knowledge, the intricacies of the molecular pathways involved in regulating the adaptation of epididymal tissue to paternal stressors remains to be fully resolved. OBJECTIVE The overall objective of this study was to investigate the direct impact of corticosterone challenge on a tractable epididymal epithelial cell line (i.e., mECap18 cells), in terms of driving adaptation of the cellular proteome and phosphoproteome signaling networks. MATERIALS AND METHODS The newly developed phosphoproteomic platform EasyPhos coupled with sequencing via an Orbitrap Exploris 480 mass spectrometer, was applied to survey global changes in the mECap18 cell (phospho)proteome resulting from sub-chronic (10-day) corticosterone challenge. RESULTS The imposed corticosterone exposure regimen elicited relatively subtle modifications of the global mECap18 proteome (i.e., only 73 out of 4171 [∼1.8%] proteins displayed altered abundance). By contrast, ∼15% of the mECap18 phosphoproteome was substantially altered following corticosterone challenge. In silico analysis of the corresponding parent proteins revealed an activation of pathways linked to DNA damage repair and oxidative stress responses as well as a reciprocal inhibition of pathways associated with organismal death. Corticosterone challenge also induced the phosphorylation of several proteins linked to the biogenesis of microRNAs. Accordingly, orthogonal validation strategies confirmed an increase in DNA damage, which was ameliorated upon selective kinase inhibition, and an altered abundance profile of a subset of microRNAs in corticosterone-treated cells. CONCLUSIONS Together, these data confirm that epididymal epithelial cells are reactive to corticosterone challenge, and that their response is tightly coupled to the opposing action of cellular kinases and phosphatases.
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Affiliation(s)
- David A Skerrett-Byrne
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, Australia
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - Simone J Stanger
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, Australia
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - Natalie A Trigg
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, Australia
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - Amanda L Anderson
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, Australia
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - Petra Sipilä
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, and Turku Center for Disease Modeling, University of Turku, Turku, Finland
| | - Ilana R Bernstein
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, Australia
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - Tessa Lord
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, Australia
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - John E Schjenken
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, Australia
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - Heather C Murray
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - Nicole M Verrills
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - Matthew D Dun
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - Terence Y Pang
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC, Australia
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, VIC, Australia
| | - Brett Nixon
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, Australia
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
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Kramárek M, Souček P, Réblová K, Grodecká L, Freiberger T. Splicing analysis of STAT3 tandem donor suggests non-canonical binding registers for U1 and U6 snRNAs. Nucleic Acids Res 2024; 52:5959-5974. [PMID: 38426935 PMCID: PMC11162779 DOI: 10.1093/nar/gkae147] [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: 10/10/2022] [Revised: 02/02/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
Tandem donor splice sites (5'ss) are unique regions with at least two GU dinucleotides serving as splicing cleavage sites. The Δ3 tandem 5'ss are a specific subclass of 5'ss separated by 3 nucleotides which can affect protein function by inserting/deleting a single amino acid. One 5'ss is typically preferred, yet factors governing particular 5'ss choice are not fully understood. A highly conserved exon 21 of the STAT3 gene was chosen as a model to study Δ3 tandem 5'ss splicing mechanisms. Based on multiple lines of experimental evidence, endogenous U1 snRNA most likely binds only to the upstream 5'ss. However, the downstream 5'ss is used preferentially, and the splice site choice is not dependent on the exact U1 snRNA binding position. Downstream 5'ss usage was sensitive to exact nucleotide composition and dependent on the presence of downstream regulatory region. The downstream 5'ss usage could be best explained by two novel interactions with endogenous U6 snRNA. U6 snRNA enables the downstream 5'ss usage in STAT3 exon 21 by two mechanisms: (i) binding in a novel non-canonical register and (ii) establishing extended Watson-Crick base pairing with the downstream regulatory region. This study suggests that U6:5'ss interaction is more flexible than previously thought.
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Affiliation(s)
- Michal Kramárek
- Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Přemysl Souček
- Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Kamila Réblová
- Centre of Molecular Biology and Genetics, University Hospital and Masaryk University, Brno, Czech Republic
| | - Lucie Kajan Grodecká
- Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic
| | - Tomáš Freiberger
- Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
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3
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Zhang W, Zhang X, Zhan X, Bai R, Lei J, Yan C, Shi Y. Structural insights into human exon-defined spliceosome prior to activation. Cell Res 2024; 34:428-439. [PMID: 38658629 PMCID: PMC11143319 DOI: 10.1038/s41422-024-00949-w] [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: 01/25/2024] [Accepted: 03/01/2024] [Indexed: 04/26/2024] Open
Abstract
Spliceosome is often assembled across an exon and undergoes rearrangement to span a neighboring intron. Most states of the intron-defined spliceosome have been structurally characterized. However, the structure of a fully assembled exon-defined spliceosome remains at large. During spliceosome assembly, the pre-catalytic state (B complex) is converted from its precursor (pre-B complex). Here we report atomic structures of the exon-defined human spliceosome in four sequential states: mature pre-B, late pre-B, early B, and mature B. In the previously unknown late pre-B state, U1 snRNP is already released but the remaining proteins are still in the pre-B state; unexpectedly, the RNAs are in the B state, with U6 snRNA forming a duplex with 5'-splice site and U5 snRNA recognizing the 3'-end of the exon. In the early and mature B complexes, the B-specific factors are stepwise recruited and specifically recognize the exon 3'-region. Our study reveals key insights into the assembly of the exon-defined spliceosomes and identifies mechanistic steps of the pre-B-to-B transition.
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Affiliation(s)
- Wenyu Zhang
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaofeng Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Xiechao Zhan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Rui Bai
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Jianlin Lei
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Chuangye Yan
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Yigong Shi
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
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4
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Zhang X, Zhan X, Bian T, Yang F, Li P, Lu Y, Xing Z, Fan R, Zhang QC, Shi Y. Structural insights into branch site proofreading by human spliceosome. Nat Struct Mol Biol 2024; 31:835-845. [PMID: 38196034 DOI: 10.1038/s41594-023-01188-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/23/2023] [Indexed: 01/11/2024]
Abstract
Selection of the pre-mRNA branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is crucial to prespliceosome (A complex) assembly. The RNA helicase PRP5 proofreads BS selection but the underlying mechanism remains unclear. Here we report the atomic structures of two sequential complexes leading to prespliceosome assembly: human 17S U2 snRNP and a cross-exon pre-A complex. PRP5 is anchored on 17S U2 snRNP mainly through occupation of the RNA path of SF3B1 by an acidic loop of PRP5; the helicase domain of PRP5 associates with U2 snRNA; the BS-interacting stem-loop (BSL) of U2 snRNA is shielded by TAT-SF1, unable to engage the BS. In the pre-A complex, an initial U2-BS duplex is formed; the translocated helicase domain of PRP5 stays with U2 snRNA and the acidic loop still occupies the RNA path. The pre-A conformation is specifically stabilized by the splicing factors SF1, DNAJC8 and SF3A2. Cancer-derived mutations in SF3B1 damage its association with PRP5, compromising BS proofreading. Together, these findings reveal key insights into prespliceosome assembly and BS selection or proofreading by PRP5.
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Affiliation(s)
- Xiaofeng Zhang
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China.
- Division of Reproduction and Genetics, The First Affiliated Hospital of USTC; MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Xiechao Zhan
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
| | - Tong Bian
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- College of Life Sciences, Fudan University, Shanghai, China
| | - Fenghua Yang
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- College of Life Sciences, Fudan University, Shanghai, China
| | - Pan Li
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure; Tsinghua-Peking Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China
| | - Yichen Lu
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- College of Life Sciences, Fudan University, Shanghai, China
| | - Zhihan Xing
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
| | - Rongyan Fan
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
| | - Qiangfeng Cliff Zhang
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure; Tsinghua-Peking Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China
| | - Yigong Shi
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China.
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure; Tsinghua-Peking Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China.
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5
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Atkinson R, Georgiou M, Yang C, Szymanska K, Lahat A, Vasconcelos EJR, Ji Y, Moya Molina M, Collin J, Queen R, Dorgau B, Watson A, Kurzawa-Akanbi M, Laws R, Saxena A, Shyan Beh C, Siachisumo C, Goertler F, Karwatka M, Davey T, Inglehearn CF, McKibbin M, Lührmann R, Steel DH, Elliott DJ, Armstrong L, Urlaub H, Ali RR, Grellscheid SN, Johnson CA, Mozaffari-Jovin S, Lako M. PRPF8-mediated dysregulation of hBrr2 helicase disrupts human spliceosome kinetics and 5´-splice-site selection causing tissue-specific defects. Nat Commun 2024; 15:3138. [PMID: 38605034 PMCID: PMC11009313 DOI: 10.1038/s41467-024-47253-0] [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: 09/21/2023] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
The carboxy-terminus of the spliceosomal protein PRPF8, which regulates the RNA helicase Brr2, is a hotspot for mutations causing retinitis pigmentosa-type 13, with unclear role in human splicing and tissue-specificity mechanism. We used patient induced pluripotent stem cells-derived cells, carrying the heterozygous PRPF8 c.6926 A > C (p.H2309P) mutation to demonstrate retinal-specific endophenotypes comprising photoreceptor loss, apical-basal polarity and ciliary defects. Comprehensive molecular, transcriptomic, and proteomic analyses revealed a role of the PRPF8/Brr2 regulation in 5'-splice site (5'SS) selection by spliceosomes, for which disruption impaired alternative splicing and weak/suboptimal 5'SS selection, and enhanced cryptic splicing, predominantly in ciliary and retinal-specific transcripts. Altered splicing efficiency, nuclear speckles organisation, and PRPF8 interaction with U6 snRNA, caused accumulation of active spliceosomes and poly(A)+ mRNAs in unique splicing clusters located at the nuclear periphery of photoreceptors. Collectively these elucidate the role of PRPF8/Brr2 regulatory mechanisms in splicing and the molecular basis of retinal disease, informing therapeutic approaches.
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Affiliation(s)
| | - Maria Georgiou
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Chunbo Yang
- Biosciences Institute, Newcastle University, Newcastle, UK
| | | | - Albert Lahat
- Department of Biosciences, Durham University, Durham, UK
| | | | - Yanlong Ji
- Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Marina Moya Molina
- Biosciences Institute, Newcastle University, Newcastle, UK
- Newcells Biotech, Newcastle, UK
| | - Joseph Collin
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Rachel Queen
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Birthe Dorgau
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Avril Watson
- Biosciences Institute, Newcastle University, Newcastle, UK
- Newcells Biotech, Newcastle, UK
| | | | - Ross Laws
- Electron Microscopy Research Services, Newcastle University, Newcastle, UK
| | - Abhijit Saxena
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Chia Shyan Beh
- Biosciences Institute, Newcastle University, Newcastle, UK
| | | | | | | | - Tracey Davey
- Electron Microscopy Research Services, Newcastle University, Newcastle, UK
| | | | - Martin McKibbin
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Reinhard Lührmann
- Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - David H Steel
- Biosciences Institute, Newcastle University, Newcastle, UK
| | | | - Lyle Armstrong
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Henning Urlaub
- Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
- Göttingen Center for Molecular Biosciences, Georg August University of Göttingen, Göttingen, Germany
| | - Robin R Ali
- Centre for Cell and Gene Therapy, Kings College London, London, UK
| | - Sushma-Nagaraja Grellscheid
- Department of Biosciences, Durham University, Durham, UK
- Department of Informatics, University of Bergen, Bergen, Norway
| | - Colin A Johnson
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK.
| | - Sina Mozaffari-Jovin
- Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany.
- Department of Medical Genetics and Medical Genetics Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Majlinda Lako
- Biosciences Institute, Newcastle University, Newcastle, UK.
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6
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Cheng F, Chapman T, Zhang S, Morsch M, Chung R, Lee A, Rayner SL. Understanding age-related pathologic changes in TDP-43 functions and the consequence on RNA splicing and signalling in health and disease. Ageing Res Rev 2024; 96:102246. [PMID: 38401571 DOI: 10.1016/j.arr.2024.102246] [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: 10/26/2023] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 02/26/2024]
Abstract
TAR DNA binding protein-43 (TDP-43) is a key component in RNA splicing which plays a crucial role in the aging process. In neurodegenerative diseases such as amyotrophic lateral sclerosis, frontotemporal dementia and limbic-predominant age-related TDP-43 encephalopathy, TDP-43 can be mutated, mislocalised out of the nucleus of neurons and glial cells and form cytoplasmic inclusions. These TDP-43 alterations can lead to its RNA splicing dysregulation and contribute to mis-splicing of various types of RNA, such as mRNA, microRNA, and circular RNA. These changes can result in the generation of an altered transcriptome and proteome within cells, ultimately changing the diversity and quantity of gene products. In this review, we summarise the findings of novel atypical RNAs resulting from TDP-43 dysfunction and their potential as biomarkers or targets for therapeutic development.
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Affiliation(s)
- Flora Cheng
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia.
| | - Tyler Chapman
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Selina Zhang
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Marco Morsch
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Roger Chung
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Albert Lee
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia
| | - Stephanie L Rayner
- Motor Neuron Disease Research Centre, Macquarie Medical School, Macquarie University, Sydney, Australia.
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7
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Zhang J, Xie J, Huang J, Liu X, Xu R, Tholen J, Galej WP, Tong L, Manley JL, Liu Z. Characterization of the SF3B1-SUGP1 interface reveals how numerous cancer mutations cause mRNA missplicing. Genes Dev 2023; 37:968-983. [PMID: 37977822 PMCID: PMC10760632 DOI: 10.1101/gad.351154.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
The spliceosomal gene SF3B1 is frequently mutated in cancer. While it is known that SF3B1 hotspot mutations lead to loss of splicing factor SUGP1 from spliceosomes, the cancer-relevant SF3B1-SUGP1 interaction has not been characterized. To address this issue, we show by structural modeling that two regions flanking the SUGP1 G-patch make numerous contacts with the region of SF3B1 harboring hotspot mutations. Experiments confirmed that all the cancer-associated mutations in these regions, as well as mutations affecting other residues in the SF3B1-SUGP1 interface, not only weaken or disrupt the interaction but also alter splicing similarly to SF3B1 cancer mutations. Finally, structural modeling of a trimeric protein complex reveals that the SF3B1-SUGP1 interaction "loops out" the G-patch for interaction with the helicase DHX15. Our study thus provides an unprecedented molecular view of a protein complex essential for accurate splicing and also reveals that numerous cancer-associated mutations disrupt the critical SF3B1-SUGP1 interaction.
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Affiliation(s)
- Jian Zhang
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Jindou Xie
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji Huang
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Xiangyang Liu
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Ruihong Xu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jonas Tholen
- European Molecular Biology Laboratory, 38042 Grenoble, France
| | | | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA;
| | - Zhaoqi Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Kour R, Kim J, Roy A, Richardson B, Cameron MJ, Knott JG, Mazumder B. Loss of function of ribosomal protein L13a blocks blastocyst formation and reveals a potential nuclear role in gene expression. FASEB J 2023; 37:e23275. [PMID: 37902531 PMCID: PMC10999073 DOI: 10.1096/fj.202301475r] [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: 07/18/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 10/31/2023]
Abstract
Ribosomal proteins play diverse roles in development and disease. Most ribosomal proteins have canonical roles in protein synthesis, while some exhibit extra-ribosomal functions. Previous studies in our laboratory revealed that ribosomal protein L13a (RPL13a) is involved in the translational silencing of a cohort of inflammatory proteins in myeloid cells. This prompted us to investigate the role of RPL13a in embryonic development. Here we report that RPL13a is required for early development in mice. Crosses between Rpl13a+/- mice resulted in no Rpl13a-/- offspring. Closer examination revealed that Rpl13a-/- embryos were arrested at the morula stage during preimplantation development. RNA sequencing analysis of Rpl13a-/- morulae revealed widespread alterations in gene expression, including but not limited to several genes encoding proteins involved in the inflammatory response, embryogenesis, oocyte maturation, stemness, and pluripotency. Ex vivo analysis revealed that RPL13a was localized to the cytoplasm and nucleus between the two-cell and morula stages. RNAi-mediated depletion of RPL13a phenocopied Rpl13a-/- embryos and knockdown embryos exhibited increased expression of IL-7 and IL-17 and decreased expression of the lineage specifier genes Sox2, Pou5f1, and Cdx2. Lastly, a protein-protein interaction assay revealed that RPL13a is associated with chromatin, suggesting an extra ribosomal function in transcription. In summary, our data demonstrate that RPL13a is essential for the completion of preimplantation embryo development. The mechanistic basis of the absence of RPL13a-mediated embryonic lethality will be addressed in the future through follow-up studies on ribosome biogenesis, global protein synthesis, and identification of RPL13a target genes using chromatin immunoprecipitation and RNA-immunoprecipitation-based sequencing.
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Affiliation(s)
- Ravinder Kour
- Center for Gene Regulation in Health and Disease, Department of Biological Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, USA
| | - Jaehwan Kim
- Developmental Epigenetics Laboratory, Department of Animal Science, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA
| | - Antara Roy
- Center for Gene Regulation in Health and Disease, Department of Biological Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, USA
| | - Brian Richardson
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mark J. Cameron
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jason G. Knott
- Developmental Epigenetics Laboratory, Department of Animal Science, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA
| | - Barsanjit Mazumder
- Center for Gene Regulation in Health and Disease, Department of Biological Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, USA
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9
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Xu Y, Spear S, Ma Y, Lorentzen MP, Gruet M, McKinney F, Xu Y, Wickremesinghe C, Shepherd MR, McNeish I, Keun HC, Nijhuis A. Pharmacological depletion of RNA splicing factor RBM39 by indisulam synergizes with PARP inhibitors in high-grade serous ovarian carcinoma. Cell Rep 2023; 42:113307. [PMID: 37858464 DOI: 10.1016/j.celrep.2023.113307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/04/2023] [Accepted: 10/04/2023] [Indexed: 10/21/2023] Open
Abstract
Ovarian high-grade serous carcinoma (HGSC) is the most common subtype of ovarian cancer with limited therapeutic options and a poor prognosis. In recent years, poly-ADP ribose polymerase (PARP) inhibitors have demonstrated significant clinical benefits, especially in patients with BRCA1/2 mutations. However, acquired drug resistance and relapse is a major challenge. Indisulam (E7070) has been identified as a molecular glue that brings together splicing factor RBM39 and DCAF15 E3 ubiquitin ligase resulting in polyubiquitination, degradation, and subsequent RNA splicing defects. In this work, we demonstrate that the loss of RBM39 induces splicing defects in key DNA damage repair genes in ovarian cancer, leading to increased sensitivity to cisplatin and various PARP inhibitors. The addition of indisulam also improved olaparib response in mice bearing PARP inhibitor-resistant tumors. These findings demonstrate that combining RBM39 degraders and PARP inhibitors is a promising therapeutic approach to improve PARP inhibitor response in ovarian HGSC.
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Affiliation(s)
- Yuewei Xu
- Department of Surgery & Cancer, Imperial College London, London, UK
| | - Sarah Spear
- Department of Surgery & Cancer, Imperial College London, London, UK; Ovarian Cancer Action Research Centre, Department of Surgery & Cancer, Imperial College London, London, UK
| | - Yurui Ma
- Department of Surgery & Cancer, Imperial College London, London, UK
| | - Marc P Lorentzen
- Department of Surgery & Cancer, Imperial College London, London, UK; Ovarian Cancer Action Research Centre, Department of Surgery & Cancer, Imperial College London, London, UK
| | - Michael Gruet
- Department of Surgery & Cancer, Imperial College London, London, UK
| | - Flora McKinney
- Department of Surgery & Cancer, Imperial College London, London, UK
| | - Yitao Xu
- Department of Surgery & Cancer, Imperial College London, London, UK
| | - Chiharu Wickremesinghe
- Department of Surgery & Cancer, Imperial College London, London, UK; Ovarian Cancer Action Research Centre, Department of Surgery & Cancer, Imperial College London, London, UK
| | | | - Iain McNeish
- Department of Surgery & Cancer, Imperial College London, London, UK; Ovarian Cancer Action Research Centre, Department of Surgery & Cancer, Imperial College London, London, UK
| | - Hector C Keun
- Department of Surgery & Cancer, Imperial College London, London, UK; Ovarian Cancer Action Research Centre, Department of Surgery & Cancer, Imperial College London, London, UK.
| | - Anke Nijhuis
- Department of Surgery & Cancer, Imperial College London, London, UK; Ovarian Cancer Action Research Centre, Department of Surgery & Cancer, Imperial College London, London, UK.
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10
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Chen J, Zhang X, Tan X, Liu P. Somatic gain-of-function mutations in BUD13 promote oncogenesis by disrupting Fbw7 function. J Exp Med 2023; 220:e20222056. [PMID: 37382881 PMCID: PMC10309187 DOI: 10.1084/jem.20222056] [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: 11/30/2022] [Revised: 04/13/2023] [Accepted: 05/19/2023] [Indexed: 06/30/2023] Open
Abstract
Somatic mutations occurring on key enzymes are extensively studied and targeted therapies are developed with clinical promises. However, context-dependent enzyme function through distinct substrates complicated targeting a given enzyme. Here, we develop an algorithm to elucidate a new class of somatic mutations occurring on enzyme-recognizing motifs that cancer may hijack to facilitate tumorigenesis. We validate BUD13-R156C and -R230Q mutations evading RSK3-mediated phosphorylation with enhanced oncogenicity in promoting colon cancer growth. Further mechanistic studies reveal BUD13 as an endogenous Fbw7 inhibitor that stabilizes Fbw7 oncogenic substrates, while cancerous BUD13-R156C or -R230Q interferes with Fbw7Cul1 complex formation. We also find this BUD13 regulation plays a critical role in responding to mTOR inhibition, which can be used to guide therapy selections. We hope our studies reveal the landscape of enzyme-recognizing motif mutations with a publicly available resource and provide novel insights for somatic mutations cancer hijacks to promote tumorigenesis with the potential for patient stratification and cancer treatment.
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Affiliation(s)
- Jianfeng Chen
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill , Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xinyi Zhang
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill , Chapel Hill, NC, USA
| | - Xianming Tan
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill , Chapel Hill, NC, USA
- Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Pengda Liu
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill , Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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11
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Lu J, Zheng KQ, Bertrand RE, Quinlan J, Ferdous S, Srinivasan T, Oh S, Wang K, Chen R. Gene augmentation therapy to rescue degenerative photoreceptors in a Cwc27 mutant mouse model. Exp Eye Res 2023; 234:109596. [PMID: 37479075 DOI: 10.1016/j.exer.2023.109596] [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: 04/24/2023] [Revised: 06/18/2023] [Accepted: 07/18/2023] [Indexed: 07/23/2023]
Abstract
Previous reports have demonstrated that defects in the spliceosome-associated protein CWC27 can lead to the degeneration of retinal cells in Cwc27 mutant mouse models. However, it is unknown whether gene replacement therapy can rescue this phenotype. The purpose of this study was to evaluate whether AAV based gene therapy could rescue the retinal degeneration observed in Cwc27 mutant mice. By 6 months of age, Cwc27 mutant mice show a retinal degenerative phenotype, including morphological and functional abnormalities, primarily driven by the death of photoreceptors. We hypothesize that subretinal injection of AAV8 to drive exogenous CWC27 protein expression will improve the retinal phenotype. We evaluated these improvements after gene therapy with electroretinography (ERG) and histology, either hematoxylin and eosin (H&E) or immunostaining. In this study, we demonstrated that subretinal injection of AAV8-GRK-Cwc27-FLAG in mutant mice can improve the functionality and morphology of the retina. Immunostaining analyses revealed a notable decrease in photoreceptor degeneration, including cone cell degeneration, in the AAV-injected eyes compared to the PBS-injected eyes. Based on these results, gene replacement therapy could be a promising method for treating retinal degeneration caused by mutations in Cwc27.
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Affiliation(s)
- Jiaxiong Lu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA; Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Karen Q Zheng
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of BioSciences, Rice University, Houston, TX, USA
| | - Renae Elaine Bertrand
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA; Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Joseph Quinlan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Bioengineering, Rice University, Houston, TX, USA
| | - Salma Ferdous
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tanmay Srinivasan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of BioSciences, Rice University, Houston, TX, USA
| | - Soo Oh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Keqing Wang
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Rui Chen
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA; Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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12
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Hecker M, Fitzner B, Boxberger N, Putscher E, Engelmann R, Bergmann W, Müller M, Ludwig-Portugall I, Schwartz M, Meister S, Dudesek A, Winkelmann A, Koczan D, Zettl UK. Transcriptome alterations in peripheral blood B cells of patients with multiple sclerosis receiving immune reconstitution therapy. J Neuroinflammation 2023; 20:181. [PMID: 37533036 PMCID: PMC10394872 DOI: 10.1186/s12974-023-02859-x] [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: 10/12/2022] [Accepted: 07/25/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Multiple sclerosis (MS) is a chronic, inflammatory and neurodegenerative disease that leads to irreversible damage to the brain and spinal cord. The goal of so-called "immune reconstitution therapies" (IRTs) is to achieve long-term disease remission by eliminating a pathogenic immune repertoire through intense short-term immune cell depletion. B cells are major targets for effective immunotherapy in MS. OBJECTIVES The aim of this study was to analyze the gene expression pattern of B cells before and during IRT (i.e., before B-cell depletion and after B-cell repopulation) to better understand the therapeutic effects and to identify biomarker candidates of the clinical response to therapy. METHODS B cells were obtained from blood samples of patients with relapsing-remitting MS (n = 50), patients with primary progressive MS (n = 13) as well as healthy controls (n = 28). The patients with relapsing MS received either monthly infusions of natalizumab (n = 29) or a pulsed IRT with alemtuzumab (n = 15) or cladribine (n = 6). B-cell subpopulation frequencies were determined by flow cytometry, and transcriptome profiling was performed using Clariom D arrays. Differentially expressed genes (DEGs) between the patient groups and controls were examined with regard to their functions and interactions. We also tested for differences in gene expression between patients with and without relapse following alemtuzumab administration. RESULTS Patients treated with alemtuzumab or cladribine showed on average a > 20% lower proportion of memory B cells as compared to before IRT. This was paralleled by profound transcriptome shifts, with > 6000 significant DEGs after adjustment for multiple comparisons. The top DEGs were found to regulate apoptosis, cell adhesion and RNA processing, and the most highly connected nodes in the network of encoded proteins were ESR2, PHB and RC3H1. Higher mRNA levels of BCL2, IL13RA1 and SLC38A11 were seen in patients with relapse despite IRT, though these differences did not pass the false discovery rate correction. CONCLUSIONS We show that B cells circulating in the blood of patients with MS undergoing IRT present a distinct gene expression signature, and we delineated the associated biological processes and gene interactions. Moreover, we identified genes whose expression may be an indicator of relapse risk, but further studies are needed to verify their potential value as biomarkers.
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Affiliation(s)
- Michael Hecker
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany.
| | - Brit Fitzner
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Nina Boxberger
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Elena Putscher
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Robby Engelmann
- Clinic III (Hematology, Oncology and Palliative Medicine), Special Hematology Laboratory, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany
| | - Wendy Bergmann
- Core Facility for Cell Sorting and Cell Analysis, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | - Michael Müller
- Core Facility for Cell Sorting and Cell Analysis, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | | | - Margit Schwartz
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Stefanie Meister
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Ales Dudesek
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Alexander Winkelmann
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Dirk Koczan
- Institute of Immunology, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | - Uwe Klaus Zettl
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
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13
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Flemr M, Schwaiger M, Hess D, Iesmantavicius V, Ahel J, Tuck AC, Mohn F, Bühler M. Mouse nuclear RNAi-defective 2 promotes splicing of weak 5' splice sites. RNA (NEW YORK, N.Y.) 2023; 29:1140-1165. [PMID: 37137667 PMCID: PMC10351895 DOI: 10.1261/rna.079465.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/19/2023] [Indexed: 05/05/2023]
Abstract
Removal of introns during pre-mRNA splicing, which is central to gene expression, initiates by base pairing of U1 snRNA with a 5' splice site (5'SS). In mammals, many introns contain weak 5'SSs that are not efficiently recognized by the canonical U1 snRNP, suggesting alternative mechanisms exist. Here, we develop a cross-linking immunoprecipitation coupled to a high-throughput sequencing method, BCLIP-seq, to identify NRDE2 (nuclear RNAi-defective 2), and CCDC174 (coiled-coil domain-containing 174) as novel RNA-binding proteins in mouse ES cells that associate with U1 snRNA and 5'SSs. Both proteins bind directly to U1 snRNA independently of canonical U1 snRNP-specific proteins, and they are required for the selection and effective processing of weak 5'SSs. Our results reveal that mammalian cells use noncanonical splicing factors bound directly to U1 snRNA to effectively select suboptimal 5'SS sequences in hundreds of genes, promoting proper splice site choice, and accurate pre-mRNA splicing.
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Affiliation(s)
- Matyas Flemr
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Michaela Schwaiger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | | | - Josip Ahel
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Alex Charles Tuck
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Fabio Mohn
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- University of Basel, 4003 Basel, Switzerland
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14
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Enders M, Neumann P, Dickmanns A, Ficner R. Structure and function of spliceosomal DEAH-box ATPases. Biol Chem 2023; 404:851-866. [PMID: 37441768 DOI: 10.1515/hsz-2023-0157] [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: 03/10/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023]
Abstract
Splicing of precursor mRNAs is a hallmark of eukaryotic cells, performed by a huge macromolecular machine, the spliceosome. Four DEAH-box ATPases are essential components of the spliceosome, which play an important role in the spliceosome activation, the splicing reaction, the release of the spliced mRNA and intron lariat, and the disassembly of the spliceosome. An integrative approach comprising X-ray crystallography, single particle cryo electron microscopy, single molecule FRET, and molecular dynamics simulations provided deep insights into the structure, dynamics and function of the spliceosomal DEAH-box ATPases.
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Affiliation(s)
- Marieke Enders
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Achim Dickmanns
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
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15
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Beusch I, Rao B, Studer MK, Luhovska T, Šukytė V, Lei S, Oses-Prieto J, SeGraves E, Burlingame A, Jonas S, Madhani HD. Targeted high-throughput mutagenesis of the human spliceosome reveals its in vivo operating principles. Mol Cell 2023; 83:2578-2594.e9. [PMID: 37402368 PMCID: PMC10484158 DOI: 10.1016/j.molcel.2023.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 03/15/2023] [Accepted: 06/02/2023] [Indexed: 07/06/2023]
Abstract
The spliceosome is a staggeringly complex machine, comprising, in humans, 5 snRNAs and >150 proteins. We scaled haploid CRISPR-Cas9 base editing to target the entire human spliceosome and investigated the mutants using the U2 snRNP/SF3b inhibitor, pladienolide B. Hypersensitive substitutions define functional sites in the U1/U2-containing A complex but also in components that act as late as the second chemical step after SF3b is dissociated. Viable resistance substitutions map not only to the pladienolide B-binding site but also to the G-patch domain of SUGP1, which lacks orthologs in yeast. We used these mutants and biochemical approaches to identify the spliceosomal disassemblase DHX15/hPrp43 as the ATPase ligand for SUGP1. These and other data support a model in which SUGP1 promotes splicing fidelity by triggering early spliceosome disassembly in response to kinetic blocks. Our approach provides a template for the analysis of essential cellular machines in humans.
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Affiliation(s)
- Irene Beusch
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, USA
| | - Beiduo Rao
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, USA
| | - Michael K Studer
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Tetiana Luhovska
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Viktorija Šukytė
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Susan Lei
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, USA
| | - Juan Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, USA
| | - Em SeGraves
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, USA
| | - Alma Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, USA
| | - Stefanie Jonas
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, USA.
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16
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Zhu G, Khalid F, Zhang D, Cao Z, Maity P, Kestler HA, Orioli D, Scharffetter-Kochanek K, Iben S. Ribosomal Dysfunction Is a Common Pathomechanism in Different Forms of Trichothiodystrophy. Cells 2023; 12:1877. [PMID: 37508541 PMCID: PMC10377840 DOI: 10.3390/cells12141877] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/07/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Mutations in a broad variety of genes can provoke the severe childhood disorder trichothiodystrophy (TTD) that is classified as a DNA repair disease or a transcription syndrome of RNA polymerase II. In an attempt to identify the common underlying pathomechanism of TTD we performed a knockout/knockdown of the two unrelated TTD factors TTDN1 and RNF113A and investigated the consequences on ribosomal biogenesis and performance. Interestingly, interference with these TTD factors created a nearly uniform impact on RNA polymerase I transcription with downregulation of UBF, disturbed rRNA processing and reduction of the backbone of the small ribosomal subunit rRNA 18S. This was accompanied by a reduced quality of decoding in protein translation and the accumulation of misfolded and carbonylated proteins, indicating a loss of protein homeostasis (proteostasis). As the loss of proteostasis by the ribosome has been identified in the other forms of TTD, here we postulate that ribosomal dysfunction is a common underlying pathomechanism of TTD.
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Affiliation(s)
- Gaojie Zhu
- Department of Dermatology and Allergic Diseases, Ulm University, 89081 Ulm, Germany
| | - Fatima Khalid
- Department of Dermatology and Allergic Diseases, Ulm University, 89081 Ulm, Germany
| | - Danhui Zhang
- Department of Dermatology and Allergic Diseases, Ulm University, 89081 Ulm, Germany
| | - Zhouli Cao
- Department of Dermatology and Allergic Diseases, Ulm University, 89081 Ulm, Germany
| | - Pallab Maity
- Department of Dermatology and Allergic Diseases, Ulm University, 89081 Ulm, Germany
| | - Hans A Kestler
- Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Donata Orioli
- Istituto di Genetica Molecolare L.L. Cavalli-Sforza CNR, 27100 Pavia, Italy
| | | | - Sebastian Iben
- Department of Dermatology and Allergic Diseases, Ulm University, 89081 Ulm, Germany
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17
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Salvato I, Ricciardi L, Dal Col J, Nigro A, Giurato G, Memoli D, Sellitto A, Lamparelli EP, Crescenzi MA, Vitale M, Vatrella A, Nucera F, Brun P, Caicci F, Dama P, Stiff T, Castellano L, Idrees S, Johansen MD, Faiz A, Wark PA, Hansbro PM, Adcock IM, Caramori G, Stellato C. Expression of targets of the RNA-binding protein AUF-1 in human airway epithelium indicates its role in cellular senescence and inflammation. Front Immunol 2023; 14:1192028. [PMID: 37483631 PMCID: PMC10360199 DOI: 10.3389/fimmu.2023.1192028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/06/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction The RNA-binding protein AU-rich-element factor-1 (AUF-1) participates to posttranscriptional regulation of genes involved in inflammation and cellular senescence, two pathogenic mechanisms of chronic obstructive pulmonary disease (COPD). Decreased AUF-1 expression was described in bronchiolar epithelium of COPD patients versus controls and in vitro cytokine- and cigarette smoke-challenged human airway epithelial cells, prompting the identification of epithelial AUF-1-targeted transcripts and function, and investigation on the mechanism of its loss. Results RNA immunoprecipitation-sequencing (RIP-Seq) identified, in the human airway epithelial cell line BEAS-2B, 494 AUF-1-bound mRNAs enriched in their 3'-untranslated regions for a Guanine-Cytosine (GC)-rich binding motif. AUF-1 association with selected transcripts and with a synthetic GC-rich motif were validated by biotin pulldown. AUF-1-targets' steady-state levels were equally affected by partial or near-total AUF-1 loss induced by cytomix (TNFα/IL1β/IFNγ/10 nM each) and siRNA, respectively, with differential transcript decay rates. Cytomix-mediated decrease in AUF-1 levels in BEAS-2B and primary human small-airways epithelium (HSAEC) was replicated by treatment with the senescence- inducer compound etoposide and associated with readouts of cell-cycle arrest, increase in lysosomal damage and senescence-associated secretory phenotype (SASP) factors, and with AUF-1 transfer in extracellular vesicles, detected by transmission electron microscopy and immunoblotting. Extensive in-silico and genome ontology analysis found, consistent with AUF-1 functions, enriched RIP-Seq-derived AUF-1-targets in COPD-related pathways involved in inflammation, senescence, gene regulation and also in the public SASP proteome atlas; AUF-1 target signature was also significantly represented in multiple transcriptomic COPD databases generated from primary HSAEC, from lung tissue and from single-cell RNA-sequencing, displaying a predominant downregulation of expression. Discussion Loss of intracellular AUF-1 may alter posttranscriptional regulation of targets particularly relevant for protection of genomic integrity and gene regulation, thus concurring to airway epithelial inflammatory responses related to oxidative stress and accelerated aging. Exosomal-associated AUF-1 may in turn preserve bound RNA targets and sustain their function, participating to spreading of inflammation and senescence to neighbouring cells.
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Affiliation(s)
- Ilaria Salvato
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Luca Ricciardi
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Jessica Dal Col
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Annunziata Nigro
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Giorgio Giurato
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Domenico Memoli
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Assunta Sellitto
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Erwin Pavel Lamparelli
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Maria Assunta Crescenzi
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Monica Vitale
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Alessandro Vatrella
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Francesco Nucera
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Paola Brun
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | | | - Paola Dama
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Thomas Stiff
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Leandro Castellano
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Sobia Idrees
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Matt D. Johansen
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Alen Faiz
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Peter A. Wark
- Immune Health, Hunter Medical Research Institute and The University of Newcastle, Newcastle, NSW, Australia
| | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
- Immune Health, Hunter Medical Research Institute and The University of Newcastle, Newcastle, NSW, Australia
| | - Ian M. Adcock
- National Heart and Lung Institute, Imperial College London and the National Institute for Health and Care Research (NIHR) Imperial Biomedical Research Centre, London, United Kingdom
| | - Gaetano Caramori
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Cristiana Stellato
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
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18
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Chang J, Yan S, Geng Z, Wang Z. Inhibition of splicing factors SF3A3 and SRSF5 contributes to As 3+/Se 4+ combination-mediated proliferation suppression and apoptosis induction in acute promyelocytic leukemia cells. Arch Biochem Biophys 2023; 743:109677. [PMID: 37356608 DOI: 10.1016/j.abb.2023.109677] [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: 04/17/2023] [Revised: 05/28/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
The low-dose combination of Arsenite (As3+) and selenite (Se4+) has the advantages of lower biological toxicity and better curative effects for acute promyelocytic leukemia (APL) therapy. However, the underlying mechanisms remain unclear. Here, based on the fact that the combination of 2 μM A3+ plus 4 μM Se4+ possessed a stronger anti-leukemic effect on APL cell line NB4 as compared with each individual, we employed iTRAQ-based quantitative proteomics to identify a total of 58 proteins that were differentially expressed after treatment with As3+/Se4+ combination rather than As3+ or Se4+ alone, the majority of which were involved in spliceosome pathway. Among them, eight proteins stood out by virtue of their splicing function and significant changes. They were validated as being decreased in mRNA and protein levels under As3+/Se4+ combination treatment. Further functional studies showed that only knockdown of two splicing factors, SF3A3 and SRSF5, suppressed the growth of NB4 cells. The reduction of SF3A3 was found to cause G1/S cell cycle arrest, which resulted in proliferation inhibition. Moreover, SRSF5 downregulation induced cell apoptosis through the activation of caspase-3. Taken together, these findings indicate that SF3A3 and SRSF5 function as pro-leukemic factors and can be potential novel therapeutic targets for APL.
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Affiliation(s)
- Jiayin Chang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, PR China
| | - Shihai Yan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, PR China
| | - Zhirong Geng
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210046, PR China.
| | - Zhilin Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, PR China.
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19
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Jung H, Park HJ, Jo SH, Lee A, Lee HJ, Kim HS, Jung C, Cho HS. Nuclear OsFKBP20-1b maintains SR34 stability and promotes the splicing of retained introns upon ABA exposure in rice. THE NEW PHYTOLOGIST 2023; 238:2476-2494. [PMID: 36942934 DOI: 10.1111/nph.18892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/16/2023] [Indexed: 05/19/2023]
Abstract
Alternative splicing (AS) is a critical means by which plants respond to changes in the environment, but few splicing factors contributing to AS have been reported and functionally characterized in rice (Oryza sativa L.). Here, we explored the function and molecular mechanism of the spliceosome-associated protein OsFKBP20-1b during AS. We determined the AS landscape of wild-type and osfkbp20-1b knockout plants upon abscisic acid (ABA) treatment by transcriptome deep sequencing. To capture the dynamics of translating intron-containing mRNAs, we blocked transcription with cordycepin and performed polysome profiling. We also analyzed whether OsFKBP20-1b and the splicing factors OsSR34 and OsSR45 function together in AS using protoplast transfection assays. We show that OsFKBP20-1b interacts with OsSR34 and regulates its stability, suggesting a role as a chaperone-like protein in the spliceosome. OsFKBP20-1b facilitates the splicing of mRNAs with retained introns after ABA treatment; some of these mRNAs are translatable and encode functional transcriptional regulators of stress-responsive genes. In addition, interacting proteins, OsSR34 and OsSR45, regulate the splicing of the same retained introns as OsFKBP20-1b after ABA treatment. Our findings reveal that spliceosome-associated immunophilin functions in alternative RNA splicing in rice by positively regulating the splicing of retained introns to limit ABA response.
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Affiliation(s)
- Haemyeong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, South Korea
| | - Hyun Ji Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea
| | - Seung Hee Jo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, South Korea
| | - Areum Lee
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, South Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea
- Department of Functional Genomics, KRIBB School of Bioscience, UST, Daejeon, 34113, South Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, South Korea
| | - Choonkyun Jung
- Department of International Agricultural Technology and Crop Biotechnology Institute/Green Bio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- Department of Agriculture, Forestry, and Bioresources and Integrated Major in Global Smart Farm, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, South Korea
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20
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Schmitzová J, Cretu C, Dienemann C, Urlaub H, Pena V. Structural basis of catalytic activation in human splicing. Nature 2023; 617:842-850. [PMID: 37165190 PMCID: PMC10208982 DOI: 10.1038/s41586-023-06049-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 04/04/2023] [Indexed: 05/12/2023]
Abstract
Pre-mRNA splicing follows a pathway driven by ATP-dependent RNA helicases. A crucial event of the splicing pathway is the catalytic activation, which takes place at the transition between the activated Bact and the branching-competent B* spliceosomes. Catalytic activation occurs through an ATP-dependent remodelling mediated by the helicase PRP2 (also known as DHX16)1-3. However, because PRP2 is observed only at the periphery of spliceosomes3-5, its function has remained elusive. Here we show that catalytic activation occurs in two ATP-dependent stages driven by two helicases: PRP2 and Aquarius. The role of Aquarius in splicing has been enigmatic6,7. Here the inactivation of Aquarius leads to the stalling of a spliceosome intermediate-the BAQR complex-found halfway through the catalytic activation process. The cryogenic electron microscopy structure of BAQR reveals how PRP2 and Aquarius remodel Bact and BAQR, respectively. Notably, PRP2 translocates along the intron while it strips away the RES complex, opens the SF3B1 clamp and unfastens the branch helix. Translocation terminates six nucleotides downstream of the branch site through an assembly of PPIL4, SKIP and the amino-terminal domain of PRP2. Finally, Aquarius enables the dissociation of PRP2, plus the SF3A and SF3B complexes, which promotes the relocation of the branch duplex for catalysis. This work elucidates catalytic activation in human splicing, reveals how a DEAH helicase operates and provides a paradigm for how helicases can coordinate their activities.
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Affiliation(s)
- Jana Schmitzová
- Macromolecular Crystallography, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Constantin Cretu
- Macromolecular Crystallography, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Research Group Mechanisms and Regulation of Splicing, The Institute of Cancer Research, London, UK
- Cluster of Excellence Multiscale Bioimaging (MBExC), Universitätsmedizin Göttingen, Göttingen, Germany
| | - Christian Dienemann
- 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, University Medical Center Sciences, Göttingen, Germany
| | - Vladimir Pena
- Macromolecular Crystallography, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
- Research Group Mechanisms and Regulation of Splicing, The Institute of Cancer Research, London, UK.
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21
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Lee A, Park HJ, Jo SH, Jung H, Kim HS, Lee HJ, Kim YS, Jung C, Cho HS. The spliceophilin CYP18-2 is mainly involved in the splicing of retained introns under heat stress in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1113-1133. [PMID: 36636802 DOI: 10.1111/jipb.13450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 01/12/2023] [Indexed: 05/13/2023]
Abstract
Peptidyl-prolyl isomerase-like 1 (PPIL1) is associated with the human spliceosome complex. However, its function in pre-mRNA splicing remains unclear. In this study, we show that Arabidopsis thaliana CYCLOPHILIN 18-2 (AtCYP18-2), a PPIL1 homolog, plays an essential role in heat tolerance by regulating pre-mRNA splicing. Under heat stress conditions, AtCYP18-2 expression was upregulated in mature plants and GFP-tagged AtCYP18-2 redistributed to nuclear and cytoplasmic puncta. We determined that AtCYP18-2 interacts with several spliceosome complex BACT components in nuclear puncta and is primarily associated with the small nuclear RNAs U5 and U6 in response to heat stress. The AtCYP18-2 loss-of-function allele cyp18-2 engineered by CRISPR/Cas9-mediated gene editing exhibited a hypersensitive phenotype to heat stress relative to the wild type. Moreover, global transcriptome profiling showed that the cyp18-2 mutation affects alternative splicing of heat stress-responsive genes under heat stress conditions, particularly intron retention (IR). The abundance of most intron-containing transcripts of a subset of genes essential for thermotolerance decreased in cyp18-2 compared to the wild type. Furthermore, the intron-containing transcripts of two heat stress-related genes, HEAT SHOCK PROTEIN 101 (HSP101) and HEAT SHOCK FACTOR A2 (HSFA2), produced functional proteins. HSP101-IR-GFP localization was responsive to heat stress, and HSFA2-III-IR interacted with HSF1 and HSP90.1 in plant cells. Our findings reveal that CYP18-2 functions as a splicing factor within the BACT spliceosome complex and is crucial for ensuring the production of adequate levels of alternatively spliced transcripts to enhance thermotolerance.
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Affiliation(s)
- Areum Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Hyun Ji Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Seung Hee Jo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34141, Korea
| | - Haemyeong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34141, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, UST, Daejeon, 34113, Korea
| | - Youn-Sung Kim
- Department of Biotechnology, NongWoo Bio, Anseong, 17558, Korea
| | - Choonkyun Jung
- Department of International Agricultural Technology and Crop Biotechnology Institute/Green Bio Science and Technology, Seoul National University, Pyeongchang, 25354, Korea
- Department of Agriculture, Forestry, and Bioresources and Integrated Major in Global Smart Farm, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34141, Korea
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22
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Phylogenetic Analysis of Spliceosome SF3a2 in Different Plant Species. Int J Mol Sci 2023; 24:ijms24065232. [PMID: 36982311 PMCID: PMC10049718 DOI: 10.3390/ijms24065232] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
The formation of mature mRNA requires cutting introns and splicing exons. The occurrence of splicing involves the participation of the spliceosome. Common spliceosomes mainly include five snRNPs: U1, U2, U4/U6, and U5. SF3a2, an essential component of spliceosome U2 snRNP, participates in splicing a series of genes. There is no definition of SF3a2 in plants. The paper elaborated on SF3a2s from a series of plants through protein sequence similarity. We constructed the evolutionary relationship of SF3a2s in plants. Moreover, we analyzed the similarities and differences in gene structure, protein structure, the cis-element of the promoter, and expression pattern; we predicted their interacting proteins and constructed their collinearity. We have preliminarily analyzed SF3a2s in plants and clarified the evolutionary relationship between different species; these studies can better serve for in-depth research on the members of the spliceosome in plants.
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23
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Rodrigues KS, Petroski LP, Utumi PH, Ferrasa A, Herai RH. IARA: a complete and curated atlas of the biogenesis of spliceosome machinery during RNA splicing. Life Sci Alliance 2023; 6:e202201593. [PMID: 36609432 PMCID: PMC9834665 DOI: 10.26508/lsa.202201593] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 01/09/2023] Open
Abstract
Splicing is one of the most important post-transcriptional processing systems and is responsible for the generation of transcriptome diversity in all living eukaryotes. Splicing is regulated by the spliceosome machinery, which is responsible for each step of primary RNA processing. However, current molecules and stages involved in RNA splicing are still spread over different studies. Thus, a curated atlas of spliceosome-related molecules and all involved stages during RNA processing can provide all researchers with a reliable resource to better investigate this important mechanism. Here, we present IARA (website access: https://pucpr-bioinformatics.github.io/atlas/), an extensively curated and constantly updated catalog of molecules involved in spliceosome machinery. IARA has a map of the steps involved in the human splicing mechanism, and it allows a detailed overview of the molecules involved throughout the distinct steps of splicing.
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Affiliation(s)
- Kelren S Rodrigues
- Laboratory of Bioinformatics and Neurogenetics, Graduate Program in Health Sciences (PPGCS), School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | - Luiz P Petroski
- Laboratory of Bioinformatics and Neurogenetics, Graduate Program in Health Sciences (PPGCS), School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | - Paulo H Utumi
- Laboratory of Bioinformatics and Neurogenetics, Graduate Program in Health Sciences (PPGCS), School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | - Adriano Ferrasa
- Informatics Department, Universidade Estadual de Ponta GrossaPonta Grossa, Brazil
| | - Roberto H Herai
- Laboratory of Bioinformatics and Neurogenetics, Graduate Program in Health Sciences (PPGCS), School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
- Research Division, Buko Kaesemodel Institute, Curitiba, Brazil
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24
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Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly. Nat Commun 2023; 14:897. [PMID: 36797247 PMCID: PMC9935549 DOI: 10.1038/s41467-023-36489-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 02/03/2023] [Indexed: 02/18/2023] Open
Abstract
Three RNA helicases - DDX42, DDX46 and DHX15 - are found to be associated with human U2 snRNP, but their roles and mechanisms in U2 snRNP and spliceosome assembly are insufficiently understood. Here we report the cryo-electron microscopy (cryo-EM) structures of the DDX42-SF3b complex and a putative assembly precursor of 17S U2 snRNP that contains DDX42 (DDX42-U2 complex). DDX42 is anchored on SF3B1 through N-terminal sequences, with its N-plug occupying the RNA path of SF3B1. The binding mode of DDX42 to SF3B1 is in striking analogy to that of DDX46. In the DDX42-U2 complex, the N-terminus of DDX42 remains anchored on SF3B1, but the helicase domain has been displaced by U2 snRNA and TAT-SF1. Through in vitro assays, we show DDX42 and DDX46 are mutually exclusive in terms of binding to SF3b. Cancer-driving mutations of SF3B1 target the residues in the RNA path that directly interact with DDX42 and DDX46. These findings reveal the distinct roles of DDX42 and DDX46 in assembly of 17S U2 snRNP and provide insights into the mechanisms of SF3B1 cancer mutations.
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25
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Samy A, Ozdemir MK, Alhajj R. Studying the connection between SF3B1 and four types of cancer by analyzing networks constructed based on published research. Sci Rep 2023; 13:2704. [PMID: 36792691 PMCID: PMC9932172 DOI: 10.1038/s41598-023-29777-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Splicing factor 3B subunit 1 (SF3B1) is the largest component of SF3b protein complex which is involved in the pre-mRNA splicing mechanism. Somatic mutations of SF3B1 were shown to be associated with aberrant splicing, producing abnormal transcripts that drive cancer development and/or prognosis. In this study, we focus on the relationship between SF3B1 and four types of cancer, namely myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), and chronic lymphocytic leukemia (CLL) and breast cancer (BC). For this purpose, we identified from the Pubmed library only articles which mentioned SF3B1 in connection with the investigated types of cancer for the period 2007 to 2018 to reveal how the connection has developed over time. We left out all published articles which mentioned SF3B1 in other contexts. We retrieved the target articles and investigated the association between SF3B1 and the mentioned four types of cancer. For this we utilized some of the publicly available databases to retrieve gene/variant/disease information related to SF3B1. We used the outcome to derive and analyze a variety of complex networks that reflect the correlation between the considered diseases and variants associated with SF3B1. The results achieved based on the analyzed articles and reported in this article illustrated that SF3B1 is associated with hematologic malignancies, such as MDS, AML, and CLL more than BC. We found that different gene networks may be required for investigating the impact of mutant splicing factors on cancer development based on the target cancer type. Additionally, based on the literature analyzed in this study, we highlighted and summarized what other researchers have reported as the set of genes and cellular pathways that are affected by aberrant splicing in cancerous cells.
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Affiliation(s)
- Asmaa Samy
- grid.411781.a0000 0004 0471 9346The Graduate School of Engineering and Natural Science, Istanbul Medipol University, Istanbul, Turkey
| | - Mehmet Kemal Ozdemir
- grid.411781.a0000 0004 0471 9346School of Engineering and Natural Science, Istanbul Medipol University, Istanbul, Turkey
| | - Reda Alhajj
- School of Engineering and Natural Science, Istanbul Medipol University, Istanbul, Turkey. .,Department of Computer Science, University of Calgary, Calgary, AB, Canada. .,Department of Heath Informatics, University of Southern Denmark, Odense, Denmark.
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26
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Tholen J, Galej WP. Structural studies of the spliceosome: Bridging the gaps. Curr Opin Struct Biol 2022; 77:102461. [PMID: 36116369 PMCID: PMC9762485 DOI: 10.1016/j.sbi.2022.102461] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 02/07/2023]
Abstract
The spliceosome is a multi-megadalton RNA-protein complex responsible for the removal of non-coding introns from pre-mRNAs. Due to its complexity and dynamic nature, it has proven to be a very challenging target for structural studies. Developments in single particle cryo-EM have overcome these previous limitations and paved the way towards a structural characterisation of the splicing machinery. Despite tremendous progress, many aspects of spliceosome structure and function remain elusive. In particular, the events leading to the definition of exon-intron boundaries, alternative and non-canonical splicing events, and cross-talk with other cellular machineries. Efforts are being made to address these knowledge gaps and further our mechanistic understanding of the spliceosome. Here, we summarise recent progress in the structural and functional analysis of the spliceosome.
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Affiliation(s)
- J Tholen
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France. https://twitter.com/@Structjon
| | - W P Galej
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France.
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27
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Parker MT, Soanes BK, Kusakina J, Larrieu A, Knop K, Joy N, Breidenbach F, Sherwood AV, Barton GJ, Fica SM, Davies BH, Simpson GG. m 6A modification of U6 snRNA modulates usage of two major classes of pre-mRNA 5' splice site. eLife 2022; 11:e78808. [PMID: 36409063 PMCID: PMC9803359 DOI: 10.7554/elife.78808] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/20/2022] [Indexed: 11/23/2022] Open
Abstract
Alternative splicing of messenger RNAs is associated with the evolution of developmentally complex eukaryotes. Splicing is mediated by the spliceosome, and docking of the pre-mRNA 5' splice site into the spliceosome active site depends upon pairing with the conserved ACAGA sequence of U6 snRNA. In some species, including humans, the central adenosine of the ACAGA box is modified by N6 methylation, but the role of this m6A modification is poorly understood. Here, we show that m6A modified U6 snRNA determines the accuracy and efficiency of splicing. We reveal that the conserved methyltransferase, FIONA1, is required for Arabidopsis U6 snRNA m6A modification. Arabidopsis fio1 mutants show disrupted patterns of splicing that can be explained by the sequence composition of 5' splice sites and cooperative roles for U5 and U6 snRNA in splice site selection. U6 snRNA m6A influences 3' splice site usage. We generalise these findings to reveal two major classes of 5' splice site in diverse eukaryotes, which display anti-correlated interaction potential with U5 snRNA loop 1 and the U6 snRNA ACAGA box. We conclude that U6 snRNA m6A modification contributes to the selection of degenerate 5' splice sites crucial to alternative splicing.
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Affiliation(s)
- Matthew T Parker
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Beth K Soanes
- Centre for Plant Sciences, School of Biology, Faculty of Biological Sciences, University of LeedsLeedsUnited Kingdom
| | - Jelena Kusakina
- Centre for Plant Sciences, School of Biology, Faculty of Biological Sciences, University of LeedsLeedsUnited Kingdom
| | - Antoine Larrieu
- Centre for Plant Sciences, School of Biology, Faculty of Biological Sciences, University of LeedsLeedsUnited Kingdom
| | - Katarzyna Knop
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Nisha Joy
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Friedrich Breidenbach
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld UniversityBielefeldGermany
| | - Anna V Sherwood
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | | | - Sebastian M Fica
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Brendan H Davies
- Centre for Plant Sciences, School of Biology, Faculty of Biological Sciences, University of LeedsLeedsUnited Kingdom
| | - Gordon G Simpson
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
- Cell & Molecular Sciences, James Hutton InstituteInvergowrieUnited Kingdom
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Gao C, Lu S, Zhou R, Ding J, Fan J, Han B, Chen M, Wang B, Cao Y. Phylogenetic analysis and stress response of the plant U2 small nuclear ribonucleoprotein B″ gene family. BMC Genomics 2022; 23:744. [DOI: 10.1186/s12864-022-08956-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Alternative splicing (AS) is an important channel for gene expression regulation and protein diversification, in addition to a major reason for the considerable differences in the number of genes and proteins in eukaryotes. In plants, U2 small nuclear ribonucleoprotein B″ (U2B″), a component of splicing complex U2 snRNP, plays an important role in AS. Currently, few studies have investigated plant U2B″, and its mechanism remains unclear.
Result
Phylogenetic analysis, including gene and protein structures, revealed that U2B″ is highly conserved in plants and typically contains two RNA recognition motifs. Subcellular localisation showed that OsU2B″ is located in the nucleus and cytoplasm, indicating that it has broad functions throughout the cell. Elemental analysis of the promoter region showed that it responded to numerous external stimuli, including hormones, stress, and light. Subsequent qPCR experiments examining response to stress (cold, salt, drought, and heavy metal cadmium) corroborated the findings. The prediction results of protein–protein interactions showed that its function is largely through a single pathway, mainly through interaction with snRNP proteins.
Conclusion
U2B″ is highly conserved in the plant kingdom, functions in the nucleus and cytoplasm, and participates in a wide range of processes in plant growth and development.
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Hluchý M, Gajdušková P, Ruiz de Los Mozos I, Rájecký M, Kluge M, Berger BT, Slabá Z, Potěšil D, Weiß E, Ule J, Zdráhal Z, Knapp S, Paruch K, Friedel CC, Blazek D. CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1. Nature 2022; 609:829-834. [PMID: 36104565 DOI: 10.1038/s41586-022-05204-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 08/08/2022] [Indexed: 11/09/2022]
Abstract
RNA splicing, the process of intron removal from pre-mRNA, is essential for the regulation of gene expression. It is controlled by the spliceosome, a megadalton RNA-protein complex that assembles de novo on each pre-mRNA intron through an ordered assembly of intermediate complexes1,2. Spliceosome activation is a major control step that requires substantial protein and RNA rearrangements leading to a catalytically active complex1-5. Splicing factor 3B subunit 1 (SF3B1) protein-a subunit of the U2 small nuclear ribonucleoprotein6-is phosphorylated during spliceosome activation7-10, but the kinase that is responsible has not been identified. Here we show that cyclin-dependent kinase 11 (CDK11) associates with SF3B1 and phosphorylates threonine residues at its N terminus during spliceosome activation. The phosphorylation is important for the association between SF3B1 and U5 and U6 snRNAs in the activated spliceosome, termed the Bact complex, and the phosphorylation can be blocked by OTS964, a potent and selective inhibitor of CDK11. Inhibition of CDK11 prevents spliceosomal transition from the precatalytic complex B to the activated complex Bact and leads to widespread intron retention and accumulation of non-functional spliceosomes on pre-mRNAs and chromatin. We demonstrate a central role of CDK11 in spliceosome assembly and splicing regulation and characterize OTS964 as a highly selective CDK11 inhibitor that suppresses spliceosome activation and splicing.
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Affiliation(s)
- Milan Hluchý
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Pavla Gajdušková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Igor Ruiz de Los Mozos
- The Francis Crick Institute, London, UK
- Department of Personalized Medicine, NASERTIC, Government of Navarra, Pamplona, Spain
- Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Michal Rájecký
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Michael Kluge
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
| | - Benedict-Tilman Berger
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Zuzana Slabá
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - David Potěšil
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Elena Weiß
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
| | - Jernej Ule
- The Francis Crick Institute, London, UK
- UK Dementia Research Institute, King's College London, London, UK
| | - Zbyněk Zdráhal
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Stefan Knapp
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Kamil Paruch
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St Anne's University Hospital in Brno, Brno, Czech Republic
| | - Caroline C Friedel
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
| | - Dalibor Blazek
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.
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Xiong F, Ren JJ, Wang YY, Zhou Z, Qi HD, Otegui MS, Wang XL. An Arabidopsis Retention and Splicing complex regulates root and embryo development through pre-mRNA splicing. PLANT PHYSIOLOGY 2022; 190:621-639. [PMID: 35640107 PMCID: PMC9434225 DOI: 10.1093/plphys/kiac256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/08/2022] [Indexed: 05/30/2023]
Abstract
Pre-mRNA splicing is an important step in the posttranscriptional processing of transcripts and a key regulator of development. The heterotrimeric retention and splicing (RES) complex plays vital roles in the growth and development of yeast, zebrafish, and humans by mediating pre-mRNA splicing of multiple genes. However, whether the RES complex is conserved in plants and what specific functions it has remain unknown. In this study, we identified Arabidopsis (Arabidopsis thaliana) BUD13 (AtBUD13), GROWTH, DEVELOPMENT AND SPLICING 1 (GDS1), and DAWDLE (DDL) as the counterparts of the yeast RES complex subunits Bud site selection protein 13 (Bud13), U2 snRNP component Snu17 (Snu17), and Pre-mRNA leakage protein 1, respectively. Moreover, we showed that RES is an ancient complex evolutionarily conserved in eukaryotes. GDS1 directly interacts with both AtBUD13 and DDL in nuclear speckles. The BUD13 domain of AtBUD13 and the RNA recognition motif domain of GDS1 are necessary and sufficient for AtBUD13-GDS1 interaction. Mutants of AtBUD13, GDS1, and DDL failed to properly splice multiple genes involved in cell proliferation and showed defects in early embryogenesis and root development. In addition, we found that GDS1 and DDL interact, respectively, with the U2 small nuclear ribonucleoproteins auxiliary factor AtU2AF65B and the NineTeen Complex-related splicing factor SKIP, which are essential for early steps of spliceosome assembly and recognition of splice sites. Altogether, our work reveals that the Arabidopsis RES complex is important for root and early embryo development by modulating pre-mRNA splicing.
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Affiliation(s)
- Feng Xiong
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Jing-Jing Ren
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Yu-Yi Wang
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Zhou Zhou
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Hao-Dong Qi
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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31
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Zhang F, Chen L. Molecular Threat of Splicing Factor Mutations to Myeloid Malignancies and Potential Therapeutic Modulations. Biomedicines 2022; 10:biomedicines10081972. [PMID: 36009519 PMCID: PMC9405558 DOI: 10.3390/biomedicines10081972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 11/21/2022] Open
Abstract
Splicing factors are frequently mutated in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). These mutations are presumed to contribute to oncogenic transformation, but the underlying mechanisms remain incompletely understood. While no specific treatment option is available for MDS/AML patients with spliceosome mutations, novel targeting strategies are actively explored, leading to clinical trials of small molecule inhibitors that target the spliceosome, DNA damage response pathway, and immune response pathway. Here, we review recent progress in mechanistic understanding of splicing factor mutations promoting disease progression and summarize potential therapeutic strategies, which, if successful, would provide clinical benefit to patients carrying splicing factor mutations.
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32
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The SWI/SNF chromatin remodeling factor DPF3 regulates metastasis of ccRCC by modulating TGF-β signaling. Nat Commun 2022; 13:4680. [PMID: 35945219 PMCID: PMC9363427 DOI: 10.1038/s41467-022-32472-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 08/02/2022] [Indexed: 12/23/2022] Open
Abstract
DPF3, a component of the SWI/SNF chromatin remodeling complex, has been associated with clear cell renal cell carcinoma (ccRCC) in a genome-wide association study. However, the functional role of DPF3 in ccRCC development and progression remains unknown. In this study, we demonstrate that DPF3a, the short isoform of DPF3, promotes kidney cancer cell migration both in vitro and in vivo, consistent with the clinical observation that DPF3a is significantly upregulated in ccRCC patients with metastases. Mechanistically, DPF3a specifically interacts with SNIP1, via which it forms a complex with SMAD4 and p300 histone acetyltransferase (HAT), the major transcriptional regulators of TGF-β signaling pathway. Moreover, the binding of DPF3a releases the repressive effect of SNIP1 on p300 HAT activity, leading to the increase in local histone acetylation and the activation of cell movement related genes. Overall, our findings reveal a metastasis-promoting function of DPF3, and further establish the link between SWI/SNF components and ccRCC. The functional role of DPF3, a component of the SWI/SNF chromatin remodelling complex associated with clear cell renal cell carcinoma (ccRCC), remains unknown. Here, the authors characterise the mechanism by which DPF3 promotes metastasis via the activation of the TGF-β signalling pathway in ccRCC.
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Galardi JW, Bela VN, Jeffery N, He X, Glasser E, Loerch S, Jenkins JL, Pulvino MJ, Boutz PL, Kielkopf CL. A UHM - ULM interface with unusual structural features contributes to U2AF2 and SF3B1 association for pre-mRNA splicing. J Biol Chem 2022; 298:102224. [PMID: 35780835 PMCID: PMC9364107 DOI: 10.1016/j.jbc.2022.102224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 11/30/2022] Open
Abstract
During spliceosome assembly, the 3′ splice site is recognized by sequential U2AF2 complexes, first with Splicing Factor 1 (SF1) and second by the SF3B1 subunit of the U2 small nuclear ribonuclear protein particle. The U2AF2–SF1 interface is well characterized, comprising a U2AF homology motif (UHM) of U2AF2 bound to a U2AF ligand motif (ULM) of SF1. However, the structure of the U2AF2–SF3B1 interface and its importance for pre-mRNA splicing are unknown. To address this knowledge gap, we determined the crystal structure of the U2AF2 UHM bound to a SF3B1 ULM site at 1.8-Å resolution. We discovered a distinctive trajectory of the SF3B1 ULM across the U2AF2 UHM surface, which differs from prior UHM/ULM structures and is expected to modulate the orientations of the full-length proteins. We established that the binding affinity of the U2AF2 UHM for the cocrystallized SF3B1 ULM rivals that of a nearly full-length U2AF2 protein for an N-terminal SF3B1 region. An additional SF3B6 subunit had no detectable effect on the U2AF2–SF3B1 binding affinities. We further showed that key residues at the U2AF2 UHM–SF3B1 ULM interface contribute to coimmunoprecipitation of the splicing factors. Moreover, disrupting the U2AF2–SF3B1 interface changed splicing of representative human transcripts. From analysis of genome-wide data, we found that many of the splice sites coregulated by U2AF2 and SF3B1 differ from those coregulated by U2AF2 and SF1. Taken together, these findings support distinct structural and functional roles for the U2AF2—SF1 and U2AF2—SF3B1 complexes during the pre-mRNA splicing process.
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Affiliation(s)
- Justin W Galardi
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Victoria N Bela
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Nazish Jeffery
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Xueyang He
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Eliezra Glasser
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Sarah Loerch
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Jermaine L Jenkins
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Mary J Pulvino
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Paul L Boutz
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Clara L Kielkopf
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA.
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34
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Kumar J, Lackey L, Waldern JM, Dey A, Mustoe AM, Weeks KM, Mathews DH, Laederach A. Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing. eLife 2022; 11:73888. [PMID: 35695373 PMCID: PMC9236610 DOI: 10.7554/elife.73888] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 06/12/2022] [Indexed: 11/29/2022] Open
Abstract
Splicing is highly regulated and is modulated by numerous factors. Quantitative predictions for how a mutation will affect precursor mRNA (pre-mRNA) structure and downstream function are particularly challenging. Here, we use a novel chemical probing strategy to visualize endogenous precursor and mature MAPT mRNA structures in cells. We used these data to estimate Boltzmann suboptimal structural ensembles, which were then analyzed to predict consequences of mutations on pre-mRNA structure. Further analysis of recent cryo-EM structures of the spliceosome at different stages of the splicing cycle revealed that the footprint of the Bact complex with pre-mRNA best predicted alternative splicing outcomes for exon 10 inclusion of the alternatively spliced MAPT gene, achieving 74% accuracy. We further developed a β-regression weighting framework that incorporates splice site strength, RNA structure, and exonic/intronic splicing regulatory elements capable of predicting, with 90% accuracy, the effects of 47 known and 6 newly discovered mutations on inclusion of exon 10 of MAPT. This combined experimental and computational framework represents a path forward for accurate prediction of splicing-related disease-causing variants.
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Affiliation(s)
- Jayashree Kumar
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Lela Lackey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics and Biochemistry, Center for Human Genetics, Clemson University, Greenwood, United States
| | - Justin M Waldern
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Abhishek Dey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Anthony M Mustoe
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center (THINC), and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, United States
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
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35
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Zhan X, Lu Y, Zhang X, Yan C, Shi Y. Mechanism of exon ligation by human spliceosome. Mol Cell 2022; 82:2769-2778.e4. [PMID: 35705093 DOI: 10.1016/j.molcel.2022.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/07/2022] [Accepted: 05/18/2022] [Indexed: 11/18/2022]
Abstract
Pre-mRNA splicing involves two sequential reactions: branching and exon ligation. The C complex after branching undergoes remodeling to become the C∗ complex, which executes exon ligation. Here, we report cryo-EM structures of two intermediate human spliceosomal complexes, pre-C∗-I and pre-C∗-II, both at 3.6 Å. In both structures, the 3' splice site is already docked into the active site, the ensuing 3' exon sequences are anchored on PRP8, and the step II factor FAM192A contacts the duplex between U2 snRNA and the branch site. In the transition of pre-C∗-I to pre-C∗-II, the step II factors Cactin, FAM32A, PRKRIP1, and SLU7 are recruited. Notably, the RNA helicase PRP22 is positioned quite differently in the pre-C∗-I, pre-C∗-II, and C∗ complexes, suggesting a role in 3' exon binding and proofreading. Together with information on human C and C∗ complexes, our studies recapitulate a molecular choreography of the C-to-C∗ transition, revealing mechanistic insights into exon ligation.
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Affiliation(s)
- Xiechao Zhan
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
| | - Yichen Lu
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; College of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xiaofeng Zhang
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Chuangye Yan
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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36
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Neuhaus D. Zinc finger structure determination by NMR: Why zinc fingers can be a handful. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 130-131:62-105. [PMID: 36113918 PMCID: PMC7614390 DOI: 10.1016/j.pnmrs.2022.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/09/2022] [Accepted: 07/10/2022] [Indexed: 06/07/2023]
Abstract
Zinc fingers can be loosely defined as protein domains containing one or more tetrahedrally-co-ordinated zinc ions whose role is to stabilise the structure rather than to be involved in enzymatic chemistry; such zinc ions are often referred to as "structural zincs". Although structural zincs can occur in proteins of any size, they assume particular significance for very small protein domains, where they are often essential for maintaining a folded state. Such small structures, that sometimes have only marginal stability, can present particular difficulties in terms of sample preparation, handling and structure determination, and early on they gained a reputation for being resistant to crystallisation. As a result, NMR has played a more prominent role in structural studies of zinc finger proteins than it has for many other types of proteins. This review will present an overview of the particular issues that arise for structure determination of zinc fingers by NMR, and ways in which these may be addressed.
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Affiliation(s)
- David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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37
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Jo SH, Park HJ, Lee A, Jung H, Park JM, Kwon SY, Kim HS, Lee HJ, Kim YS, Jung C, Cho HS. The Arabidopsis cyclophilin CYP18-1 facilitates PRP18 dephosphorylation and the splicing of introns retained under heat stress. THE PLANT CELL 2022; 34:2383-2403. [PMID: 35262729 PMCID: PMC9134067 DOI: 10.1093/plcell/koac084] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 03/05/2022] [Indexed: 05/13/2023]
Abstract
In plants, heat stress induces changes in alternative splicing, including intron retention; these events can rapidly alter proteins or downregulate protein activity, producing nonfunctional isoforms or inducing nonsense-mediated decay of messenger RNA (mRNA). Nuclear cyclophilins (CYPs) are accessory proteins in the spliceosome complexes of multicellular eukaryotes. However, whether plant CYPs are involved in pre-mRNA splicing remain unknown. Here, we found that Arabidopsis thaliana CYP18-1 is necessary for the efficient removal of introns that are retained in response to heat stress during germination. CYP18-1 interacts with Step II splicing factors (PRP18a, PRP22, and SWELLMAP1) and associates with the U2 and U5 small nuclear RNAs in response to heat stress. CYP18-1 binds to phospho-PRP18a, and increasing concentrations of CYP18-1 are associated with increasing dephosphorylation of PRP18a. Furthermore, interaction and protoplast transfection assays revealed that CYP18-1 and the PP2A-type phosphatase PP2A B'η co-regulate PRP18a dephosphorylation. RNA-seq and RT-qPCR analysis confirmed that CYP18-1 is essential for splicing introns that are retained under heat stress. Overall, we reveal the mechanism of action by which CYP18-1 activates the dephosphorylation of PRP18 and show that CYP18-1 is crucial for the efficient splicing of retained introns and rapid responses to heat stress in plants.
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Affiliation(s)
- Seung Hee Jo
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology,
Korea University of Science and Technology, Daejeon 34113, Korea
| | - Hyun Ji Park
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Areum Lee
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology,
Korea University of Science and Technology, Daejeon 34113, Korea
| | - Haemyeong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology,
Korea University of Science and Technology, Daejeon 34113, Korea
| | - Jeong Mee Park
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University
of Science and Technology, Daejeon 34113, Korea
| | - Youn-Sung Kim
- Department of Biotechnology, NongWoo
Bio, Anseong 17558, Korea
| | - Choonkyun Jung
- Department of International Agricultural Technology and Crop Biotechnology
Institute/Green Bio Science and Technology, Seoul National University,
Pyeongchang 25354, Korea
- Department of Agriculture, Forestry, and Bioresources and Integrated Major
in Global Smart Farm, College of Agriculture and Life Sciences, Seoul National
University, Seoul 08826, Korea
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38
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Pellegrina D, Bahcheli AT, Krassowski M, Reimand J. Human phospho-signaling networks of SARS-CoV-2 infection are rewired by population genetic variants. Mol Syst Biol 2022; 18:e10823. [PMID: 35579274 PMCID: PMC9112486 DOI: 10.15252/msb.202110823] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 11/23/2022] Open
Abstract
SARS-CoV-2 infection hijacks signaling pathways and induces protein-protein interactions between human and viral proteins. Human genetic variation may impact SARS-CoV-2 infection and COVID-19 pathology; however, the genetic variation in these signaling networks remains uncharacterized. Here, we studied human missense single nucleotide variants (SNVs) altering phosphorylation sites modulated by SARS-CoV-2 infection, using machine learning to identify amino acid substitutions altering kinase-bound sequence motifs. We found 2,033 infrequent phosphorylation-associated SNVs (pSNVs) that are enriched in sequence motif alterations, potentially reflecting the evolution of signaling networks regulating host defenses. Proteins with pSNVs are involved in viral life cycle and host responses, including RNA splicing, interferon response (TRIM28), and glucose homeostasis (TBC1D4) with potential associations with COVID-19 comorbidities. pSNVs disrupt CDK and MAPK substrate motifs and replace these with motifs of Tank Binding Kinase 1 (TBK1) involved in innate immune responses, indicating consistent rewiring of signaling networks. Several pSNVs associate with severe COVID-19 and hospitalization (STARD13, ARFGEF2). Our analysis highlights potential genetic factors contributing to inter-individual variation of SARS-CoV-2 infection and COVID-19 and suggests leads for mechanistic and translational studies.
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Affiliation(s)
- Diogo Pellegrina
- Computational Biology ProgramOntario Institute for Cancer ResearchTorontoONCanada
| | - Alexander T Bahcheli
- Computational Biology ProgramOntario Institute for Cancer ResearchTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | - Michal Krassowski
- Medical Sciences DivisionNuffield Department of Women's and Reproductive HealthUniversity of OxfordOxfordUK
| | - Jüri Reimand
- Computational Biology ProgramOntario Institute for Cancer ResearchTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
- Department of Medical BiophysicsUniversity of TorontoTorontoONCanada
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Tsampoula M, Tarampoulous I, Manolakou T, Ninou E, Politis PK. The neurodevelopmental disorders associated gene Rnf113a regulates survival and differentiation properties of neural stem cells. Stem Cells 2022; 40:678-690. [DOI: 10.1093/stmcls/sxac030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/23/2022] [Indexed: 11/15/2022]
Abstract
Abstract
RNF113A (Ring Finger Protein 113A) is genetically associated with autism spectrum disorders and X-linked trichothiodystrophy (TTD) syndrome. Loss-of-function mutations in human RNF113A are causally linked to TTD, which is characterized by abnormal development of central nervous system (CNS) and mental retardation. How loss of RNF113A activity affects brain development is not known. Here we identify Rnf113a1 as a critical regulator of cell death and neurogenesis during mouse brain development. Rnf113a1 gene exhibits widespread expression in the embryonic CNS. Knockdown studies in embryonic cortical neural stem/progenitor cells (NSCs) and the mouse cortex suggest that Rnf113a1 controls survival, proliferation and differentiation properties of progenitor cells. Importantly, Rnf113a1 deficiency triggers cell apoptosis via a combined action on essential regulators of cell survival, including p53, Nupr1 and Rad51. Collectively, these observations establish Rnf113a1 as a regulatory factor in CNS development and provide insights for its role in neurodevelopmental defects associated with TTD and autism.
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Affiliation(s)
- Matina Tsampoula
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Isaak Tarampoulous
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Theodora Manolakou
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Elpinickie Ninou
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Panagiotis K Politis
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- School of Medicine, European University Cyprus, Nicosia, Cyprus
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Sherill-Rofe D, Raban O, Findlay S, Rahat D, Unterman I, Samiei A, Yasmeen A, Kaiser Z, Kuasne H, Park M, Foulkes WD, Bloch I, Zick A, Gotlieb WH, Tabach Y, Orthwein A. Multi-omics data integration analysis identifies the spliceosome as a key regulator of DNA double-strand break repair. NAR Cancer 2022; 4:zcac013. [PMID: 35399185 PMCID: PMC8991968 DOI: 10.1093/narcan/zcac013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/25/2022] [Accepted: 03/23/2022] [Indexed: 11/14/2022] Open
Abstract
DNA repair by homologous recombination (HR) is critical for the maintenance of genome stability. Germline and somatic mutations in HR genes have been associated with an increased risk of developing breast (BC) and ovarian cancers (OvC). However, the extent of factors and pathways that are functionally linked to HR with clinical relevance for BC and OvC remains unclear. To gain a broader understanding of this pathway, we used multi-omics datasets coupled with machine learning to identify genes that are associated with HR and to predict their sub-function. Specifically, we integrated our phylogenetic-based co-evolution approach (CladePP) with 23 distinct genetic and proteomic screens that monitored, directly or indirectly, DNA repair by HR. This omics data integration analysis yielded a new database (HRbase) that contains a list of 464 predictions, including 76 gold standard HR genes. Interestingly, the spliceosome machinery emerged as one major pathway with significant cross-platform interactions with the HR pathway. We functionally validated 6 spliceosome factors, including the RNA helicase SNRNP200 and its co-factor SNW1. Importantly, their RNA expression correlated with BC/OvC patient outcome. Altogether, we identified novel clinically relevant DNA repair factors and delineated their specific sub-function by machine learning. Our results, supported by evolutionary and multi-omics analyses, suggest that the spliceosome machinery plays an important role during the repair of DNA double-strand breaks (DSBs).
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Affiliation(s)
- Dana Sherill-Rofe
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Oded Raban
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
| | - Steven Findlay
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
| | - Dolev Rahat
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Irene Unterman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Arash Samiei
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
| | - Amber Yasmeen
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
| | - Zafir Kaiser
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Hellen Kuasne
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Morag Park
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - William D Foulkes
- The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Idit Bloch
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Aviad Zick
- Department of Oncology, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Ein-Kerem, Jerusalem 91120, Israel
| | - Walter H Gotlieb
- Division of Gynecology Oncology, Segal Cancer Center, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada
| | - Yuval Tabach
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem 91120, Israel
| | - Alexandre Orthwein
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1E2, Canada
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Liu KL, Yin YW, Lu BS, Niu YL, Wang DD, Shi B, Zhang H, Guo PY, Yang Z, Li W. E2F6/KDM5C promotes SF3A3 expression and bladder cancer progression through a specific hypomethylated DNA promoter. Cancer Cell Int 2022; 22:109. [PMID: 35248043 PMCID: PMC8897952 DOI: 10.1186/s12935-022-02475-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/18/2022] [Indexed: 12/01/2022] Open
Abstract
Background Abnormal expression of splicing factor 3A subunit 3 (SF3A3), a component of the spliceosome, has been confirmed to be related to the occurrence and development of various cancers. However, the expression and function of SF3A3 in bladder cancer (BC) remains unclear. Methods The SF3A3 mRNA and protein level were measured in clinical samples and cell lines by quantitative real-time PCR, Western blot and immunofluorescence staining. Evaluate the clinical correlation between SF3A3 expression and clinicopathological characteristics through statistical analysis in BC patients. The function of SF3A3 in BC cells was determined in vitro using MTT and colony analysis. Co-immunoprecipitation (CoIP) assay was used to detected E2F6 and KDM5C interaction. Luciferase reporter and chromatin immunoprecipitation (ChIP) were used to examine the relationship between E2F6/KDM5C and SF3A3 expression. Results In the present study, we demonstrated that expression of SF3A3 was elevated in BC tissue compared to the normal bladder tissue. Importantly, the upregulation of SF3A3 in patients was correlated with poor prognosis. Additionally, overexpression of SF3A3 promoted while depletion of SF3A3 reduced the growth of BC cells in vivo and in vitro. Data from the TCGA database and clinical samples revealed that hypomethylation of the DNA promoter leads to high expression of SF3A3 in BC tissue. We found that upregulation of lysine-specific demethylase 5C (KDM5C) promotes SF3A3 expression via hypomethylation of the DNA promoter. The transcription factor E2F6 interacts with KDM5C, recruits KDM5C to the SF3A3 promoter, and demethylates the GpC island of H3K4me2, leading to high SF3A3 expression and BC progression. Conclusions The results demonstrated that depletion of the KDM5C/SF3A3 prevents the growth of BC in vivo and in vitro. The E2F6/KDM5C/SF3A3 pathway may be a potential therapeutic target for BC treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02475-4.
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Bergfort A, Preußner M, Kuropka B, Ilik İA, Hilal T, Weber G, Freund C, Aktaş T, Heyd F, Wahl MC. A multi-factor trafficking site on the spliceosome remodeling enzyme BRR2 recruits C9ORF78 to regulate alternative splicing. Nat Commun 2022; 13:1132. [PMID: 35241646 PMCID: PMC8894380 DOI: 10.1038/s41467-022-28754-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/10/2022] [Indexed: 11/09/2022] Open
Abstract
The intrinsically unstructured C9ORF78 protein was detected in spliceosomes but its role in splicing is presently unclear. We find that C9ORF78 tightly interacts with the spliceosome remodeling factor, BRR2, in vitro. Affinity purification/mass spectrometry and RNA UV-crosslinking analyses identify additional C9ORF78 interactors in spliceosomes. Cryogenic electron microscopy structures reveal how C9ORF78 and the spliceosomal B complex protein, FBP21, wrap around the C-terminal helicase cassette of BRR2 in a mutually exclusive manner. Knock-down of C9ORF78 leads to alternative NAGNAG 3'-splice site usage and exon skipping, the latter dependent on BRR2. Inspection of spliceosome structures shows that C9ORF78 could contact several detected spliceosome interactors when bound to BRR2, including the suggested 3'-splice site regulating helicase, PRPF22. Together, our data establish C9ORF78 as a late-stage splicing regulatory protein that takes advantage of a multi-factor trafficking site on BRR2, providing one explanation for suggested roles of BRR2 during splicing catalysis and alternative splicing.
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Affiliation(s)
- Alexandra Bergfort
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Berlin, Germany.,Yale University, Molecular Biophysics and Biochemistry, New Haven, CT, USA
| | - Marco Preußner
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Berlin, Germany
| | - Benno Kuropka
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Protein Biochemistry, Berlin, Germany.,Freie Universität Berlin, Institute of Chemistry and Biochemistry, Core Facility BioSupraMol, Berlin, Germany
| | | | - Tarek Hilal
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Berlin, Germany.,Freie Universität Berlin, Institute of Chemistry and Biochemistry, Core Facility BioSupraMol, Berlin, Germany.,Freie Universität Berlin, Institute of Chemistry and Biochemistry, Research Center of Electron Microscopy and Core Facility BioSupraMol, Berlin, Germany
| | - Gert Weber
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Berlin, Germany
| | - Christian Freund
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Protein Biochemistry, Berlin, Germany
| | - Tuğçe Aktaş
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Florian Heyd
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Berlin, Germany
| | - Markus C Wahl
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Berlin, Germany. .,Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Berlin, Germany.
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43
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Gañez-Zapater A, Mackowiak SD, Guo Y, Tarbier M, Jordán-Pla A, Friedländer MR, Visa N, Östlund Farrants AK. The SWI/SNF subunit BRG1 affects alternative splicing by changing RNA binding factor interactions with nascent RNA. Mol Genet Genomics 2022; 297:463-484. [PMID: 35187582 PMCID: PMC8960663 DOI: 10.1007/s00438-022-01863-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/23/2022] [Indexed: 11/29/2022]
Abstract
BRG1 and BRM are ATPase core subunits of the human SWI/SNF chromatin remodelling complexes mainly associated with transcriptional initiation. They also have a role in alternative splicing, which has been shown for BRM-containing SWI/SNF complexes at a few genes. Here, we have identified a subset of genes which harbour alternative exons that are affected by SWI/SNF ATPases by expressing the ATPases BRG1 and BRM in C33A cells, a BRG1- and BRM-deficient cell line, and analysed the effect on splicing by RNA sequencing. BRG1- and BRM-affected sub-sets of genes favouring both exon inclusion and exon skipping, with only a minor overlap between the ATPase. Some of the changes in alternative splicing induced by BRG1 and BRM expression did not require the ATPase activity. The BRG1-ATPase independent included exons displayed an exon signature of a high GC content. By investigating three genes with exons affected by the BRG-ATPase-deficient variant, we show that these exons accumulated phosphorylated RNA pol II CTD, both serine 2 and serine 5 phosphorylation, without an enrichment of the RNA polymerase II. The ATPases were recruited to the alternative exons, together with both core and signature subunits of SWI/SNF complexes, and promoted the binding of RNA binding factors to chromatin and RNA at the alternative exons. The interaction with the nascent RNP, however, did not reflect the association to chromatin. The hnRNPL, hnRNPU and SAM68 proteins associated with chromatin in cells expressing BRG1 and BRM wild type, but the binding of hnRNPU to the nascent RNP was excluded. This suggests that SWI/SNF can regulate alternative splicing by interacting with splicing-RNA binding factor and influence their binding to the nascent pre-mRNA particle.
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Affiliation(s)
- Antoni Gañez-Zapater
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
- Center for Genomic Regulation, 08003, Barcelona, Spain
| | - Sebastian D Mackowiak
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Yuan Guo
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - Antonio Jordán-Pla
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencies Biológicas, Valencia University, C/Dr. Moliner, 50, 46100, Burjassot, Spain
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
| | - Ann-Kristin Östlund Farrants
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden.
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Idrissou M, Maréchal A. The PRP19 Ubiquitin Ligase, Standing at the Cross-Roads of mRNA Processing and Genome Stability. Cancers (Basel) 2022; 14:cancers14040878. [PMID: 35205626 PMCID: PMC8869861 DOI: 10.3390/cancers14040878] [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: 12/22/2021] [Revised: 02/01/2022] [Accepted: 02/04/2022] [Indexed: 12/07/2022] Open
Abstract
mRNA processing factors are increasingly being recognized as important regulators of genome stability. By preventing and resolving RNA:DNA hybrids that form co-transcriptionally, these proteins help avoid replication-transcription conflicts and thus contribute to genome stability through their normal function in RNA maturation. Some of these factors also have direct roles in the activation of the DNA damage response and in DNA repair. One of the most intriguing cases is that of PRP19, an evolutionarily conserved essential E3 ubiquitin ligase that promotes mRNA splicing, but also participates directly in ATR activation, double-strand break resection and mitosis. Here, we review historical and recent work on PRP19 and its associated proteins, highlighting their multifarious cellular functions as central regulators of spliceosome activity, R-loop homeostasis, DNA damage signaling and repair and cell division. Finally, we discuss open questions that are bound to shed further light on the functions of PRP19-containing complexes in both normal and cancer cells.
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Affiliation(s)
- Mouhamed Idrissou
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N3, Canada
| | - Alexandre Maréchal
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N3, Canada
- Correspondence:
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A genetic screen in C. elegans reveals roles for KIN17 and PRCC in maintaining 5' splice site identity. PLoS Genet 2022; 18:e1010028. [PMID: 35143478 PMCID: PMC8865678 DOI: 10.1371/journal.pgen.1010028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 02/23/2022] [Accepted: 01/10/2022] [Indexed: 01/11/2023] Open
Abstract
Pre-mRNA splicing is an essential step of eukaryotic gene expression carried out by a series of dynamic macromolecular protein/RNA complexes, known collectively and individually as the spliceosome. This series of spliceosomal complexes define, assemble on, and catalyze the removal of introns. Molecular model snapshots of intermediates in the process have been created from cryo-EM data, however, many aspects of the dynamic changes that occur in the spliceosome are not fully understood. Caenorhabditis elegans follow the GU-AG rule of splicing, with almost all introns beginning with 5’ GU and ending with 3’ AG. These splice sites are identified early in the splicing cycle, but as the cycle progresses and “custody” of the pre-mRNA splice sites is passed from factor to factor as the catalytic site is built, the mechanism by which splice site identity is maintained or re-established through these dynamic changes is unclear. We performed a genetic screen in C. elegans for factors that are capable of changing 5’ splice site choice. We report that KIN17 and PRCC are involved in splice site choice, the first functional splicing role proposed for either of these proteins. Previously identified suppressors of cryptic 5’ splicing promote distal cryptic GU splice sites, however, mutations in KIN17 and PRCC instead promote usage of an unusual proximal 5’ splice site which defines an intron beginning with UU, separated by 1nt from a GU donor. We performed high-throughput mRNA sequencing analysis and found that mutations in PRCC, and to a lesser extent KIN17, changed alternative 5’ splice site usage at native sites genome-wide, often promoting usage of nearby non-consensus sites. Our work has uncovered both fine and coarse mechanisms by which the spliceosome maintains splice site identity during the complex assembly process. Pre-messenger RNA splicing is an important regulator of eukaryotic gene expression, changing the content, frame, and functionality of both coding and non-coding transcripts. Our understanding of how the spliceosome chooses where to cut has focused on the initial identification of splice sites. However, our results suggest that the spliceosome also relies on other components in later steps to maintain the identity of the splice donor sites. We are currently in the midst of a “resolution revolution”, with ever-clearer cryo-EM snapshots of stalled complexes, allowing researchers to visualize moments in time in the splicing cycle. These models are illuminating, but do not always elucidate mechanistic functioning of a highly dynamic ribonucleoprotein complex. Therefore, our lab takes a complementary approach, using the power of genetics in a multicellular animal to gain functional insights into the spliceosome. Using a C.elegans genetic screen, we have found novel functional splicing roles for two proteins, KIN17 and PRCC. Mutations in PRCC in particular promote nearby alternative 5’ splice sites at native loci. This work improves our understanding of how the spliceosome maintains the identity of where to cut the pre-mRNA, and thus how genes are expressed and used in multicellular animals.
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Xu W, Biswas J, Singer RH, Rosbash M. Targeted RNA editing: novel tools to study post-transcriptional regulation. Mol Cell 2022; 82:389-403. [PMID: 34739873 PMCID: PMC8792254 DOI: 10.1016/j.molcel.2021.10.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 01/22/2023]
Abstract
RNA binding proteins (RBPs) regulate nearly all post-transcriptional processes within cells. To fully understand RBP function, it is essential to identify their in vivo targets. Standard techniques for profiling RBP targets, such as crosslinking immunoprecipitation (CLIP) and its variants, are limited or suboptimal in some situations, e.g. when compatible antibodies are not available and when dealing with small cell populations such as neuronal subtypes and primary stem cells. This review summarizes and compares several genetic approaches recently designed to identify RBP targets in such circumstances. TRIBE (targets of RNA binding proteins identified by editing), RNA tagging, and STAMP (surveying targets by APOBEC-mediated profiling) are new genetic tools useful for the study of post-transcriptional regulation and RBP identification. We describe the underlying RNA base editing technology, recent applications, and therapeutic implications.
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Affiliation(s)
- Weijin Xu
- Howard Hughes Medical Institute, Department of Biology, Brandeis University, Waltham, MA 02451, USA
| | - Jeetayu Biswas
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute, Department of Biology, Brandeis University, Waltham, MA 02451, USA.
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Yazhini A, Srinivasan N, Sandhya S. Sequence Divergence and Functional Specializations of the Ancient Spliceosomal SF3b: Implications in Flexibility and Adaptations of the Multi-Protein Complex. Front Genet 2022; 12:747344. [PMID: 35082828 PMCID: PMC8785561 DOI: 10.3389/fgene.2021.747344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/07/2021] [Indexed: 11/17/2022] Open
Abstract
Multi-protein assemblies are complex molecular systems that perform highly sophisticated biochemical functions in an orchestrated manner. They are subject to changes that are governed by the evolution of individual components. We performed a comparative analysis of the ancient and functionally conserved spliceosomal SF3b complex, to recognize molecular signatures that contribute to sequence divergence and functional specializations. For this, we recognized homologous sequences of individual SF3b proteins distributed across 10 supergroups of eukaryotes and identified all seven protein components of the complex in 578 eukaryotic species. Using sequence and structural analysis, we establish that proteins occurring on the surface of the SF3b complex harbor more sequence variation than the proteins that lie in the core. Further, we show through protein interface conservation patterns that the extent of conservation varies considerably between interacting partners. When we analyze phylogenetic distributions of individual components of the complex, we find that protein partners that are known to form independent subcomplexes are observed to share similar profiles, reaffirming the link between differential conservation of interface regions and their inter-dependence. When we extend our analysis to individual protein components of the complex, we find taxa-specific variability in molecular signatures of the proteins. These trends are discussed in the context of proline-rich motifs of SF3b4, functional and drug binding sites of SF3b1. Further, we report key protein-protein interactions between SF3b1 and SF3b6 whose presence is observed to be lineage-specific across eukaryotes. Together, our studies show the association of protein location within the complex and subcomplex formation patterns with the sequence conservation of SF3b proteins. In addition, our study underscores evolutionarily flexible elements that appear to confer adaptive features in individual components of the multi-protein SF3b complexes and may contribute to its functional adaptability.
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Affiliation(s)
- Arangasamy Yazhini
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | | - Sankaran Sandhya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Department of Biotechnology, Faculty of Life and Allied Health Sciences, M. S. Ramaiah University of Applied Sciences, Bengaluru, India
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48
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Abstract
Recognition of the intron branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is a critical event during spliceosome assembly. In mammals, BS sequences are poorly conserved, and unambiguous intron recognition cannot be achieved solely through a base-pairing mechanism. We isolated human 17S U2 snRNP and reconstituted in vitro its adenosine 5´-triphosphate (ATP)–dependent remodeling and binding to the pre–messenger RNA substrate. We determined a series of high-resolution (2.0 to 2.2 angstrom) structures providing snapshots of the BS selection process. The substrate-bound U2 snRNP shows that SF3B6 stabilizes the BS:U2 snRNA duplex, which could aid binding of introns with poor sequence complementarity. ATP-dependent remodeling uncoupled from substrate binding captures U2 snRNA in a conformation that competes with BS recognition, providing a selection mechanism based on branch helix stability.
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Affiliation(s)
- Jonas Tholen
- European Molecular Biology Laboratory; 71 Avenue des Martyrs, 38042 Grenoble, France
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Michal Razew
- European Molecular Biology Laboratory; 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Felix Weis
- European Molecular Biology Laboratory, Structural and Computational Biology Unit; Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Wojciech P. Galej
- European Molecular Biology Laboratory; 71 Avenue des Martyrs, 38042 Grenoble, France
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49
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Abstract
In Eukarya, immature mRNA transcripts (pre-mRNA) often contain coding sequences, or exons, interleaved by non-coding sequences, or introns. Introns are removed upon splicing, and further regulation of the retained exons leads to alternatively spliced mRNA. The splicing reaction requires the stepwise assembly of the spliceosome, a macromolecular machine composed of small nuclear ribonucleoproteins (snRNPs). This review focuses on the early stage of spliceosome assembly, when U1 snRNP defines each intron 5’-splice site (5ʹss) in the pre-mRNA. We first introduce the splicing reaction and the impact of alternative splicing on gene expression regulation. Thereafter, we extensively discuss splicing descriptors that influence the 5ʹss selection by U1 snRNP, such as sequence determinants, and interactions mediated by U1-specific proteins or U1 small nuclear RNA (U1 snRNA). We also include examples of diseases that affect the 5ʹss selection by U1 snRNP, and discuss recent therapeutic advances that manipulate U1 snRNP 5ʹss selectivity with antisense oligonucleotides and small-molecule splicing switches.
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Affiliation(s)
- Florian Malard
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
| | - Cameron D Mackereth
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
| | - Sébastien Campagne
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
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50
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Bergfort A, Hilal T, Kuropka B, Ilik İA, Weber G, Aktaş T, Freund C, Wahl MC. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2938-2958. [PMID: 35188580 PMCID: PMC8934646 DOI: 10.1093/nar/gkac087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/21/2022] [Accepted: 01/26/2022] [Indexed: 11/16/2022] Open
Abstract
Biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and their recycling after splicing require numerous assembly/recycling factors whose modes of action are often poorly understood. The intrinsically disordered TSSC4 protein has been identified as a nuclear-localized U5 snRNP and U4/U6-U5 tri-snRNP assembly/recycling factor, but how TSSC4’s intrinsic disorder supports TSSC4 functions remains unknown. Using diverse interaction assays and cryogenic electron microscopy-based structural analysis, we show that TSSC4 employs four conserved, non-contiguous regions to bind the PRPF8 Jab1/MPN domain and the SNRNP200 helicase at functionally important sites. It thereby inhibits SNRNP200 helicase activity, spatially aligns the proteins, coordinates formation of a U5 sub-module and transiently blocks premature interaction of SNRNP200 with at least three other spliceosomal factors. Guided by the structure, we designed a TSSC4 variant that lacks stable binding to the PRPF8 Jab1/MPN domain or SNRNP200 in vitro. Comparative immunoprecipitation/mass spectrometry from HEK293 nuclear extract revealed distinct interaction profiles of wild type TSSC4 and the variant deficient in PRPF8/SNRNP200 binding with snRNP proteins, other spliceosomal proteins as well as snRNP assembly/recycling factors and chaperones. Our findings elucidate molecular strategies employed by an intrinsically disordered protein to promote snRNP assembly, and suggest multiple TSSC4-dependent stages during snRNP assembly/recycling.
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Affiliation(s)
- Alexandra Bergfort
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany
| | - Tarek Hilal
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Research Center of Electron Microscopy, Fabeckstr. 36a, 14195 Berlin, Germany
| | - Benno Kuropka
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Protein Biochemistry, Thielallee 63, D-14195, Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Core Facility BioSupraMol, Thielallee 63, D-14195, Berlin, Germany
| | - İbrahim Avşar Ilik
- Max Planck Institute for Molecular Genetics, Ihnestr. 63, D-14195 Berlin, Germany
| | - Gert Weber
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Tuğçe Aktaş
- Max Planck Institute for Molecular Genetics, Ihnestr. 63, D-14195 Berlin, Germany
| | - Christian Freund
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Protein Biochemistry, Thielallee 63, D-14195, Berlin, Germany
| | - Markus C Wahl
- To whom correspondence should be addressed. Tel: +49 30 838 53456; Fax: +49 30 8384 53456;
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