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Anastassov S, Filo M, Khammash M. Inteins: A Swiss army knife for synthetic biology. Biotechnol Adv 2024; 73:108349. [PMID: 38552727 DOI: 10.1016/j.biotechadv.2024.108349] [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: 12/18/2023] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/13/2024]
Abstract
Inteins are proteins found in nature that execute protein splicing. Among them, split inteins stand out for their versatility and adaptability, presenting creative solutions for addressing intricate challenges in various biological applications. Their exquisite attributes, including compactness, reliability, orthogonality, low toxicity, and irreversibility, make them of interest to various fields including synthetic biology, biotechnology and biomedicine. In this review, we delve into the inherent challenges of using inteins, present approaches for overcoming these challenges, and detail their reliable use for specific cellular tasks. We will discuss the use of conditional inteins in areas like cancer therapy, drug screening, patterning, infection treatment, diagnostics and biocontainment. Additionally, we will underscore the potential of inteins in executing basic logical operations with practical implications. We conclude by showcasing their potential in crafting complex genetic circuits for performing computations and feedback control that achieves robust perfect adaptation.
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Affiliation(s)
- Stanislav Anastassov
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4056, Switzerland
| | - Maurice Filo
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4056, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4056, Switzerland.
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2
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Yellamaty R, Sharma S. Critical Cellular Functions and Mechanisms of Action of the RNA Helicase UAP56. J Mol Biol 2024; 436:168604. [PMID: 38729260 DOI: 10.1016/j.jmb.2024.168604] [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: 03/06/2024] [Revised: 04/24/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024]
Abstract
Posttranscriptional maturation and export from the nucleus to the cytoplasm are essential steps in the normal processing of many cellular RNAs. The RNA helicase UAP56 (U2AF associated protein 56; also known as DDX39B) has emerged as a critical player in facilitating and co-transcriptionally linking these steps. Originally identified as a helicase involved in pre-mRNA splicing, UAP56 has been shown to facilitate formation of the A complex during spliceosome assembly. Additionally, it has been found to be critical for interactions between components of the exon junction and transcription and export complexes to promote the loading of export receptors. Although it appears to be structurally similar to other helicase superfamily 2 members, UAP56's ability to interact with multiple different protein partners allows it to perform its various cellular functions. Herein, we describe the structure-activity relationship studies that identified protein interactions of UAP56 and its human paralog URH49 (UAP56-related helicase 49; also known as DDX39A) and are beginning to reveal molecular mechanisms by which interacting proteins and substrate RNAs may regulate these helicases. We also provide an overview of reports that have demonstrated less well-characterized roles for UAP56, including R-loop resolution and telomere maintenance. Finally, we discuss studies that indicate a potential pathogenic effect of UAP56 in the development of autoimmune diseases and cancer, and identify the association of somatic and genetic mutations in UAP56 with neurodevelopmental disorders.
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Affiliation(s)
- Ryan Yellamaty
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA
| | - Shalini Sharma
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA.
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3
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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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4
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Li CH, Liang SB, Huang QW, Zhou ZZ, Ding Z, Long N, Wi KC, Li L, Jiang XP, Fan YJ, Xu YZ. Minor Spliceosomal 65K/RNPC3 Interacts with ANKRD11 and Mediates HDAC3-Regulated Histone Deacetylation and Transcription. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2307804. [PMID: 38837887 DOI: 10.1002/advs.202307804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/12/2024] [Indexed: 06/07/2024]
Abstract
RNA splicing is crucial in the multilayer regulatory networks for gene expression, making functional interactions with DNA- and other RNA-processing machineries in the nucleus. However, these established couplings are all major spliceosome-related; whether the minor spliceosome is involved remains unclear. Here, through affinity purification using Drosophila lysates, an interaction is identified between the minor spliceosomal 65K/RNPC3 and ANKRD11, a cofactor of histone deacetylase 3 (HDAC3). Using a CRISPR/Cas9 system, Deletion strains are constructed and found that both Dm65KΔ/Δ and Dmankrd11Δ/Δ mutants have reduced histone deacetylation at Lys9 of histone H3 (H3K9) and Lys5 of histone H4 (H4K5) in their heads, exhibiting various neural-related defects. The 65K-ANKRD11 interaction is also conserved in human cells, and the HsANKRD11 middle-uncharacterized domain mediates Hs65K association with HDAC3. Cleavage under targets and tagmentation (CUT&Tag) assays revealed that HsANKRD11 is a bridging factor, which facilitates the synergistic common chromatin-binding of HDAC3 and Hs65K. Knockdown (KD) of HsANKRD11 simultaneously decreased their common binding, resulting in reduced deacetylation of nearby H3K9. Ultimately, this study demonstrates that expression changes of many genes caused by HsANKRD11-KD are due to the decreased common chromatin-binding of HDAC3 and Hs65K and subsequently reduced deacetylation of H3K9, illustrating a novel and conserved coupling mechanism that links the histone deacetylation with minor spliceosome for the regulation of gene expression.
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Affiliation(s)
- Chen-Hui Li
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, 430072, China
| | - Shao-Bo Liang
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, 430072, China
| | - Qi-Wei Huang
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, 430072, China
| | - Zhen-Zhen Zhou
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, 430072, China
| | - Zhan Ding
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, 430072, China
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Ni Long
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, 430072, China
| | - Kwang-Chon Wi
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, 430072, China
| | - Liang Li
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, 430072, China
| | - Xi-Ping Jiang
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, 430072, China
| | - Yu-Jie Fan
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, 430072, China
| | - Yong-Zhen Xu
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, 430072, China
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5
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Wang Y, Xu X, Zhang A, Yang S, Li H. Role of alternative splicing in fish immunity. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109601. [PMID: 38701992 DOI: 10.1016/j.fsi.2024.109601] [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: 02/07/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Alternative splicing serves as a pivotal source of complexity in the transcriptome and proteome, selectively connecting various coding elements to generate a diverse array of mRNAs. This process encodes multiple proteins with either similar or distinct functions, contributing significantly to the intricacies of cellular processes. The role of alternative splicing in mammalian immunity has been well studied. Remarkably, the immune system of fish shares substantial similarities with that of humans, and alternative splicing also emerges as a key player in the immune processes of fish. In this review, we offer an overview of alternative splicing and its associated functions in the immune processes of fish, and summarize the research progress on alternative splicing in the fish immunity. Furthermore, we review the impact of alternative splicing on the fish immune system's response to external stimuli. Finally, we present our perspectives on future directions in this field. Our aim is to provide valuable insights for the future investigations into the role of alternative splicing in immunity.
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Affiliation(s)
- Yunchao Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xinyi Xu
- Hunan Fisheries Science Institute, Changsha, 410153, China
| | - Ailong Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Shuaiqi Yang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
| | - Hongyan Li
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266003, China.
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6
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Guan J, Wu P, Mo X, Zhang X, Liang W, Zhang X, Jiang L, Li J, Cui H, Yuan J. An axonemal intron splicing program sustains Plasmodium male development. Nat Commun 2024; 15:4697. [PMID: 38824128 PMCID: PMC11144265 DOI: 10.1038/s41467-024-49002-9] [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: 12/14/2023] [Accepted: 05/15/2024] [Indexed: 06/03/2024] Open
Abstract
Differentiation of male gametocytes into flagellated fertile male gametes relies on the assembly of axoneme, a major component of male development for mosquito transmission of the malaria parasite. RNA-binding protein (RBP)-mediated post-transcriptional regulation of mRNA plays important roles in eukaryotic sexual development, including the development of female Plasmodium. However, the role of RBP in defining the Plasmodium male transcriptome and its function in male gametogenesis remains incompletely understood. Here, we performed genome-wide screening for gender-specific RBPs and identified an undescribed male-specific RBP gene Rbpm1 in the Plasmodium. RBPm1 is localized in the nucleus of male gametocytes. RBPm1-deficient parasites fail to assemble the axoneme for male gametogenesis and thus mosquito transmission. RBPm1 interacts with the spliceosome E complex and regulates the splicing initiation of certain introns in a group of 26 axonemal genes. RBPm1 deficiency results in intron retention and protein loss of these axonemal genes. Intron deletion restores axonemal protein expression and partially rectifies axonemal defects in RBPm1-null gametocytes. Further splicing assays in both reporter and endogenous genes exhibit stringent recognition of the axonemal introns by RBPm1. The splicing activator RBPm1 and its target introns constitute an axonemal intron splicing program in the post-transcriptional regulation essential for Plasmodium male development.
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Affiliation(s)
- Jiepeng Guan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Peijia Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Xiaoli Mo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Xiaolong Zhang
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Wenqi Liang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Xiaoming Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Lubin Jiang
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
| | - Jian Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China.
| | - Huiting Cui
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China.
| | - Jing Yuan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China.
- Department of Infectious Disease, Xiang'an Hospital of Xiamen University, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China.
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7
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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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8
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Greene D, Thys C, Berry IR, Jarvis J, Ortibus E, Mumford AD, Freson K, Turro E. Mutations in the U4 snRNA gene RNU4-2 cause one of the most prevalent monogenic neurodevelopmental disorders. Nat Med 2024:10.1038/s41591-024-03085-5. [PMID: 38821540 DOI: 10.1038/s41591-024-03085-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/23/2024] [Indexed: 06/02/2024]
Abstract
Most people with intellectual disability (ID) do not receive a molecular diagnosis following genetic testing. To identify new etiologies of ID, we performed a genetic association analysis comparing the burden of rare variants in 41,132 noncoding genes between 5,529 unrelated cases and 46,401 unrelated controls. RNU4-2, which encodes U4 small nuclear RNA, a critical component of the spliceosome, was the most strongly associated gene. We implicated de novo variants among 47 cases in two regions of RNU4-2 in the etiology of a syndrome characterized by ID, microcephaly, short stature, hypotonia, seizures and motor delay. We replicated this finding in three collections, bringing the number of unrelated cases to 73. Analysis of national genomic diagnostic data showed RNU4-2 to be a more common etiological gene for neurodevelopmental abnormality than any previously reported autosomal gene. Our findings add to the growing evidence of spliceosome dysfunction in the etiologies of neurological disorders.
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Affiliation(s)
- Daniel Greene
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chantal Thys
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Ian R Berry
- NHS South West Genomic Laboratory Hub, Southmead Hospital, Bristol, UK
- NHS South West Genomic Medicine Service Alliance, Bristol, UK
| | - Joanna Jarvis
- Clinical Genetics Unit, Birmingham Women's Hospital, Birmingham, UK
| | - Els Ortibus
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
- Paediatric Neurology Department, University Hospitals of KU Leuven, Leuven, Belgium
| | - Andrew D Mumford
- NHS South West Genomic Medicine Service Alliance, Bristol, UK
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Ernest Turro
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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9
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Shen A, Hencel K, Parker MT, Scott R, Skukan R, Adesina AS, Metheringham CL, Miska EA, Nam Y, Haerty W, Simpson GG, Akay A. U6 snRNA m6A modification is required for accurate and efficient splicing of C. elegans and human pre-mRNAs. Nucleic Acids Res 2024:gkae447. [PMID: 38808663 DOI: 10.1093/nar/gkae447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/30/2024] Open
Abstract
pre-mRNA splicing is a critical feature of eukaryotic gene expression. Both cis- and trans-splicing rely on accurately recognising splice site sequences by spliceosomal U snRNAs and associated proteins. Spliceosomal snRNAs carry multiple RNA modifications with the potential to affect different stages of pre-mRNA splicing. Here, we show that the conserved U6 snRNA m6A methyltransferase METT-10 is required for accurate and efficient cis- and trans-splicing of C. elegans pre-mRNAs. The absence of METT-10 in C. elegans and METTL16 in humans primarily leads to alternative splicing at 5' splice sites with an adenosine at +4 position. In addition, METT-10 is required for splicing of weak 3' cis- and trans-splice sites. We identified a significant overlap between METT-10 and the conserved splicing factor SNRNP27K in regulating 5' splice sites with +4A. Finally, we show that editing endogenous 5' splice site +4A positions to +4U restores splicing to wild-type positions in a mett-10 mutant background, supporting a direct role for U6 snRNA m6A modification in 5' splice site recognition. We conclude that the U6 snRNA m6A modification is important for accurate and efficient pre-mRNA splicing.
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Affiliation(s)
- Aykut Shen
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
| | - Katarzyna Hencel
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
| | - Matthew T Parker
- School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Robyn Scott
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Roberta Skukan
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
| | | | | | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Rd, Cambridge CB2 1QN, UK
| | - Yunsun Nam
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wilfried Haerty
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Gordon G Simpson
- School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, DD2 5DA, UK
| | - Alper Akay
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
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10
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Bei M, Xu J. SR proteins in cancer: function, regulation, and small inhibitor. Cell Mol Biol Lett 2024; 29:78. [PMID: 38778254 PMCID: PMC11110342 DOI: 10.1186/s11658-024-00594-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Alternative splicing of pre-mRNAs is a fundamental step in RNA processing required for gene expression in most metazoans. Serine and arginine-rich proteins (SR proteins) comprise a family of multifunctional proteins that contain an RNA recognition motif (RRM) and the ultra-conserved arginine/serine-rich (RS) domain, and play an important role in precise alternative splicing. Increasing research supports SR proteins as also functioning in other RNA-processing-related mechanisms, such as polyadenylation, degradation, and translation. In addition, SR proteins interact with N6-methyladenosine (m6A) regulators to modulate the methylation of ncRNA and mRNA. Dysregulation of SR proteins causes the disruption of cell differentiation and contributes to cancer progression. Here, we review the distinct biological characteristics of SR proteins and their known functional mechanisms during carcinogenesis. We also summarize the current inhibitors that directly target SR proteins and could ultimately turn SR proteins into actionable therapeutic targets in cancer therapy.
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Affiliation(s)
- Mingrong Bei
- Systems Biology Laboratory, Shantou University Medical College (SUMC), 22 Xinling Road, Shantou, 515041, China
- Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Jianzhen Xu
- Systems Biology Laboratory, Shantou University Medical College (SUMC), 22 Xinling Road, Shantou, 515041, China.
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11
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Marchetto A, Leidescher S, van Hoi T, Hirschberger N, Vogel F, Köhler S, Bedei IA, Axt-Fliedner R, Shoukier M, Keil C. Prenatal Diagnosis of Fryns Syndrome through Identification of Two Novel Splice Variants in the PIGN Gene-A Case Series. Life (Basel) 2024; 14:628. [PMID: 38792648 PMCID: PMC11122441 DOI: 10.3390/life14050628] [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: 04/22/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Fryns syndrome (FS) is a multiple congenital anomaly syndrome with different multisystemic malformations. These include congenital diaphragmatic hernia, pulmonary hypoplasia, and craniofacial dysmorphic features in combination with malformations of the central nervous system such as agenesis of the corpus callosum, cerebellar hypoplasia, and enlarged ventricles. We present a non-consanguineous northern European family with two recurrent cases of FS: a boy with multiple congenital malformations who died at the age of 2.5 months and a female fetus with a complex developmental disorder with similar features in a following pregnancy. Quad whole exome analysis revealed two likely splicing-affecting disease-causing mutations in the PIGN gene: a synonymous mutation c.2619G>A, p.(Leu873=) in the last nucleotide of exon 29 and a 30 bp-deletion c.996_1023+2del (NM_176787.5) protruding into intron 12, with both mutations in trans configuration in the affected patients. Exon skipping resulting from these two variants was confirmed via RNA sequencing. Our molecular and clinical findings identified compound heterozygosity for two novel splice-affecting variants as the underlying pathomechanism for the development of FS in two patients.
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Affiliation(s)
- Aruna Marchetto
- Eurofins Humangenetik und Pränatal-Medizin MVZ GmbH, 80639 Munich, Germany (M.S.)
| | - Susanne Leidescher
- Eurofins Humangenetik und Pränatal-Medizin MVZ GmbH, 80639 Munich, Germany (M.S.)
| | - Theresia van Hoi
- Eurofins Humangenetik und Pränatal-Medizin MVZ GmbH, 80639 Munich, Germany (M.S.)
| | - Niklas Hirschberger
- Eurofins Humangenetik und Pränatal-Medizin MVZ GmbH, 80639 Munich, Germany (M.S.)
| | - Florian Vogel
- Eurofins Humangenetik und Pränatal-Medizin MVZ GmbH, 80639 Munich, Germany (M.S.)
| | - Siegmund Köhler
- Department of Prenatal Medicine and Fetal Therapy, Philipps University, 35043 Marburg, Germany;
| | - Ivonne Alexandra Bedei
- Department of Prenatal Medicine and Fetal Therapy, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Roland Axt-Fliedner
- Department of Prenatal Medicine and Fetal Therapy, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Moneef Shoukier
- Eurofins Humangenetik und Pränatal-Medizin MVZ GmbH, 80639 Munich, Germany (M.S.)
| | - Corinna Keil
- Department of Prenatal Medicine and Fetal Therapy, Philipps University, 35043 Marburg, Germany;
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12
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Martínez-Lumbreras S, Träger LK, Mulorz MM, Payr M, Dikaya V, Hipp C, König J, Sattler M. Intramolecular autoinhibition regulates the selectivity of PRPF40A tandem WW domains for proline-rich motifs. Nat Commun 2024; 15:3888. [PMID: 38719828 PMCID: PMC11079029 DOI: 10.1038/s41467-024-48004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
PRPF40A plays an important role in the regulation of pre-mRNA splicing by mediating protein-protein interactions in the early steps of spliceosome assembly. By binding to proteins at the 5´ and 3´ splice sites, PRPF40A promotes spliceosome assembly by bridging the recognition of the splices. The PRPF40A WW domains are expected to recognize proline-rich sequences in SF1 and SF3A1 in the early spliceosome complexes E and A, respectively. Here, we combine NMR, SAXS and ITC to determine the structure of the PRPF40A tandem WW domains in solution and characterize the binding specificity and mechanism for proline-rich motifs recognition. Our structure of the PRPF40A WW tandem in complex with a high-affinity SF1 peptide reveals contributions of both WW domains, which also enables tryptophan sandwiching by two proline residues in the ligand. Unexpectedly, a proline-rich motif in the N-terminal region of PRPF40A mediates intramolecular interactions with the WW tandem. Using NMR, ITC, mutational analysis in vitro, and immunoprecipitation experiments in cells, we show that the intramolecular interaction acts as an autoinhibitory filter for proof-reading of high-affinity proline-rich motifs in bona fide PRPF40A binding partners. We propose that similar autoinhibitory mechanisms are present in most WW tandem-containing proteins to enhance binding selectivity and regulation of WW/proline-rich peptide interaction networks.
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Affiliation(s)
- Santiago Martínez-Lumbreras
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
- TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany.
| | - Lena K Träger
- TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Miriam M Mulorz
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128, Mainz, Germany
| | - Marco Payr
- TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Varvara Dikaya
- TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Clara Hipp
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Julian König
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128, Mainz, Germany
| | - Michael Sattler
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
- TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany.
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13
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Shen Z, Naveed M, Bao J. Untacking small RNA profiling and RNA fragment footprinting: Approaches and challenges in library construction. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1852. [PMID: 38715192 DOI: 10.1002/wrna.1852] [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: 02/21/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 06/06/2024]
Abstract
Small RNAs (sRNAs) with sizes ranging from 15 to 50 nucleotides (nt) are critical regulators of gene expression control. Prior studies have shown that sRNAs are involved in a broad range of biological processes, such as organ development, tumorigenesis, and epigenomic regulation; however, emerging evidence unveils a hidden layer of diversity and complexity of endogenously encoded sRNAs profile in eukaryotic organisms, including novel types of sRNAs and the previously unknown post-transcriptional RNA modifications. This underscores the importance for accurate, unbiased detection of sRNAs in various cellular contexts. A multitude of high-throughput methods based on next-generation sequencing (NGS) are developed to decipher the sRNA expression and their modifications. Nonetheless, distinct from mRNA sequencing, the data from sRNA sequencing suffer frequent inconsistencies and high variations emanating from the adapter contaminations and RNA modifications, which overall skew the sRNA libraries. Here, we summarize the sRNA-sequencing approaches, and discuss the considerations and challenges for the strategies and methods of sRNA library construction. The pros and cons of sRNA sequencing have significant implications for implementing RNA fragment footprinting approaches, including CLIP-seq and Ribo-seq. We envision that this review can inspire novel improvements in small RNA sequencing and RNA fragment footprinting in future. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.
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Affiliation(s)
- Zhaokang Shen
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
| | - Muhammad Naveed
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Jianqiang Bao
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
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14
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Carvalho L, Lasek AW. It is not just about transcription: involvement of brain RNA splicing in substance use disorders. J Neural Transm (Vienna) 2024; 131:495-503. [PMID: 38396082 PMCID: PMC11055753 DOI: 10.1007/s00702-024-02740-y] [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: 09/16/2023] [Accepted: 01/04/2024] [Indexed: 02/25/2024]
Abstract
Alternative splicing is a co-transcriptional process that significantly contributes to the molecular landscape of the cell. It plays a multifaceted role in shaping gene transcription, protein diversity, and functional adaptability in response to environmental cues. Recent studies demonstrate that drugs of abuse have a profound impact on alternative splicing patterns within different brain regions. Drugs like alcohol and cocaine modify the expression of genes responsible for encoding splicing factors, thereby influencing alternative splicing of crucial genes involved in neurotransmission, neurogenesis, and neuroinflammation. Notable examples of these alterations include alcohol-induced changes in splicing factors such as HSPA6 and PCBP1, as well as cocaine's impact on PTBP1 and SRSF11. Beyond the immediate effects of drug exposure, recent research has shed light on the role of alternative splicing in contributing to the risk of substance use disorders (SUDs). This is exemplified by exon skipping events in key genes like ELOVL7, which can elevate the risk of alcohol use disorder. Lastly, drugs of abuse can induce splicing alterations through epigenetic modifications. For example, cocaine exposure leads to alterations in levels of trimethylated lysine 36 of histone H3, which exhibits a robust association with alternative splicing and serves as a reliable predictor for exon exclusion. In summary, alternative splicing has emerged as a critical player in the complex interplay between drugs of abuse and the brain, offering insights into the molecular underpinnings of SUDs.
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Affiliation(s)
- Luana Carvalho
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, 1220 E. Broad ST, Box 980613, Richmond, VA, 23298, USA.
| | - Amy W Lasek
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, 1220 E. Broad ST, Box 980613, Richmond, VA, 23298, USA
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15
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Riabov Bassat D, Visanpattanasin S, Vorländer MK, Fin L, Phillips AW, Plaschka C. Structural basis of human U5 snRNP late biogenesis and recycling. Nat Struct Mol Biol 2024; 31:747-751. [PMID: 38467876 DOI: 10.1038/s41594-024-01243-4] [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: 08/08/2023] [Accepted: 02/06/2024] [Indexed: 03/13/2024]
Abstract
Pre-mRNA splicing by the spliceosome requires the biogenesis and recycling of its small nuclear ribonucleoprotein (snRNP) complexes, which are consumed in each round of splicing. The human U5 snRNP is the ~1 MDa 'heart' of the spliceosome and is recycled through an unknown mechanism involving major architectural rearrangements and the dedicated chaperones CD2BP2 and TSSC4. Late steps in U5 snRNP biogenesis similarly involve these chaperones. Here we report cryo-electron microscopy structures of four human U5 snRNP-CD2BP2-TSSC4 complexes, revealing how a series of molecular events primes the U5 snRNP to generate the ~2 MDa U4/U6.U5 tri-snRNP, the largest building block of the spliceosome.
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Affiliation(s)
- Daria Riabov Bassat
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | | | | | - Laura Fin
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Alexander W Phillips
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Clemens Plaschka
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.
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16
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Bhat P, Chow A, Emert B, Ettlin O, Quinodoz SA, Strehle M, Takei Y, Burr A, Goronzy IN, Chen AW, Huang W, Ferrer JLM, Soehalim E, Goh ST, Chari T, Sullivan DK, Blanco MR, Guttman M. Genome organization around nuclear speckles drives mRNA splicing efficiency. Nature 2024; 629:1165-1173. [PMID: 38720076 PMCID: PMC11164319 DOI: 10.1038/s41586-024-07429-6] [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: 03/12/2023] [Accepted: 04/16/2024] [Indexed: 05/21/2024]
Abstract
The nucleus is highly organized, such that factors involved in the transcription and processing of distinct classes of RNA are confined within specific nuclear bodies1,2. One example is the nuclear speckle, which is defined by high concentrations of protein and noncoding RNA regulators of pre-mRNA splicing3. What functional role, if any, speckles might play in the process of mRNA splicing is unclear4,5. Here we show that genes localized near nuclear speckles display higher spliceosome concentrations, increased spliceosome binding to their pre-mRNAs and higher co-transcriptional splicing levels than genes that are located farther from nuclear speckles. Gene organization around nuclear speckles is dynamic between cell types, and changes in speckle proximity lead to differences in splicing efficiency. Finally, directed recruitment of a pre-mRNA to nuclear speckles is sufficient to increase mRNA splicing levels. Together, our results integrate the long-standing observations of nuclear speckles with the biochemistry of mRNA splicing and demonstrate a crucial role for dynamic three-dimensional spatial organization of genomic DNA in driving spliceosome concentrations and controlling the efficiency of mRNA splicing.
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Affiliation(s)
- Prashant Bhat
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Amy Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Benjamin Emert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Olivia Ettlin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sofia A Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Mackenzie Strehle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yodai Takei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Alex Burr
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Isabel N Goronzy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Allen W Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Wesley Huang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jose Lorenzo M Ferrer
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Elizabeth Soehalim
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Say-Tar Goh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tara Chari
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Delaney K Sullivan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mario R Blanco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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17
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Passmore LA, Zhang S. Mechanisms of transcription and RNA processing. Nat Struct Mol Biol 2024; 31:730-731. [PMID: 38744993 DOI: 10.1038/s41594-024-01312-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Affiliation(s)
| | - Suyang Zhang
- MRC Laboratory of Molecular Biology, Cambridge, UK.
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18
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Waddell BM, Wu CW. A role for the C. elegans Argonaute protein CSR-1 in small nuclear RNA 3' processing. PLoS Genet 2024; 20:e1011284. [PMID: 38743783 PMCID: PMC11125478 DOI: 10.1371/journal.pgen.1011284] [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: 10/11/2023] [Revised: 05/24/2024] [Accepted: 05/02/2024] [Indexed: 05/16/2024] Open
Abstract
The Integrator is a multi-subunit protein complex that catalyzes the maturation of snRNA transcripts via 3' cleavage, a step required for snRNA incorporation with snRNP for spliceosome biogenesis. Here we developed a GFP based in vivo snRNA misprocessing reporter as a readout of Integrator function and performed a genome-wide RNAi screen for Integrator regulators. We found that loss of the Argonaute encoding csr-1 gene resulted in widespread 3' misprocessing of snRNA transcripts that is accompanied by a significant increase in alternative splicing. Loss of the csr-1 gene down-regulates the germline expression of Integrator subunits 4 and 6 and is accompanied by a reduced protein translation efficiency of multiple Integrator catalytic and non-catalytic subunits. Through isoform and motif mutant analysis, we determined that CSR-1's effect on snRNA processing is dependent on its catalytic slicer activity but does not involve the CSR-1a isoform. Moreover, mRNA-sequencing revealed high similarity in the transcriptome profile between csr-1 and Integrator subunit knockdown via RNAi. Together, our findings reveal CSR-1 as a new regulator of the Integrator complex and implicate a novel role of this Argonaute protein in snRNA 3' processing.
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Affiliation(s)
- Brandon M. Waddell
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Cheng-Wei Wu
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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19
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Eijlers P, Al-Khafaji M, Soto-Martin E, Fasimoye R, Stead D, Wenzel M, Müller B, Pettitt J. A nematode-specific ribonucleoprotein complex mediates interactions between the major nematode spliced leader snRNP and its target pre-mRNAs. Nucleic Acids Res 2024:gkae321. [PMID: 38676950 DOI: 10.1093/nar/gkae321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
Spliced leader trans-splicing of pre-mRNAs is a critical step in the gene expression of many eukaryotes. How the spliced leader RNA and its target transcripts are brought together to form the trans-spliceosome remains an important unanswered question. Using immunoprecipitation followed by protein analysis via mass spectrometry and RIP-Seq, we show that the nematode-specific proteins, SNA-3 and SUT-1, form a complex with a set of enigmatic non-coding RNAs, the SmY RNAs. Our work redefines the SmY snRNP and shows for the first time that it is essential for nematode viability and is involved in spliced leader trans-splicing. SNA-3 and SUT-1 are associated with the 5' ends of most, if not all, nascent capped RNA polymerase II transcripts, and they also interact with components of the major nematode spliced leader (SL1) snRNP. We show that depletion of SNA-3 impairs the co-immunoprecipitation between one of the SL1 snRNP components, SNA-2, and several core spliceosomal proteins. We thus propose that the SmY snRNP recruits the SL1 snRNP to the 5' ends of nascent pre-mRNAs, an instrumental step in the assembly of the trans-spliceosome.
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Affiliation(s)
- Peter Eijlers
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Mohammed Al-Khafaji
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Eva Soto-Martin
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Rotimi Fasimoye
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - David Stead
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Rowett Institute, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Marius Wenzel
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ Scotland, UK
| | - Berndt Müller
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Jonathan Pettitt
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
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20
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Bauer M, Schöbel CM, Wickenhauser C, Seliger B, Jasinski-Bergner S. Deciphering the role of alternative splicing in neoplastic diseases for immune-oncological therapies. Front Immunol 2024; 15:1386993. [PMID: 38736877 PMCID: PMC11082354 DOI: 10.3389/fimmu.2024.1386993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/16/2024] [Indexed: 05/14/2024] Open
Abstract
Alternative splicing (AS) is an important molecular biological mechanism regulated by complex mechanisms involving a plethora of cis and trans-acting elements. Furthermore, AS is tissue specific and altered in various pathologies, including infectious, inflammatory, and neoplastic diseases. Recently developed immuno-oncological therapies include monoclonal antibodies (mAbs) and chimeric antigen receptor (CAR) T cells targeting, among others, immune checkpoint (ICP) molecules. Despite therapeutic successes have been demonstrated, only a limited number of patients showed long-term benefit from these therapies with tumor entity-related differential response rates were observed. Interestingly, splice variants of common immunotherapeutic targets generated by AS are able to completely escape and/or reduce the efficacy of mAb- and/or CAR-based tumor immunotherapies. Therefore, the analyses of splicing patterns of targeted molecules in tumor specimens prior to therapy might help correct stratification, thereby increasing therapy success by antibody panel selection and antibody dosages. In addition, the expression of certain splicing factors has been linked with the patients' outcome, thereby highlighting their putative prognostic potential. Outstanding questions are addressed to translate the findings into clinical application. This review article provides an overview of the role of AS in (tumor) diseases, its molecular mechanisms, clinical relevance, and therapy response.
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Affiliation(s)
- Marcus Bauer
- Institute of Pathology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Chiara-Maria Schöbel
- Institute for Translational Immunology, Brandenburg Medical School (MHB), Theodor Fontane, Brandenburg an der Havel, Germany
| | - Claudia Wickenhauser
- Institute of Pathology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Barbara Seliger
- Institute for Translational Immunology, Brandenburg Medical School (MHB), Theodor Fontane, Brandenburg an der Havel, Germany
- Department of Good Manufacturing Practice (GMP) Development & Advanced Therapy Medicinal Products (ATMP) Design, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
- Institute for Medical Immunology, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Simon Jasinski-Bergner
- Institute for Translational Immunology, Brandenburg Medical School (MHB), Theodor Fontane, Brandenburg an der Havel, Germany
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21
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Norppa AJ, Chowdhury I, van Rooijen LE, Ravantti JJ, Snel B, Varjosalo M, Frilander MJ. Distinct functions for the paralogous RBM41 and U11/U12-65K proteins in the minor spliceosome. Nucleic Acids Res 2024; 52:4037-4052. [PMID: 38499487 DOI: 10.1093/nar/gkae070] [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: 12/11/2023] [Revised: 01/19/2024] [Accepted: 03/11/2024] [Indexed: 03/20/2024] Open
Abstract
Here, we identify RBM41 as a novel unique protein component of the minor spliceosome. RBM41 has no previously recognized cellular function but has been identified as a paralog of U11/U12-65K, a known unique component of the U11/U12 di-snRNP. Both proteins use their highly similar C-terminal RRMs to bind to 3'-terminal stem-loops in U12 and U6atac snRNAs with comparable affinity. Our BioID data indicate that the unique N-terminal domain of RBM41 is necessary for its association with complexes containing DHX8, an RNA helicase, which in the major spliceosome drives the release of mature mRNA from the spliceosome. Consistently, we show that RBM41 associates with excised U12-type intron lariats, is present in the U12 mono-snRNP, and is enriched in Cajal bodies, together suggesting that RBM41 functions in the post-splicing steps of the minor spliceosome assembly/disassembly cycle. This contrasts with U11/U12-65K, which uses its N-terminal region to interact with U11 snRNP during intron recognition. Finally, while RBM41 knockout cells are viable, they show alterations in U12-type 3' splice site usage. Together, our results highlight the role of the 3'-terminal stem-loop of U12 snRNA as a dynamic binding platform for the U11/U12-65K and RBM41 proteins, which function at distinct stages of the assembly/disassembly cycle.
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Affiliation(s)
- Antto J Norppa
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Iftekhar Chowdhury
- Molecular Systems Biology Research Group and Proteomics Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Laura E van Rooijen
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Janne J Ravantti
- Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Markku Varjosalo
- Molecular Systems Biology Research Group and Proteomics Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Mikko J Frilander
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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22
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Bouton L, Ecoutin A, Malard F, Campagne S. Small molecules modulating RNA splicing: a review of targets and future perspectives. RSC Med Chem 2024; 15:1109-1126. [PMID: 38665842 PMCID: PMC11042171 DOI: 10.1039/d3md00685a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/03/2024] [Indexed: 04/28/2024] Open
Abstract
In eukaryotic cells, RNA splicing is crucial for gene expression. Dysregulation of this process can result in incorrect mRNA processing, leading to aberrant gene expression patterns. Such abnormalities are implicated in many inherited diseases and cancers. Historically, antisense oligonucleotides, which bind to specific RNA targets, have been used to correct these splicing abnormalities. Despite their high specificity of action, these oligonucleotides have drawbacks, such as lack of oral bioavailability and the need for chemical modifications to enhance cellular uptake and stability. As a result, recent efforts focused on the development of small organic molecules that can correct abnormal RNA splicing event under disease conditions. This review discusses known and potential targets of these molecules, including RNA structures, trans-acting splicing factors, and the spliceosome - the macromolecular complex responsible for RNA splicing. We also rely on recent advances to discuss therapeutic applications of RNA-targeting small molecules in splicing correction. Overall, this review presents an update on strategies for RNA splicing modulation, emphasizing the therapeutic promise of small molecules.
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Affiliation(s)
- Léa Bouton
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Agathe Ecoutin
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Florian Malard
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Sébastien Campagne
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
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23
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White DS, Dunyak BM, Vaillancourt FH, Hoskins AA. A Sequential Binding Mechanism for 5' Splice Site Recognition and Modulation for the Human U1 snRNP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590139. [PMID: 38659798 PMCID: PMC11042371 DOI: 10.1101/2024.04.18.590139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Splice site recognition is essential for defining the transcriptome. Drugs like risdiplam and branaplam change how U1 snRNP recognizes particular 5' splice sites (5'SS) and promote U1 snRNP binding and splicing at these locations. Despite the therapeutic potential of 5'SS modulators, the complexity of their interactions and snRNP substrates have precluded defining a mechanism for 5'SS modulation. We have determined a sequential binding mechanism for modulation of -1A bulged 5'SS by branaplam using a combination of ensemble kinetic measurements and colocalization single molecule spectroscopy (CoSMoS). Our mechanism establishes that U1-C protein binds reversibly to U1 snRNP, and branaplam binds to the U1 snRNP/U1-C complex only after it has engaged a -1A bulged 5'SS. Obligate orders of binding and unbinding explain how reversible branaplam interactions cause formation of long-lived U1 snRNP/5'SS complexes. Branaplam is a ribonucleoprotein, not RNA duplex alone, targeting drug whose action depends on fundamental properties of 5'SS recognition.
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Affiliation(s)
- David S. White
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI
- Present Address: Element Biosciences, San Diego, CA
| | | | | | - Aaron A. Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI
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24
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Beusch I, Madhani HD. Understanding the dynamic design of the spliceosome. Trends Biochem Sci 2024:S0968-0004(24)00078-1. [PMID: 38641465 DOI: 10.1016/j.tibs.2024.03.012] [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: 12/12/2023] [Revised: 03/05/2024] [Accepted: 03/19/2024] [Indexed: 04/21/2024]
Abstract
The spliceosome catalyzes the splicing of pre-mRNAs. Although the spliceosome evolved from a prokaryotic self-splicing intron and an associated protein, it is a vastly more complex and dynamic ribonucleoprotein (RNP) whose function requires at least eight ATPases and multiple RNA rearrangements. These features afford stepwise opportunities for multiple inspections of the intron substrate, coupled with spliceosome disassembly for substrates that fail inspection. Early work using splicing-defective pre-mRNAs or small nuclear (sn)RNAs in Saccharomyces cerevisiae demonstrated that such checks could occur in catalytically active spliceosomes. We review recent results on pre-mRNA splicing in various systems, including humans, suggesting that earlier steps in spliceosome assembly are also subject to such quality control. The inspection-rejection framework helps explain the dynamic nature of the spliceosome.
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Affiliation(s)
- Irene Beusch
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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25
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Damianov A, Lin CH, Huang J, Zhou L, Jami-Alahmadi Y, Peyda P, Wohlschlegel J, Black DL. The splicing regulators RBM5 and RBM10 are subunits of the U2 snRNP engaged with intron branch sites on chromatin. Mol Cell 2024; 84:1496-1511.e7. [PMID: 38537639 PMCID: PMC11057915 DOI: 10.1016/j.molcel.2024.02.039] [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: 09/08/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 04/09/2024]
Abstract
Understanding the mechanisms of pre-mRNA splicing is limited by the technical challenges to examining spliceosomes in vivo. Here, we report the isolation of RNP complexes derived from precatalytic A or B-like spliceosomes solubilized from the chromatin pellet of mammalian cell nuclei. We found that these complexes contain U2 snRNP proteins and a portion of the U2 snRNA bound with protected RNA fragments that precisely map to intronic branch sites across the transcriptome. These U2 complexes also contained the splicing regulators RBM5 and RBM10. We found RBM5 and RBM10 bound to nearly all branch site complexes and not simply those at regulated exons. The deletion of a conserved RBM5/RBM10 peptide sequence, including a zinc finger motif, disrupted U2 interaction and rendered the proteins inactive for the repression of many alternative exons. We propose a model where RBM5 and RBM10 regulate splicing as components of the U2 snRNP complex following branch site base pairing.
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Affiliation(s)
- Andrey Damianov
- Department of Microbiology, Immunology, and Molecular Genetics, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jeffrey Huang
- Department of Microbiology, Immunology, and Molecular Genetics, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Lin Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Parham Peyda
- Department of Microbiology, Immunology, and Molecular Genetics, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
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26
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Yang WQ, Ge JY, Zhang X, Zhu WY, Lin L, Shi Y, Xu B, Liu RJ. THUMPD2 catalyzes the N2-methylation of U6 snRNA of the spliceosome catalytic center and regulates pre-mRNA splicing and retinal degeneration. Nucleic Acids Res 2024; 52:3291-3309. [PMID: 38165050 PMCID: PMC11014329 DOI: 10.1093/nar/gkad1243] [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: 08/26/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024] Open
Abstract
The mechanisms by which the relatively conserved spliceosome manages the enormously large number of splicing events that occur in humans (∼200 000 versus ∼300 in yeast) are poorly understood. Here, we show deposition of one RNA modification-N2-methylguanosine (m2G) on the G72 of U6 snRNA (the catalytic center of the spliceosome) promotes efficient pre-mRNA splicing activity in human cells. This modification was identified to be conserved among vertebrates. Further, THUMPD2 was demonstrated as the methyltransferase responsible for U6 m2G72 by explicitly recognizing the U6-specific sequences and structural elements. The knock-out of THUMPD2 eliminated U6 m2G72 and impaired the pre-mRNA splicing activity, resulting in thousands of changed alternative splicing events of endogenous pre-mRNAs in human cells. Notably, the aberrantly spliced pre-mRNA population elicited the nonsense-mediated mRNA decay pathway. We further show that THUMPD2 was associated with age-related macular degeneration and retinal function. Our study thus demonstrates how an RNA epigenetic modification of the major spliceosome regulates global pre-mRNA splicing and impacts physiology and disease.
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Affiliation(s)
- Wen-Qing Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jian-Yang Ge
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiaofeng Zhang
- Division of Reproduction and Genetics, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, China
| | - Wen-Yu Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lin Lin
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yigong Shi
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou 310064,Zhejiang Province, China
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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27
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Chen Y, Dawes R, Kim HC, Stenton SL, Walker S, Ljungdahl A, Lord J, Ganesh VS, Ma J, Martin-Geary AC, Lemire G, D’Souza EN, Dong S, Ellingford JM, Adams DR, Allan K, Bakshi M, Baldwin EE, Berger SI, Bernstein JA, Brown NJ, Burrage LC, Chapman K, Compton AG, Cunningham CA, D’Souza P, Délot EC, Dias KR, Elias ER, Evans CA, Ewans L, Ezell K, Fraser JL, Gallacher L, Genetti CA, Grant CL, Haack T, Kuechler A, Lalani SR, Leitão E, Fevre AL, Leventer RJ, Liebelt JE, Lockhart PJ, Ma AS, Macnamara EF, Maurer TM, Mendez HR, Montgomery SB, Nassogne MC, Neumann S, O’Leary M, Palmer EE, Phillips J, Pitsava G, Pysar R, Rehm HL, Reuter CM, Revencu N, Riess A, Rius R, Rodan L, Roscioli T, Rosenfeld JA, Sachdev R, Simons C, Sisodiya SM, Snell P, Clair L, Stark Z, Tan TY, Tan NB, Temple SEL, Thorburn DR, Tifft CJ, Uebergang E, VanNoy GE, Vilain E, Viskochil DH, Wedd L, Wheeler MT, White SM, Wojcik M, Wolfe LA, Wolfenson Z, Xiao C, Zocche D, Rubenstein JL, Markenscoff-Papadimitriou E, Fica SM, Baralle D, Depienne C, MacArthur DG, Howson JMM, Sanders SJ, O’Donnell-Luria A, Whiffin N. De novo variants in the non-coding spliceosomal snRNA gene RNU4-2 are a frequent cause of syndromic neurodevelopmental disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.07.24305438. [PMID: 38645094 PMCID: PMC11030480 DOI: 10.1101/2024.04.07.24305438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes1. Increasingly, large genome-sequenced cohorts are improving our ability to discover new diagnoses in the non-coding genome. Here, we identify the non-coding RNA RNU4-2 as a novel syndromic NDD gene. RNU4-2 encodes the U4 small nuclear RNA (snRNA), which is a critical component of the U4/U6.U5 tri-snRNP complex of the major spliceosome2. We identify an 18 bp region of RNU4-2 mapping to two structural elements in the U4/U6 snRNA duplex (the T-loop and Stem III) that is severely depleted of variation in the general population, but in which we identify heterozygous variants in 119 individuals with NDD. The vast majority of individuals (77.3%) have the same highly recurrent single base-pair insertion (n.64_65insT). We estimate that variants in this region explain 0.41% of individuals with NDD. We demonstrate that RNU4-2 is highly expressed in the developing human brain, in contrast to its contiguous counterpart RNU4-1 and other U4 homologs, supporting RNU4-2's role as the primary U4 transcript in the brain. Overall, this work underscores the importance of non-coding genes in rare disorders. It will provide a diagnosis to thousands of individuals with NDD worldwide and pave the way for the development of effective treatments for these individuals.
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Affiliation(s)
- Yuyang Chen
- Big Data Institute, University of Oxford, Oxford, UK
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ruebena Dawes
- Big Data Institute, University of Oxford, Oxford, UK
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Hyung Chul Kim
- Big Data Institute, University of Oxford, Oxford, UK
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sarah L Stenton
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Alicia Ljungdahl
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, UK
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, USA
| | - Jenny Lord
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Vijay S Ganesh
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Jialan Ma
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexandra C Martin-Geary
- Big Data Institute, University of Oxford, Oxford, UK
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gabrielle Lemire
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Elston N D’Souza
- Big Data Institute, University of Oxford, Oxford, UK
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Shan Dong
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, UK
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, USA
| | - Jamie M Ellingford
- Genomics England, London, UK
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - David R Adams
- Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA
| | - Kirsten Allan
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
| | - Madhura Bakshi
- Department of Clinical Genetics, Liverpool Hospital, Sydney, NSW, Australia
| | - Erin E Baldwin
- Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Seth I Berger
- Center for Genetic Medicine Research, Children’s National Research Institute, Washington, DC, USA
- Division of Genetics and Metabolism, Children’s National Hospital, Washington, DC, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kimberly Chapman
- Division of Genetics and Metabolism, Children’s National Hospital, Washington, DC, USA
| | - Alison G Compton
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
- Murdoch Children’s Research Institute, Melbourne, VIC, Australia
| | - Chloe A Cunningham
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Precilla D’Souza
- Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA
| | - Emmanuèle C Délot
- Center for Genetic Medicine Research, Children’s National Research Institute, Washington, DC, USA
| | - Kerith-Rae Dias
- Neuroscience Research Australia, Sydney, NSW, Australia
- Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Ellen R Elias
- Department of Pediatrics, Children’s Hospital Colorado, Aurora, CO, USA
- University of Colorado School of Medicine, University of Colorado, Aurora, CO, USA
| | - Carey-Anne Evans
- Neuroscience Research Australia, Sydney, NSW, Australia
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Lisa Ewans
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- Centre for Clinical Genetics, Sydney Children’s Hospitals Network, Randwick, NSW, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Kimberly Ezell
- Division of Medical Genetics & Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jamie L Fraser
- Center for Genetic Medicine Research, Children’s National Research Institute, Washington, DC, USA
- Division of Genetics and Metabolism, Children’s National Hospital, Washington, DC, USA
| | - Lyndon Gallacher
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Casie A Genetti
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Christina L Grant
- Division of Genetics and Metabolism, Children’s National Hospital, Washington, DC, USA
| | - Tobias Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Rare Diseases Tübingen, University of Tübingen, Tübingen, Germany
| | - Alma Kuechler
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elsa Leitão
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Anna Le Fevre
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
| | - Richard J Leventer
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
- Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Royal Children’s Hospital, Melbourne, VIC, Australia
| | - Jan E Liebelt
- Paediatric and Reproductive Genetics Unit, South Australian Clinical Genetics Service, Women’s and Children’s Hospital, North Adelaide, SA, Australia
- Repromed, Dulwich, SA, Australia
| | - Paul J Lockhart
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
| | - Alan S Ma
- Department of Clinical Genetics, Sydney Children’s Hospitals Network Westmead, Sydney, NSW, Australia
- Specialty of Genomic Medicine, University of Sydney, Sydney, NSW, Australia
| | - Ellen F Macnamara
- Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA
| | - Taylor M Maurer
- GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Hector R Mendez
- GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine - Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen B Montgomery
- GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Department of Genetics, Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Marie-Cécile Nassogne
- Service de Neurologie Pédiatrique, Cliniques Universitaires Saint-Luc, UCLouvain, B-1200, Brussels, Belgium
- Institut des Maladies Rares, Cliniques Universitaires Saint-Luc, UCLouvain, B-1200, Brussels, Belgium
| | - Serena Neumann
- Division of Medical Genetics & Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Melanie O’Leary
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elizabeth E Palmer
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- Centre for Clinical Genetics, Sydney Children’s Hospitals Network, Randwick, NSW, Australia
| | - John Phillips
- Division of Medical Genetics & Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Georgia Pitsava
- Institute for Clinical and Translational Research, University of California, Irvine, CA, USA
| | - Ryan Pysar
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- Centre for Clinical Genetics, Sydney Children’s Hospitals Network, Randwick, NSW, Australia
- Department of Clinical Genetics, The Children’s Hospital at Westmead, Westmead, NSW, Australia
| | - Heidi L Rehm
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Chloe M Reuter
- GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine - Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicole Revencu
- Center for Human Genetics, Cliniques universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Angelika Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Rocio Rius
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Lance Rodan
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Tony Roscioli
- Neuroscience Research Australia, Sydney, NSW, Australia
- Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Rani Sachdev
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- Centre for Clinical Genetics, Sydney Children’s Hospitals Network, Randwick, NSW, Australia
| | - Cas Simons
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK
- UK and Chalfont Centre for Epilepsy, Bucks, UK
| | - Penny Snell
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
| | - Laura Clair
- Department of Clinical Genetics, Sydney Children’s Hospitals Network Westmead, Sydney, NSW, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Natalie B Tan
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
| | - Suzanna EL Temple
- Department of Clinical Genetics, Liverpool Hospital, Sydney, NSW, Australia
- School of Women’s and Childrens’s Health, University of New South Wales, Sydney, NSW, Australia
| | - David R Thorburn
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
- Murdoch Children’s Research Institute, Melbourne, VIC, Australia
| | - Cynthia J Tifft
- Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA
| | - Eloise Uebergang
- Murdoch Children’s Research Institute, Melbourne, VIC, Australia
| | - Grace E VanNoy
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric Vilain
- Institute for Clinical and Translational Science, University of California, Irvine, CA, USA
| | - David H Viskochil
- Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Laura Wedd
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Matthew T Wheeler
- GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine - Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Monica Wojcik
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Newborn Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lynne A Wolfe
- Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA
| | - Zoe Wolfenson
- Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA
| | - Changrui Xiao
- Department of Neurology, University of California, Irvine, CA, USA
| | - David Zocche
- North West Thames Regional Genetics Service, Northwick Park & St Mark’s Hospitals, London, UK
| | - John L Rubenstein
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, USA
| | - Eirene Markenscoff-Papadimitriou
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California, San Francisco, USA
| | | | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, Southampton, UK
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Joanna MM Howson
- Human Genetics Centre of Excellence, Novo Nordisk Research Centre, Oxford, UK
| | - Stephan J Sanders
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, UK
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, USA
| | - Anne O’Donnell-Luria
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicola Whiffin
- Big Data Institute, University of Oxford, Oxford, UK
- Centre for Human Genetics, University of Oxford, Oxford, UK
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Lee J, Wang ZM, Messi ML, Milligan C, Furdui CM, Delbono O. Sex differences in single neuron function and proteomics profiles examined by patch-clamp and mass spectrometry in the locus coeruleus of the adult mouse. Acta Physiol (Oxf) 2024; 240:e14123. [PMID: 38459766 PMCID: PMC11021178 DOI: 10.1111/apha.14123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/16/2024] [Accepted: 02/19/2024] [Indexed: 03/10/2024]
Abstract
AIMS This study aimed to characterize the properties of locus coeruleus (LC) noradrenergic neurons in male and female mice. We also sought to investigate sex-specific differences in membrane properties, action potential generation, and protein expression profiles to understand the mechanisms underlying neuronal excitability variations. METHODS Utilizing a genetic mouse model by crossing Dbhcre knock-in mice with tdTomato Ai14 transgenic mice, LC neurons were identified using fluorescence microscopy. Neuronal functional properties were assessed using patch-clamp recordings. Proteomic analyses of individual LC neuron soma was conducted using mass spectrometry to discern protein expression profiles. Data are available via ProteomeXchange with identifier PXD045844. RESULTS Female LC noradrenergic neurons displayed greater membrane capacitance than those in male mice. Male LC neurons demonstrated greater spontaneous and evoked action potential generation compared to females. Male LC neurons exhibited a lower rheobase and achieved higher peak frequencies with similar current injections. Proteomic analysis revealed differences in protein expression profiles between sexes, with male mice displaying a notably larger unique protein set compared to females. Notably, pathways pertinent to protein synthesis, degradation, and recycling, such as EIF2 and glucocorticoid receptor signaling, showed reduced expression in females. CONCLUSIONS Male LC noradrenergic neurons exhibit higher intrinsic excitability compared to those from females. The discernible sex-based differences in excitability could be ascribed to varying protein expression profiles, especially within pathways that regulate protein synthesis and degradation. This study lays the groundwork for future studies focusing on the interplay between proteomics and neuronal function examined in individual cells.
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Affiliation(s)
- Jingyun Lee
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157
| | - Zhong-Min Wang
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157
| | - María Laura Messi
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157
| | - Carol Milligan
- Department of Translational Neuroscience, Wake Forest University School of Medicine, Winston-Salem, NC 27157
| | - Cristina M. Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157
| | - Osvaldo Delbono
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157
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29
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Zhang Y, Gu S, Du J, Huang G, Shi J, Lu X, Wang J, Yang W, Guo X, Zhao C. Plant microphenotype: from innovative imaging to computational analysis. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:802-818. [PMID: 38217351 PMCID: PMC10955502 DOI: 10.1111/pbi.14244] [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: 03/10/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 01/15/2024]
Abstract
The microphenotype plays a key role in bridging the gap between the genotype and the complex macro phenotype. In this article, we review the advances in data acquisition and the intelligent analysis of plant microphenotyping and present applications of microphenotyping in plant science over the past two decades. We then point out several challenges in this field and suggest that cross-scale image acquisition strategies, powerful artificial intelligence algorithms, advanced genetic analysis, and computational phenotyping need to be established and performed to better understand interactions among genotype, environment, and management. Microphenotyping has entered the era of Microphenotyping 3.0 and will largely advance functional genomics and plant science.
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Affiliation(s)
- Ying Zhang
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shenghao Gu
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jianjun Du
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Guanmin Huang
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jiawei Shi
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xianju Lu
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinglu Wang
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xinyu Guo
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chunjiang Zhao
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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30
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Liu X, Zhang H, Zeng Y, Zhu X, Zhu L, Fu J. DRANetSplicer: A Splice Site Prediction Model Based on Deep Residual Attention Networks. Genes (Basel) 2024; 15:404. [PMID: 38674339 PMCID: PMC11048956 DOI: 10.3390/genes15040404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
The precise identification of splice sites is essential for unraveling the structure and function of genes, constituting a pivotal step in the gene annotation process. In this study, we developed a novel deep learning model, DRANetSplicer, that integrates residual learning and attention mechanisms for enhanced accuracy in capturing the intricate features of splice sites. We constructed multiple datasets using the most recent versions of genomic data from three different organisms, Oryza sativa japonica, Arabidopsis thaliana and Homo sapiens. This approach allows us to train models with a richer set of high-quality data. DRANetSplicer outperformed benchmark methods on donor and acceptor splice site datasets, achieving an average accuracy of (96.57%, 95.82%) across the three organisms. Comparative analyses with benchmark methods, including SpliceFinder, Splice2Deep, Deep Splicer, EnsembleSplice, and DNABERT, revealed DRANetSplicer's superior predictive performance, resulting in at least a (4.2%, 11.6%) relative reduction in average error rate. We utilized the DRANetSplicer model trained on O. sativa japonica data to predict splice sites in A. thaliana, achieving accuracies for donor and acceptor sites of (94.89%, 94.25%). These results indicate that DRANetSplicer possesses excellent cross-organism predictive capabilities, with its performance in cross-organism predictions even surpassing that of benchmark methods in non-cross-organism predictions. Cross-organism validation showcased DRANetSplicer's excellence in predicting splice sites across similar organisms, supporting its applicability in gene annotation for understudied organisms. We employed multiple methods to visualize the decision-making process of the model. The visualization results indicate that DRANetSplicer can learn and interpret well-known biological features, further validating its overall performance. Our study systematically examined and confirmed the predictive ability of DRANetSplicer from various levels and perspectives, indicating that its practical application in gene annotation is justified.
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Affiliation(s)
- Xueyan Liu
- College of Information and Intelligence, Hunan Agricultural University, Changsha 410128, China; (X.L.); (X.Z.); (L.Z.); (J.F.)
| | - Hongyan Zhang
- College of Information and Intelligence, Hunan Agricultural University, Changsha 410128, China; (X.L.); (X.Z.); (L.Z.); (J.F.)
| | - Ying Zeng
- School of Computer and Communication, Hunan Institute of Engineering, Xiangtan 411104, China;
| | - Xinghui Zhu
- College of Information and Intelligence, Hunan Agricultural University, Changsha 410128, China; (X.L.); (X.Z.); (L.Z.); (J.F.)
| | - Lei Zhu
- College of Information and Intelligence, Hunan Agricultural University, Changsha 410128, China; (X.L.); (X.Z.); (L.Z.); (J.F.)
| | - Jiahui Fu
- College of Information and Intelligence, Hunan Agricultural University, Changsha 410128, China; (X.L.); (X.Z.); (L.Z.); (J.F.)
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31
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Da Cunha D, Miro J, Van Goethem C, Notarnicola C, Hugon G, Carnac G, Cossée M, Koenig M, Tuffery-Giraud S. The exon junction complex is required for DMD gene splicing fidelity and myogenic differentiation. Cell Mol Life Sci 2024; 81:150. [PMID: 38512499 PMCID: PMC10957711 DOI: 10.1007/s00018-024-05188-1] [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: 09/10/2023] [Revised: 02/14/2024] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
Deposition of the exon junction complex (EJC) upstream of exon-exon junctions helps maintain transcriptome integrity by preventing spurious re-splicing events in already spliced mRNAs. Here we investigate the importance of EJC for the correct splicing of the 2.2-megabase-long human DMD pre-mRNA, which encodes dystrophin, an essential protein involved in cytoskeletal organization and cell signaling. Using targeted RNA-seq, we show that knock-down of the eIF4A3 and Y14 core components of EJC in a human muscle cell line causes an accumulation of mis-splicing events clustered towards the 3' end of the DMD transcript (Dp427m). This deregulation is conserved in the short Dp71 isoform expressed ubiquitously except in adult skeletal muscle and is rescued with wild-type eIF4A3 and Y14 proteins but not with an EJC assembly-defective mutant eIF4A3. MLN51 protein and EJC-associated ASAP/PSAP complexes independently modulate the inclusion of the regulated exons 71 and 78. Our data confirm the protective role of EJC in maintaining splicing fidelity, which in the DMD gene is necessary to preserve the function of the critical C-terminal protein-protein interaction domain of dystrophin present in all tissue-specific isoforms. Given the role of the EJC in maintaining the integrity of dystrophin, we asked whether the EJC could also be involved in the regulation of a mechanism as complex as skeletal muscle differentiation. We found that eIF4A3 knockdown impairs myogenic differentiation by blocking myotube formation. Collectively, our data provide new insights into the functional roles of EJC in human skeletal muscle.
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Affiliation(s)
- Dylan Da Cunha
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Julie Miro
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Charles Van Goethem
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France
- Montpellier BioInformatique Pour Le Diagnostic Clinique (MOBIDIC), Plateau de Médecine Moléculaire Et Génomique (PMMG), CHU Montpellier, 34295, Montpellier, France
| | | | - Gérald Hugon
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Gilles Carnac
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Mireille Cossée
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France
| | - Michel Koenig
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France
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32
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Osterhoudt K, Bagno O, Katzman S, Zahler AM. Spliceosomal helicases DDX41/SACY-1 and PRP22/MOG-5 both contribute to proofreading against proximal 3' splice site usage. RNA (NEW YORK, N.Y.) 2024; 30:404-417. [PMID: 38282418 PMCID: PMC10946429 DOI: 10.1261/rna.079888.123] [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: 11/07/2023] [Accepted: 01/12/2024] [Indexed: 01/30/2024]
Abstract
RNA helicases drive necessary rearrangements and ensure fidelity during the pre-mRNA splicing cycle. DEAD-box helicase DDX41 has been linked to human disease and has recently been shown to interact with DEAH-box helicase PRP22 in the spliceosomal C* complex, yet its function in splicing remains unknown. Depletion of DDX41 homolog SACY-1 from somatic cells has been previously shown to lead to changes in alternative 3' splice site (3'ss) usage. Here, we show by transcriptomic analysis of published and novel data sets that SACY-1 perturbation causes a previously unreported pattern in alternative 3' splicing in introns with pairs of 3' splice sites ≤18 nt away from each other. We find that both SACY-1 depletion and the allele sacy-1(G533R) lead to a striking unidirectional increase in the usage of the proximal (upstream) 3'ss. We previously discovered a similar alternative splicing pattern between germline tissue and somatic tissue, in which there is a unidirectional increase in proximal 3'ss usage in the germline for ∼200 events; many of the somatic SACY-1 alternative 3' splicing events overlap with these developmentally regulated events. We generated targeted mutant alleles of the Caenorhabditis elegans homolog of PRP22, mog-5, in the region of MOG-5 that is predicted to interact with SACY-1 based on the human C* structure. These viable alleles, and a mimic of the myelodysplastic syndrome-associated allele DDX41(R525H), all promote the usage of proximal alternative adjacent 3' splice sites. We show that PRP22/MOG-5 and DDX41/SACY-1 have overlapping roles in proofreading the 3'ss.
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Affiliation(s)
- Kenneth Osterhoudt
- Department of Molecular Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Orazio Bagno
- Department of Molecular Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Sol Katzman
- UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Alan M Zahler
- Department of Molecular Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
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33
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Cui H, Shi Q, Macarios CM, Schimmel P. Metabolic regulation of mRNA splicing. Trends Cell Biol 2024:S0962-8924(24)00025-4. [PMID: 38431493 DOI: 10.1016/j.tcb.2024.02.002] [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: 11/07/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 03/05/2024]
Abstract
Alternative mRNA splicing enables the diversification of the proteome from a static genome and confers plasticity and adaptiveness on cells. Although this is often explored in development, where hard-wired programs drive the differentiation and specialization, alternative mRNA splicing also offers a way for cells to react to sudden changes in outside stimuli such as small-molecule metabolites. Fluctuations in metabolite levels and availability in particular convey crucial information to which cells react and adapt. We summarize and highlight findings surrounding the metabolic regulation of mRNA splicing. We discuss the principles underlying the biochemistry and biophysical properties of mRNA splicing, and propose how these could intersect with metabolite levels. Further, we present examples in which metabolites directly influence RNA-binding proteins and splicing factors. We also discuss the interplay between alternative mRNA splicing and metabolite-responsive signaling pathways. We hope to inspire future research to obtain a holistic picture of alternative mRNA splicing in response to metabolic cues.
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Affiliation(s)
- Haissi Cui
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
| | - Qingyu Shi
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | | | - Paul Schimmel
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA.
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34
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Kienbeck K, Malfertheiner L, Zelger-Paulus S, Johannsen S, von Mering C, Sigel RKO. Identification of HDV-like theta ribozymes involved in tRNA-based recoding of gut bacteriophages. Nat Commun 2024; 15:1559. [PMID: 38378708 PMCID: PMC10879173 DOI: 10.1038/s41467-024-45653-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: 07/25/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
Trillions of microorganisms, collectively known as the microbiome, inhabit our bodies with the gut microbiome being of particular interest in biomedical research. Bacteriophages, the dominant virome constituents, can utilize suppressor tRNAs to switch to alternative genetic codes (e.g., the UAG stop-codon is reassigned to glutamine) while infecting hosts with the standard bacterial code. However, what triggers this switch and how the bacteriophage manipulates its host is poorly understood. Here, we report the discovery of a subgroup of minimal hepatitis delta virus (HDV)-like ribozymes - theta ribozymes - potentially involved in the code switch leading to the expression of recoded lysis and structural phage genes. We demonstrate their HDV-like self-scission behavior in vitro and find them in an unreported context often located with their cleavage site adjacent to tRNAs, indicating a role in viral tRNA maturation and/or regulation. Every fifth associated tRNA is a suppressor tRNA, further strengthening our hypothesis. The vast abundance of tRNA-associated theta ribozymes - we provide 1753 unique examples - highlights the importance of small ribozymes as an alternative to large enzymes that usually process tRNA 3'-ends. Our discovery expands the short list of biological functions of small HDV-like ribozymes and introduces a previously unknown player likely involved in the code switch of certain recoded gut bacteriophages.
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Affiliation(s)
- Kasimir Kienbeck
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, CH-8057, Switzerland
| | | | - Silke Johannsen
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, CH-8057, Switzerland.
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland.
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35
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Wong J, Yellamaty R, Gallante C, Lawrence E, Martelly W, Sharma S. Examining the capacity of human U1 snRNA variants to facilitate pre-mRNA splicing. RNA (NEW YORK, N.Y.) 2024; 30:271-280. [PMID: 38164604 PMCID: PMC10870369 DOI: 10.1261/rna.079892.123] [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: 11/16/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
The human U1 snRNA is encoded by a multigene family consisting of transcribed variants and defective pseudogenes. Many variant U1 (vU1) snRNAs have been demonstrated to not only be transcribed but also processed by the addition of a trimethylated guanosine cap, packaged into snRNPs, and assembled into spliceosomes; however, their capacity to facilitate pre-mRNA splicing has, so far, not been tested. A recent systematic analysis of the human snRNA genes identified 178 U1 snRNA genes that are present in the genome as either tandem arrays or single genes on multiple chromosomes. Of these, 15 were found to be expressed in human tissues and cell lines, although at significantly low levels from their endogenous loci, <0.001% of the canonical U1 snRNA. In this study, we found that placing the variants in the context of the regulatory elements of the RNU1-1 gene improves the expression of many variants to levels comparable to the canonical U1 snRNA. Application of a previously established HeLa cell-based minigene reporter assay to examine the capacity of the vU1 snRNAs to support pre-mRNA splicing revealed that even though the exogenously expressed variant snRNAs were enriched in the nucleus, only a few had a measurable effect on splicing.
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Affiliation(s)
- Jason Wong
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - Ryan Yellamaty
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - Christina Gallante
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - Ethan Lawrence
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - William Martelly
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - Shalini Sharma
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
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36
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Rinaldi S, Moroni E, Rozza R, Magistrato A. Frontiers and Challenges of Computing ncRNAs Biogenesis, Function and Modulation. J Chem Theory Comput 2024; 20:993-1018. [PMID: 38287883 DOI: 10.1021/acs.jctc.3c01239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Non-coding RNAs (ncRNAs), generated from nonprotein coding DNA sequences, constitute 98-99% of the human genome. Non-coding RNAs encompass diverse functional classes, including microRNAs, small interfering RNAs, PIWI-interacting RNAs, small nuclear RNAs, small nucleolar RNAs, and long non-coding RNAs. With critical involvement in gene expression and regulation across various biological and physiopathological contexts, such as neuronal disorders, immune responses, cardiovascular diseases, and cancer, non-coding RNAs are emerging as disease biomarkers and therapeutic targets. In this review, after providing an overview of non-coding RNAs' role in cell homeostasis, we illustrate the potential and the challenges of state-of-the-art computational methods exploited to study non-coding RNAs biogenesis, function, and modulation. This can be done by directly targeting them with small molecules or by altering their expression by targeting the cellular engines underlying their biosynthesis. Drawing from applications, also taken from our work, we showcase the significance and role of computer simulations in uncovering fundamental facets of ncRNA mechanisms and modulation. This information may set the basis to advance gene modulation tools and therapeutic strategies to address unmet medical needs.
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Affiliation(s)
- Silvia Rinaldi
- National Research Council of Italy (CNR) - Institute of Chemistry of OrganoMetallic Compounds (ICCOM), c/o Area di Ricerca CNR di Firenze Via Madonna del Piano 10, 50019 Sesto Fiorentino, Florence, Italy
| | - Elisabetta Moroni
- National Research Council of Italy (CNR) - Institute of Chemical Sciences and Technologies (SCITEC), via Mario Bianco 9, 20131 Milano, Italy
| | - Riccardo Rozza
- National Research Council of Italy (CNR) - Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
| | - Alessandra Magistrato
- National Research Council of Italy (CNR) - Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
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37
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Carrocci TJ, DeMario S, He K, Zeps NJ, Harkner CT, Chanfreau G, Hoskins AA. Functional Analysis of the Zinc Finger Modules of the S. cerevisiae Splicing Factor Luc7. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578419. [PMID: 38352541 PMCID: PMC10862913 DOI: 10.1101/2024.02.04.578419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Identification of splice sites is a critical step in pre-mRNA splicing since definition of the exon/intron boundaries controls what nucleotides are incorporated into mature mRNAs. The intron boundary with the upstream exon is initially identified through interactions with the U1 snRNP. This involves both base pairing between the U1 snRNA and the pre-mRNA as well as snRNP proteins interacting with the 5' splice site/snRNA duplex. In yeast, this duplex is buttressed by two conserved protein factors, Yhc1 and Luc7. Luc7 has three human paralogs (LUC7L, LUC7L2, and LUC7L3) which play roles in alternative splicing. What domains of these paralogs promote splicing at particular sites is not yet clear. Here, we humanized the zinc finger domains of the yeast Luc7 protein in order to understand their roles in splice site selection using reporter assays, transcriptome analysis, and genetic interactions. While we were unable to determine a function for the first zinc finger domain, humanization of the second zinc finger domain to mirror that found in LUC7L or LUC7L2 resulted in altered usage of nonconsensus 5' splice sites. In contrast, the corresponding zinc finger domain of LUC7L3 could not support yeast viability. Further, humanization of Luc7 can suppress mutation of the ATPase Prp28, which is involved in U1 release and exchange for U6 at the 5' splice site. Our work reveals a role for the second zinc finger of Luc7 in splice site selection and suggests that different zinc finger domains may have different ATPase requirements for release by Prp28.
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Affiliation(s)
- Tucker J. Carrocci
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Samuel DeMario
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kevin He
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Natalie J. Zeps
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Cade T. Harkner
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Guillaume Chanfreau
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aaron A. Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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38
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Tao Y, Zhang Q, Wang H, Yang X, Mu H. Alternative splicing and related RNA binding proteins in human health and disease. Signal Transduct Target Ther 2024; 9:26. [PMID: 38302461 PMCID: PMC10835012 DOI: 10.1038/s41392-024-01734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Alternative splicing (AS) serves as a pivotal mechanism in transcriptional regulation, engendering transcript diversity, and modifications in protein structure and functionality. Across varying tissues, developmental stages, or under specific conditions, AS gives rise to distinct splice isoforms. This implies that these isoforms possess unique temporal and spatial roles, thereby associating AS with standard biological activities and diseases. Among these, AS-related RNA-binding proteins (RBPs) play an instrumental role in regulating alternative splicing events. Under physiological conditions, the diversity of proteins mediated by AS influences the structure, function, interaction, and localization of proteins, thereby participating in the differentiation and development of an array of tissues and organs. Under pathological conditions, alterations in AS are linked with various diseases, particularly cancer. These changes can lead to modifications in gene splicing patterns, culminating in changes or loss of protein functionality. For instance, in cancer, abnormalities in AS and RBPs may result in aberrant expression of cancer-associated genes, thereby promoting the onset and progression of tumors. AS and RBPs are also associated with numerous neurodegenerative diseases and autoimmune diseases. Consequently, the study of AS across different tissues holds significant value. This review provides a detailed account of the recent advancements in the study of alternative splicing and AS-related RNA-binding proteins in tissue development and diseases, which aids in deepening the understanding of gene expression complexity and offers new insights and methodologies for precision medicine.
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Affiliation(s)
- Yining Tao
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Haoyu Wang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Xiyu Yang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Haoran Mu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
- Shanghai Bone Tumor Institution, 200000, Shanghai, China.
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Best C, Mennigen JA, Gilmour KM. Exploring transcriptional and post-transcriptional epigenetic regulation of crf and 11βhsd2 in rainbow trout brain during chronic social stress. Comp Biochem Physiol A Mol Integr Physiol 2024; 288:111557. [PMID: 38043640 DOI: 10.1016/j.cbpa.2023.111557] [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: 10/15/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
Using dominance hierarchies in juvenile rainbow trout (Oncorhynchus mykiss) as a model of chronic social stress in fish, we explored whether epigenetic transcriptional and post-transcriptional mechanisms are involved in the gene expression of corticotropin-releasing factor (crf) and 11β-hydroxysteroid dehydrogenase (11βhsd2), key factors involved in the regulation of the endocrine stress axis response. In juvenile rainbow trout pairs, subordinate individuals display sustained elevation of circulating cortisol concentrations. Cortisol production is controlled by the hypothalamic-pituitary-interrenal (HPI) axis in fish and initiated by CRF release from the preoptic area (POA). Given that crf is modulated during chronic social stress, and that such stress has been implicated in the epigenetic regulation of crf in other taxa, we probed a role for epigenetic regulation of crf transcript abundance in chronically stressed rainbow trout. We also investigated the regulation of the cortisol-metabolising enzyme 11βhsd2 in the POA, which is upregulated in subordinates. The potential involvement of DNA methylation and microRNAs (miRNAs) in the regulation of crf transcript abundance was investigated during social stress in the POA of fish, as was the potential involvement of miRNAs in 11βhsd2 regulation. Although transcript abundances of crf were elevated in subordinate fish after 4 days, DNA methylation profiles within putative promoter sequences upstream of the crf gene were not significantly affected by chronic stress. An inverse relationship between crf and its predicted posttranscriptional regulator miR-103a-3p in the POA suggests that miRNAs may be involved in mediating the effects of chronic social stress on key components of the endocrine stress axis.
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Affiliation(s)
- Carol Best
- Department of Biology, University of Ottawa, Ottawa, ON, Canada.
| | - Jan A Mennigen
- Department of Biology, University of Ottawa, Ottawa, ON, Canada.
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Hunter O, Talkish J, Quick-Cleveland J, Igel H, Tan A, Kuersten S, Katzman S, Donohue JP, S Jurica M, Ares M. Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain. RNA (NEW YORK, N.Y.) 2024; 30:149-170. [PMID: 38071476 PMCID: PMC10798247 DOI: 10.1261/rna.079866.123] [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: 10/05/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023]
Abstract
Intron branchpoint (BP) recognition by the U2 snRNP is a critical step of splicing, vulnerable to recurrent cancer mutations and bacterial natural product inhibitors. The BP binds a conserved pocket in the SF3B1 (human) or Hsh155 (yeast) U2 snRNP protein. Amino acids that line this pocket affect the binding of splicing inhibitors like Pladienolide-B (Plad-B), such that organisms differ in their sensitivity. To study the mechanism of splicing inhibitor action in a simplified system, we modified the naturally Plad-B resistant yeast Saccharomyces cerevisiae by changing 14 amino acids in the Hsh155 BP pocket to those from human. This humanized yeast grows normally, and splicing is largely unaffected by the mutation. Splicing is inhibited within minutes after the addition of Plad-B, and different introns appear inhibited to different extents. Intron-specific inhibition differences are also observed during cotranscriptional splicing in Plad-B using single-molecule intron tracking to minimize gene-specific transcription and decay rates that cloud estimates of inhibition by standard RNA-seq. Comparison of Plad-B intron sensitivities to those of the structurally distinct inhibitor Thailanstatin-A reveals intron-specific differences in sensitivity to different compounds. This work exposes a complex relationship between the binding of different members of this class of inhibitors to the spliceosome and intron-specific rates of BP recognition and catalysis. Introns with variant BP sequences seem particularly sensitive, echoing observations from mammalian cells, where monitoring individual introns is complicated by multi-intron gene architecture and alternative splicing. The compact yeast system may hasten the characterization of splicing inhibitors, accelerating improvements in selectivity and therapeutic efficacy.
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Affiliation(s)
- Oarteze Hunter
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Jason Talkish
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Jen Quick-Cleveland
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Haller Igel
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Asako Tan
- Illumina, Inc., Madison, Wisconsin 53719, USA
| | | | - Sol Katzman
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - John Paul Donohue
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Melissa S Jurica
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Manuel Ares
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
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Shilo A, Pegoraro G, Misteli T. High-Throughput RNA-HCR-FISH Detection of Endogenous Pre-mRNA Splice Variants. Methods Mol Biol 2024; 2784:133-146. [PMID: 38502483 DOI: 10.1007/978-1-0716-3766-1_9] [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] [Indexed: 03/21/2024]
Abstract
RNA-fluorescence in situ hybridization (RNA-FISH) is an essential and widely used tool for visualizing RNA molecules in intact cells. Recent advances have increased RNA-FISH sensitivity, signal detection efficiency, and throughput. However, detection of endogenous mRNA splice variants has been challenging due to the limits of visualization of RNA-FISH fluorescence signals and due to the limited number of RNA-FISH probes per target. HiFENS (high-throughput FISH detection of endogenous pre-mRNA splicing isoforms) is a method that enables visualization and relative quantification of mRNA splice variants at single-cell resolution in an automated high-throughput manner. HiFENS incorporates HCR (hybridization chain reaction) signal amplification strategies to enhance the fluorescence signal generated by low abundance transcripts or a small number of FISH probes targeting short stretches of RNA, such as single exons. The technique offers a significant advance in high-throughput FISH-based RNA detection and provides a powerful tool that can be used as a readout in functional genomics screens to discover and dissect cellular pathways regulating gene expression and alternative pre-mRNA splicing events.
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Affiliation(s)
- Asaf Shilo
- Cell Biology of Genomes, Center for Cancer Research (CCR), National Cancer Institute, NIH, Bethesda, MD, USA
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility (HiTIF), Center for Cancer Research (CCR), National Cancer Institute, NIH, Bethesda, MD, USA
| | - Tom Misteli
- Cell Biology of Genomes, Center for Cancer Research (CCR), National Cancer Institute, NIH, Bethesda, MD, USA.
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Abrhámová K, Groušlová M, Valentová A, Hao X, Liu B, Převorovský M, Gahura O, Půta F, Sunnerhagen P, Folk P. Truncating the spliceosomal 'rope protein' Prp45 results in Htz1 dependent phenotypes. RNA Biol 2024; 21:1-17. [PMID: 38711165 PMCID: PMC11085953 DOI: 10.1080/15476286.2024.2348896] [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] [Accepted: 04/24/2024] [Indexed: 05/08/2024] Open
Abstract
Spliceosome assembly contributes an important but incompletely understood aspect of splicing regulation. Prp45 is a yeast splicing factor which runs as an extended fold through the spliceosome, and which may be important for bringing its components together. We performed a whole genome analysis of the genetic interaction network of the truncated allele of PRP45 (prp45(1-169)) using synthetic genetic array technology and found chromatin remodellers and modifiers as an enriched category. In agreement with related studies, H2A.Z-encoding HTZ1, and the components of SWR1, INO80, and SAGA complexes represented prominent interactors, with htz1 conferring the strongest growth defect. Because the truncation of Prp45 disproportionately affected low copy number transcripts of intron-containing genes, we prepared strains carrying intronless versions of SRB2, VPS75, or HRB1, the most affected cases with transcription-related function. Intron removal from SRB2, but not from the other genes, partly repaired some but not all the growth phenotypes identified in the genetic screen. The interaction of prp45(1-169) and htz1Δ was detectable even in cells with SRB2 intron deleted (srb2Δi). The less truncated variant, prp45(1-330), had a synthetic growth defect with htz1Δ at 16°C, which also persisted in the srb2Δi background. Moreover, htz1Δ enhanced prp45(1-330) dependent pre-mRNA hyper-accumulation of both high and low efficiency splicers, genes ECM33 and COF1, respectively. We conclude that while the expression defects of low expression intron-containing genes contribute to the genetic interactome of prp45(1-169), the genetic interactions between prp45 and htz1 alleles demonstrate the sensitivity of spliceosome assembly, delayed in prp45(1-169), to the chromatin environment.
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Affiliation(s)
- Kateřina Abrhámová
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Martina Groušlová
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Anna Valentová
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Xinxin Hao
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Beidong Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - František Půta
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Petr Folk
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
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Polvèche H, Valat J, Fontrodona N, Lapendry A, Clerc V, Janczarski S, Mortreux F, Auboeuf D, Bourgeois CF. SplicingLore: a web resource for studying the regulation of cassette exons by human splicing factors. Database (Oxford) 2023; 2023:baad091. [PMID: 38128543 PMCID: PMC10735282 DOI: 10.1093/database/baad091] [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: 07/09/2023] [Revised: 11/06/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
One challenge faced by scientists from the alternative RNA splicing field is to decode the cooperative or antagonistic effects of splicing factors (SFs) to understand and eventually predict splicing outcomes on a genome-wide scale. In this manuscript, we introduce SplicingLore, an open-access database and web resource that help to fill this gap in a straightforward manner. The database contains a collection of RNA-sequencing-derived lists of alternative exons regulated by a total of 75 different SFs. All datasets were processed in a standardized manner, ensuring valid comparisons and correlation analyses. The user can easily retrieve a factor-specific set of differentially included exons from the database or provide a list of exons and search which SF(s) control(s) their inclusion. Our simple workflow is fast and easy to run, and it ensures a reliable calculation of correlation scores between the tested datasets. As a proof of concept, we predicted and experimentally validated a novel functional cooperation between the RNA helicases DDX17 and DDX5 and the heterogeneous nuclear ribonucleoprotein C (HNRNPC) protein. SplicingLore is available at https://splicinglore.ens-lyon.fr/. Database URL: https://splicinglore.ens-lyon.fr/.
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Affiliation(s)
| | - Jessica Valat
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Nicolas Fontrodona
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Audrey Lapendry
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Valentine Clerc
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Stéphane Janczarski
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
| | - Franck Mortreux
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Didier Auboeuf
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Cyril F Bourgeois
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
- CECS/AFM, I-STEM, 28 rue Henri Desbrueres, Corbeil-Essonnes F-91100, France
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Perchlik M, Sasse A, Mostafavi S, Fields S, Cuperus JT. Impact on splicing in Saccharomyces cerevisiae of random 50-base sequences inserted into an intron. RNA (NEW YORK, N.Y.) 2023; 30:52-67. [PMID: 37879864 PMCID: PMC10726166 DOI: 10.1261/rna.079752.123] [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: 06/21/2023] [Accepted: 10/18/2023] [Indexed: 10/27/2023]
Abstract
Intron splicing is a key regulatory step in gene expression in eukaryotes. Three sequence elements required for splicing-5' and 3' splice sites and a branchpoint-are especially well-characterized in Saccharomyces cerevisiae, but our understanding of additional intron features that impact splicing in this organism is incomplete, due largely to its small number of introns. To overcome this limitation, we constructed a library in S. cerevisiae of random 50-nt (N50) elements individually inserted into the intron of a reporter gene and quantified canonical splicing and the use of cryptic splice sites by sequencing analysis. More than 70% of approximately 140,000 N50 elements reduced splicing by at least 20%. N50 features, including higher GC content, presence of GU repeats, and stronger predicted secondary structure of its pre-mRNA, correlated with reduced splicing efficiency. A likely basis for the reduced splicing of such a large proportion of variants is the formation of RNA structures that pair N50 bases-such as the GU repeats-with other bases specifically within the reporter pre-mRNA analyzed. However, multiple models were unable to explain more than a small fraction of the variance in splicing efficiency across the library, suggesting that complex nonlinear interactions in RNA structures are not accurately captured by RNA structure prediction methods. Our results imply that the specific context of a pre-mRNA may determine the bases allowable in an intron to prevent secondary structures that reduce splicing. This large data set can serve as a resource for further exploration of splicing mechanisms.
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Affiliation(s)
- Molly Perchlik
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Alexander Sasse
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Sara Mostafavi
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
- Department of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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Lee S, Aubee JI, Lai EC. Regulation of alternative splicing and polyadenylation in neurons. Life Sci Alliance 2023; 6:e202302000. [PMID: 37793776 PMCID: PMC10551640 DOI: 10.26508/lsa.202302000] [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: 02/19/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
Cell-type-specific gene expression is a fundamental feature of multicellular organisms and is achieved by combinations of regulatory strategies. Although cell-restricted transcription is perhaps the most widely studied mechanism, co-transcriptional and post-transcriptional processes are also central to the spatiotemporal control of gene functions. One general category of expression control involves the generation of multiple transcript isoforms from an individual gene, whose balance and cell specificity are frequently tightly regulated via diverse strategies. The nervous system makes particularly extensive use of cell-specific isoforms, specializing the neural function of genes that are expressed more broadly. Here, we review regulatory strategies and RNA-binding proteins that direct neural-specific isoform processing. These include various classes of alternative splicing and alternative polyadenylation events, both of which broadly diversify the neural transcriptome. Importantly, global alterations of splicing and alternative polyadenylation are characteristic of many neural pathologies, and recent genetic studies demonstrate how misregulation of individual neural isoforms can directly cause mutant phenotypes.
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Affiliation(s)
- Seungjae Lee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Joseph I Aubee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
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46
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García Morato J, Gloeckner CJ, Kahle PJ. Proteomics elucidating physiological and pathological functions of TDP-43. Proteomics 2023; 23:e2200410. [PMID: 37671599 DOI: 10.1002/pmic.202200410] [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: 05/19/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 09/07/2023]
Abstract
Trans-activation response DNA binding protein of 43 kDa (TDP-43) regulates a great variety of cellular processes in the nucleus and cytosol. In addition, a defined subset of neurodegenerative diseases is characterized by nuclear depletion of TDP-43 as well as cytosolic mislocalization and aggregation. To perform its diverse functions TDP-43 can associate with different ribonucleoprotein complexes. Combined with transcriptomics, MS interactome studies have unveiled associations between TDP-43 and the spliceosome machinery, polysomes and RNA granules. Moreover, the highly dynamic, low-valency interactions regulated by its low-complexity domain calls for innovative proximity labeling methodologies. In addition to protein partners, the analysis of post-translational modifications showed that they may play a role in the nucleocytoplasmic shuttling, RNA binding, liquid-liquid phase separation and protein aggregation of TDP-43. Here we review the various TDP-43 ribonucleoprotein complexes characterized so far, how they contribute to the diverse functions of TDP-43, and roles of post-translational modifications. Further understanding of the fluid dynamic properties of TDP-43 in ribonucleoprotein complexes, RNA granules, and self-assemblies will advance the understanding of RNA processing in cells and perhaps help to develop novel therapeutic approaches for TDPopathies.
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Affiliation(s)
- Jorge García Morato
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, German Center of Neurodegenerative Diseases and Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Christian Johannes Gloeckner
- Research Group Functional Neuroproteomics, German Center of Neurodegenerative Diseases, Tübingen, Germany
- Core Facility for Medical Bioanalytics, Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Philipp J Kahle
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, German Center of Neurodegenerative Diseases and Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Department of Biochemistry, University of Tübingen, Tübingen, Germany
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47
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Jobbins AM, Yu S, Paterson HAB, Maude H, Kefala-Stavridi A, Speck C, Cebola I, Vernia S. Pre-RNA splicing in metabolic homeostasis and liver disease. Trends Endocrinol Metab 2023; 34:823-837. [PMID: 37673766 DOI: 10.1016/j.tem.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023]
Abstract
The liver plays a key role in sensing nutritional and hormonal inputs to maintain metabolic homeostasis. Recent studies into pre-mRNA splicing and alternative splicing (AS) and their effects on gene expression have revealed considerable transcriptional complexity in the liver, both in health and disease. While the contribution of these mechanisms to cell and tissue identity is widely accepted, their role in physiological and pathological contexts within tissues is just beginning to be appreciated. In this review, we showcase recent studies on the splicing and AS of key genes in metabolic pathways in the liver, the effect of metabolic signals on the spliceosome, and therapeutic intervention points based on RNA splicing.
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Affiliation(s)
- Andrew M Jobbins
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Sijia Yu
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Helen A B Paterson
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Hannah Maude
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Antonia Kefala-Stavridi
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Christian Speck
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Santiago Vernia
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
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Yandrapally S, Sarkar S, Banerjee S. HIV-1 Tat commandeers nuclear export of Rev-viral RNA complex by controlling hnRNPA2-mediated splicing. J Virol 2023; 97:e0104423. [PMID: 37905837 PMCID: PMC10688328 DOI: 10.1128/jvi.01044-23] [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: 07/13/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE HIV-infected host cells impose varied degrees of regulation on viral replication, from very high to abortive. Proliferation of HIV in astrocytes is limited when compared to immune cells, such as CD4+ T lymphocytes. Understanding such differential regulation is one of the key questions in the field as these cells permit HIV persistence and rebound viremia, challenging HIV treatment and clinical cure. This study focuses on understanding the molecular mechanism behind such cell-specific disparities. We show that one of the key mechanisms is the regulation of heterogenous nuclear ribonucleoprotein A2, a host factor involved in alternative splicing and RNA processing, by HIV-1 Tat in CD4+ T lymphocytes, not observed in astrocytes. This regulation causes an increase in the levels of unspliced/partially spliced viral RNA and nuclear export of Rev-RNA complexes which results in high viral propagation in CD4+ T lymphocytes. The study reveals a new mechanism imposed by HIV on host cells that determines the fate of infection.
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Affiliation(s)
- Sriram Yandrapally
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Satarupa Sarkar
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Sharmistha Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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Asada R, Dominguez A, Montpetit B. Single-molecule quantitation of RNA-binding protein occupancy and stoichiometry defines a role for Yra1 (Aly/REF) in nuclear mRNP organization. Cell Rep 2023; 42:113415. [PMID: 37963019 PMCID: PMC10841842 DOI: 10.1016/j.celrep.2023.113415] [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: 03/27/2023] [Revised: 10/09/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023] Open
Abstract
RNA-binding proteins (RBPs) interact with mRNA to form supramolecular complexes called messenger ribonucleoprotein (mRNP) particles. These dynamic assemblies direct and regulate individual steps of gene expression; however, their composition and functional importance remain largely unknown. Here, we develop a total internal reflection fluorescence-based single-molecule imaging assay to investigate stoichiometry and co-occupancy of 15 RBPs within mRNPs from Saccharomyces cerevisiae. We show compositional heterogeneity of single mRNPs and plasticity across different growth conditions, with major co-occupants of mRNPs containing the nuclear cap-binding complex identified as Yra1 (1-10 copies), Nab2 (1-6 copies), and Npl3 (1-6 copies). Multicopy Yra1-bound mRNPs are specifically co-occupied by the THO complex and assembled on mRNAs biased by transcript length and RNA secondary structure. Yra1 depletion results in decreased compaction of nuclear mRNPs demonstrating a packaging function. Together, we provide a quantitative framework for gene- and condition-dependent RBP occupancy and stoichiometry in individual nuclear mRNPs.
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Affiliation(s)
- Ryuta Asada
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Andrew Dominguez
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA; Biochemistry, Molecular, Cellular, and Developmental Biology Graduate Group, University of California, Davis, Davis, CA 95616, USA
| | - Ben Montpetit
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA; Biochemistry, Molecular, Cellular, and Developmental Biology Graduate Group, University of California, Davis, Davis, CA 95616, USA.
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Du Y, Cao L, Wang S, Guo L, Tan L, Liu H, Feng Y, Wu W. Differences in alternative splicing and their potential underlying factors between animals and plants. J Adv Res 2023:S2090-1232(23)00354-5. [PMID: 37981087 DOI: 10.1016/j.jare.2023.11.017] [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: 05/07/2023] [Revised: 08/16/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Alternative splicing (AS), a posttranscriptional process, contributes to the complexity of transcripts from a limited number of genes in a genome, and AS is considered a great source of genetic and phenotypic diversity in eukaryotes. In animals, AS is tightly regulated during the processes of cell growth and differentiation, and its dysregulation is involved in many diseases, including cancers. Likewise, in plants, AS occurs in all stages of plant growth and development, and it seems to play important roles in the rapid reprogramming of genes in response to environmental stressors. To date, the prevalence and functional roles of AS have been extensively reviewed in animals and plants. However, AS differences between animals and plants, especially their underlying molecular mechanisms and impact factors, are anecdotal and rarely reviewed. AIM OF REVIEW This review aims to broaden our understanding of AS roles in a variety of biological processes and provide insights into the underlying mechanisms and impact factors likely leading to AS differences between animals and plants. KEY SCIENTIFIC CONCEPTS OF REVIEW We briefly summarize the roles of AS regulation in physiological and biochemical activities in animals and plants. Then, we underline the differences in the process of AS between plants and animals and especially analyze the potential impact factors, such as gene exon/intron architecture, 5'/3' untranslated regions (UTRs), spliceosome components, chromatin dynamics and transcription speeds, splicing factors [serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs)], noncoding RNAs, and environmental stimuli, which might lead to the differences. Moreover, we compare the nonsense-mediated mRNA decay (NMD)-mediated turnover of the transcripts with a premature termination codon (PTC) in animals and plants. Finally, we summarize the current AS knowledge published in animals versus plants and discuss the potential development of disease therapies and superior crops in the future.
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Affiliation(s)
- Yunfei Du
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Lu Cao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Lingling Tan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Hua Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Ying Feng
- Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health (SINH), Chinese Academy of Sciences (CAS), Shanghai 200032, China.
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China.
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