1
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Manara V, Radoani M, Belli R, Peroni D, Destefanis F, Angheben L, Tome G, Tebaldi T, Bellosta P. NOC1 is a direct MYC target, and its protein interactome dissects its activity in controlling nucleolar function. Front Cell Dev Biol 2023; 11:1293420. [PMID: 38213308 PMCID: PMC10782387 DOI: 10.3389/fcell.2023.1293420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024] Open
Abstract
The nucleolus is a subnuclear compartment critical in ribosome biogenesis and cellular stress responses. These mechanisms are governed by a complex interplay of proteins, including NOC1, a member of the NOC family of nucleolar proteins responsible for controlling rRNA processing and ribosomal maturation. This study reveals a novel relationship between NOC1 and MYC transcription factor, known for its crucial role in controlling ribosomal biogenesis, cell growth, and proliferation. Here, we demonstrate that NOC1 functions as a direct target of MYC, as it is transcriptionally induced through a functional MYC-binding E-box sequence in the NOC1 promoter region. Furthermore, protein interactome analysis reveals that NOC1-complex includes the nucleolar proteins NOC2 and NOC3 and other nucleolar components such as Nucleostemin1 Ns1 transporters of ribosomal subunits and components involved in rRNA processing and maturation. In response to MYC, NOC1 expression and localization within the nucleolus significantly increase, suggesting a direct functional link between MYC activity and NOC1 function. Notably, NOC1 over-expression leads to the formation of large nuclear granules and enlarged nucleoli, which co-localize with nucleolar fibrillarin and Ns1. Additionally, we demonstrate that NOC1 expression is necessary for Ns1 nucleolar localization, suggesting a role for NOC1 in maintaining nucleolar structure. Finally, the co-expression of NOC1 and MYC enhances nucleolus size and maintains their co-localization, outlining another aspect of the cooperation between NOC1 and MYC in nucleolar dynamics. This study also reveals an enrichment with NOC1 with few proteins involved in RNA processing, modification, and splicing. Moreover, proteins such as Ythdc1, Flacc, and splenito are known to mediate N6-methyladenosine (m6A) methylation of mRNAs in nuclear export, revealing NOC1's potential involvement in coordinating RNA splicing and nuclear mRNA export. In summary, we uncovered novel roles for NOC1 in nucleolar homeostasis and established its direct connection with MYC in the network governing nucleolar structure and function. These findings also highlight NOC1's interaction with proteins relevant to specific RNA functions, suggesting a broader role in addition to its control of nucleolar homeostasis and providing new insight that can be further investigated.
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Affiliation(s)
- Valeria Manara
- Department of Computational, Cellular, Integrative Biology CIBIO, University of Trento, Trento, Italy
| | - Marco Radoani
- Department of Computational, Cellular, Integrative Biology CIBIO, University of Trento, Trento, Italy
| | - Romina Belli
- Department of Computational, Cellular, Integrative Biology CIBIO, University of Trento, Trento, Italy
| | - Daniele Peroni
- Department of Computational, Cellular, Integrative Biology CIBIO, University of Trento, Trento, Italy
| | - Francesca Destefanis
- Department of Computational, Cellular, Integrative Biology CIBIO, University of Trento, Trento, Italy
- Institute of Evolutionary Biology CSIC Universitat Pompeu Fabra, Barcelona, Spain
| | - Luca Angheben
- Department of Computational, Cellular, Integrative Biology CIBIO, University of Trento, Trento, Italy
| | - Gabriele Tome
- Department of Computational, Cellular, Integrative Biology CIBIO, University of Trento, Trento, Italy
| | - Toma Tebaldi
- Department of Computational, Cellular, Integrative Biology CIBIO, University of Trento, Trento, Italy
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Paola Bellosta
- Department of Computational, Cellular, Integrative Biology CIBIO, University of Trento, Trento, Italy
- Department of Medicine, NYU Langone Medical Center, New York, NY, United States
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2
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Zhu Z, Huo F, Zhang J, Shan H, Pei D. Crosstalk between m6A modification and alternative splicing during cancer progression. Clin Transl Med 2023; 13:e1460. [PMID: 37850412 PMCID: PMC10583157 DOI: 10.1002/ctm2.1460] [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: 05/30/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 10/19/2023] Open
Abstract
Background N6-methyladenosine (m6A), the most prevalent internal mRNA modification in eukaryotes, is added by m6A methyltransferases, removed by m6A demethylases and recognised by m6A-binding proteins. This modification significantly influences carious facets of RNA metabolism and plays a pivotal role in cellular and physiological processes. Main body Pre-mRNA alternative splicing, a process that generates multiple splice isoforms from multi-exon genes, contributes significantly to the protein diversity in mammals. Moreover, the presence of crosstalk between m6A modification and alternative splicing, with m6A modifications on pre-mRNAs exerting regulatory control, has been established. The m6A modification modulates alternative splicing patterns by recruiting specific RNA-binding proteins (RBPs) that regulate alternative splicing or by directly influencing the interaction between RBPs and their target RNAs. Conversely, alternative splicing can impact the deposition or recognition of m6A modification on mRNAs. The integration of m6A modifications has expanded the scope of therapeutic strategies for cancer treatment, while alternative splicing offers novel insights into the mechanistic role of m6A methylation in cancer initiation and progression. Conclusion This review aims to highlight the biological functions of alternative splicing of m6A modification machinery and its implications in tumourigenesis. Furthermore, we discuss the clinical relevance of understanding m6A-dependent alternative splicing in tumour therapies.
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Affiliation(s)
- Zhi‐Man Zhu
- Department of PathologyXuzhou Medical UniversityXuzhouJiangsuChina
| | - Fu‐Chun Huo
- Department of PathologyXuzhou Medical UniversityXuzhouJiangsuChina
| | - Jian Zhang
- Department of Respiratory MedicineSecond Affiliated Hospital of Xuzhou Medical UniversityXuzhouJiangsuChina
| | - Hong‐Jian Shan
- Department of OrthopedicsThe Affiliated Jiangning Hospital with Nanjing Medical UniversityNanjingJiangsuChina
| | - Dong‐Sheng Pei
- Department of PathologyXuzhou Medical UniversityXuzhouJiangsuChina
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3
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The RNA m 6A writer WTAP in diseases: structure, roles, and mechanisms. Cell Death Dis 2022; 13:852. [PMID: 36207306 PMCID: PMC9546849 DOI: 10.1038/s41419-022-05268-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/11/2022] [Accepted: 09/14/2022] [Indexed: 11/05/2022]
Abstract
N6-methyladenosine (m6A) is a widely investigated RNA modification in studies on the "epigenetic regulation" of mRNAs that is ubiquitously present in eukaryotes. Abnormal changes in m6A levels are closely related to the regulation of RNA metabolism, heat shock stress, tumor occurrence, and development. m6A modifications are catalyzed by the m6A writer complex, which contains RNA methyltransferase-like 3 (METTL3), methyltransferase-like 14 (METTL14), Wilms tumor 1-associated protein (WTAP), and other proteins with methyltransferase (MTase) capability, such as RNA-binding motif protein 15 (RBM15), KIAA1429 and zinc finger CCCH-type containing 13 (ZC3H13). Although METTL3 is the main catalytic subunit, WTAP is a regulatory subunit whose function is to recruit the m6A methyltransferase complex to the target mRNA. Specifically, WTAP is required for the accumulation of METTL3 and METTL14 in nuclear speckles. In this paper, we briefly introduce the molecular mechanism of m6A modification. Then, we focus on WTAP, a component of the m6A methyltransferase complex, and introduce its structure, localization, and physiological functions. Finally, we describe its roles and mechanisms in cancer.
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4
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The Critical Role of RNA m6A Methylation in Gliomas: Targeting the Hallmarks of Cancer. Cell Mol Neurobiol 2022:10.1007/s10571-022-01283-8. [DOI: 10.1007/s10571-022-01283-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/04/2022] [Indexed: 11/03/2022]
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5
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Horiuchi K, Kawamura T, Hamakubo T. Wilms' Tumor 1-Associating Protein complex regulates alternative splicing and polyadenylation at potential G-quadruplex-forming splice site sequences. J Biol Chem 2021; 297:101248. [PMID: 34582888 PMCID: PMC8605363 DOI: 10.1016/j.jbc.2021.101248] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 11/14/2022] Open
Abstract
Wilms’ tumor 1-associating protein (WTAP) is a core component of the N6-methyladenosine (m6A)-methyltransferase complex, along with VIRMA, CBLL1, ZC3H13 (KIAA0853), RBM15/15B, and METTL3/14, which generate m6A, a key RNA modification that affects various processes of RNA metabolism. WTAP also interacts with splicing factors; however, despite strong evidence suggesting a role of Drosophila WTAP homolog fl(2)d in alternative splicing (AS), its role in splicing regulation in mammalian cells remains elusive. Here we demonstrate using RNAi coupled with RNA-seq that WTAP, VIRMA, CBLL1, and ZC3H13 modulate AS, promoting exon skipping and intron retention in AS events that involve short introns/exons with higher GC content and introns with weaker polypyrimidine-tract and branch points. Further analysis of GC-rich sequences involved in AS events regulated by WTAP, together with minigene assay analysis, revealed potential G-quadruplex formation at splice sites where WTAP has an inhibitory effect. We also found that several AS events occur in the last exon of one isoform of MSL1 and WTAP, leading to competition for polyadenylation. Proteomic analysis also suggested that WTAP/CBLL1 interaction promotes recruitment of the 3′-end processing complex. Taken together, our results indicate that the WTAP complex regulates AS and alternative polyadenylation via inhibitory mechanisms in GC-rich sequences.
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Affiliation(s)
- Keiko Horiuchi
- Department of Protein-Protein Interaction Research, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, 113-0011, Japan.
| | - Takeshi Kawamura
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Takao Hamakubo
- Department of Protein-Protein Interaction Research, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, 113-0011, Japan.
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6
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Loss of WTAP Impairs Early Parthenogenetic Embryo Development. Animals (Basel) 2021; 11:ani11061675. [PMID: 34199793 PMCID: PMC8229322 DOI: 10.3390/ani11061675] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/29/2021] [Accepted: 06/02/2021] [Indexed: 12/14/2022] Open
Abstract
m6A is one of the most common and abundant modifications of RNA molecules present in eukaryotes. The methyltransferase complex, consisting of methyltransferase-like 3 (METTL3), METTL14, and WTAP, is responsible for the m6A modification of RNA. WTAP was identified as an mRNA splicing regulator. Its role as a regulatory subunit of the m6A methyltransferase complex in embryonic development remains largely unknown. To investigate the role of WTAP in porcine early embryonic development, si-WTAP was microinjected into porcine parthenogenetic zygotes. WTAP knockdown significantly reduced the blastocyst rate and global m6A levels, but did not affect the cleavage rate. Betaine was supplemented into the in vitro culture (IVC) to increase the m6A levels. Betaine significantly increased the global m6A levels but did not affect the blastocyst rate. Furthermore, the pluripotency genes, including OCT4, SOX2, and NANOG, were downregulated following WTAP knockdown. The apoptotic genes BAX and CASPASE 3 were upregulated, while the anti-apoptotic gene BCL2 was downregulated in WTAP knockdown blastocysts. TUNEL staining revealed that the number of apoptotic cells was significantly increased following WTAP knockdown. Our study indicated that WTAP has an indispensable role in porcine early embryonic development.
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7
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Wang Y, Zhang L, Ren H, Ma L, Guo J, Mao D, Lu Z, Lu L, Yan D. Role of Hakai in m 6A modification pathway in Drosophila. Nat Commun 2021; 12:2159. [PMID: 33846330 PMCID: PMC8041851 DOI: 10.1038/s41467-021-22424-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 03/14/2021] [Indexed: 12/13/2022] Open
Abstract
N6-methyladenosine (m6A), the most abundant internal modification in eukaryotic mRNA, is installed by a multi-component writer complex; however, the exact roles of each component remain poorly understood. Here we show that a potential E3 ubiquitin ligase Hakai colocalizes and interacts with other m6A writer components, and Hakai mutants exhibit typical m6A pathway defects in Drosophila, such as lowered m6A levels in mRNA, aberrant Sxl alternative splicing, wing and behavior defects. Hakai, Vir, Fl(2)d and Flacc form a stable complex, and disruption of either Hakai, Vir or Fl(2)d led to the degradation of the other three components. Furthermore, MeRIP-seq indicates that the effective m6A modification is mostly distributed in 5’ UTRs in Drosophila, in contrast to the mammalian system. Interestingly, we demonstrate that m6A modification is deposited onto the Sxl mRNA in a sex-specific fashion, which depends on the m6A writer. Together, our work not only advances the understanding of mechanism and regulation of the m6A writer complex, but also provides insights into how Sxl cooperate with the m6A pathway to control its own splicing. Drosophila m6A writer complex regulates alternative splicing of the Sex-lethal gene. Here the authors show that a potential E3 ligase Hakai interacts with the fly m6A writer complex and that m6A level is reduced in Hakai mutant flies.
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Affiliation(s)
- Yanhua Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Lifeng Zhang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Hang Ren
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Lijuan Ma
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Jian Guo
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Decai Mao
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Zhongwen Lu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Lijun Lu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Dong Yan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
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8
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Jensen P, Patel B, Smith S, Sabnis R, Kaboord B. Improved Immunoprecipitation to Mass Spectrometry Method for the Enrichment of Low-Abundant Protein Targets. Methods Mol Biol 2021; 2261:229-246. [PMID: 33420993 DOI: 10.1007/978-1-0716-1186-9_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Immunoprecipitation (IP) is commonly used upstream of mass spectrometry (MS) as an enrichment tool for low-abundant protein targets. However, several aspects of the classical IP procedure such as nonspecific protein binding to the isolation matrix, detergents or high salt concentrations in wash and elution buffers, and antibody chain contamination in elution fractions render it incompatible with downstream mass spectrometry analysis. Here, we discuss an improved IP-MS workflow that is designed to minimize sample prep time and these contaminants. The method employs biotinylated antibodies to the targets of interest and streptavidin magnetic beads that exhibit low background binding. In addition, alterations in the elution protocol and subsequent MS sample prep were made to reduce time and antibody leaching in the eluent, minimizing potential ion suppression effects and thereby maximizing detection of multiple target antigens and interacting proteins.
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Affiliation(s)
| | | | | | - Renuka Sabnis
- Nisarga Biotech Pvt. Ltd., Satara, Maharashtra, India
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9
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Chen J, Fang X, Zhong P, Song Z, Hu X. N6-methyladenosine modifications: interactions with novel RNA-binding proteins and roles in signal transduction. RNA Biol 2019; 16:991-1000. [PMID: 31107151 DOI: 10.1080/15476286.2019.1620060] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
RNA epigenetics has received a great deal of attention in recent years, and the reversible N6-methyladenosine (m6A) modification on messenger RNAs (mRNAs) has emerged as a widespread phenomenon. The vital roles of m6A in diverse biological processes are dependent on many RNA-binding proteins (RBPs) with 'reader' or 'nonreader' functions. Moreover, m6A effector proteins affect cellular processes, such as stem cell differentiation, tumor development and the immune response by controlling signal transduction. This review provides an overview of the interactions of m6A with various RBPs, including the 'reader' proteins (excluding the YT521-B homology (YTH) domain proteins and the heterogeneous nuclear ribonucleoproteins (hnRNPs)), and the functional 'nonreader' proteins, and this review focuses on their specific RNA-binding domains and their associations with other m6A effectors. Furthermore, we summarize key m6A-marked targets in distinct signaling pathways, leading to a better understanding of the cellular m6A machinery.
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Affiliation(s)
- Jiaxin Chen
- a Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province , Sir Run Shaw Hospital, Zhejiang University , Hangzhou , China
| | - Xiao Fang
- b Department of Anesthesiology and Key Laboratory of Biotherapy of Zhejiang Province , Sir Run Shaw Hospital, Zhejiang University , Hangzhou , China
| | - Pengcheng Zhong
- a Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province , Sir Run Shaw Hospital, Zhejiang University , Hangzhou , China
| | - Zhangfa Song
- c Department of Colorectal Surgery and Key Laboratory of Biotherapy of Zhejiang Province , Sir Run Shaw Hospital, Zhejiang University , Hangzhou , China
| | - Xiaotong Hu
- a Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province , Sir Run Shaw Hospital, Zhejiang University , Hangzhou , China
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Abstract
The central dogma of molecular biology introduced by Crick describes a linear flow of information from DNA to mRNA to protein. Since then it has become evident that RNA undergoes several maturation steps such as capping, splicing, 3'-end processing, and editing. Likewise, nucleotide modifications are common in mRNA and are present in all organisms impacting on the regulation of gene expression. The most abundant modification found in mRNA is N6-methyladenosine (m6A). Deposition of m6A is a nuclear process and is performed by a megadalton writer complex primarily on mRNAs, but also on microRNAs and lncRNAs. The m6A methylosome is composed of the enzymatic core components METTL3 and METTL14, and several auxiliary proteins necessary for its correct positioning and functioning, which are WTAP, VIRMA, FLACC, RBM15, and HAKAI. The m6A epimark is decoded by YTH domain-containing reader proteins YTHDC and YTHDF, but METTLs can act as "readers" as well. Eraser proteins, such as FTO and ALKBH5, can remove the methyl group. Here we review recent progress on the role of m6A in regulating gene expression in light of Crick's central dogma of molecular biology. In particular, we address the complexity of the writer complex from an evolutionary perspective to obtain insights into the mechanism of ancient m6A methylation and its regulation.
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Affiliation(s)
- Dario L Balacco
- School of Biosciences, College of Life and Environmental Sciences , University of Birmingham , Edgbaston, Birmingham B15 2TT , United Kingdom
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences , University of Birmingham , Edgbaston, Birmingham B15 2TT , United Kingdom
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11
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Martinez NM, Gilbert WV. Pre-mRNA modifications and their role in nuclear processing. QUANTITATIVE BIOLOGY 2018; 6:210-227. [PMID: 30533247 DOI: 10.1007/s40484-018-0147-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Background Cellular non-coding RNAs are extensively modified post-transcriptionally, with more than 100 chemically distinct nucleotides identified to date. In the past five years, new sequencing based methods have revealed widespread decoration of eukaryotic messenger RNA with diverse RNA modifications whose functions in mRNA metabolism are only beginning to be known. Results Since most of the identified mRNA modifying enzymes are present in the nucleus, these modifications have the potential to function in nuclear pre-mRNA processing including alternative splicing. Here we review recent progress towards illuminating the role of pre-mRNA modifications in splicing and highlight key areas for future investigation in this rapidly growing field. Conclusions Future studies to identify which modifications are added to nascent pre-mRNA and to interrogate the direct effects of individual modifications are likely to reveal new mechanisms by which nuclear pre-mRNA processing is regulated.
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Affiliation(s)
- Nicole M Martinez
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Wendy V Gilbert
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
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12
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Dynamic transcriptomic m 6A decoration: writers, erasers, readers and functions in RNA metabolism. Cell Res 2018; 28:616-624. [PMID: 29789545 PMCID: PMC5993786 DOI: 10.1038/s41422-018-0040-8] [Citation(s) in RCA: 958] [Impact Index Per Article: 159.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 04/22/2018] [Indexed: 02/06/2023] Open
Abstract
N6-methyladenosine (m6A) is a chemical modification present in multiple RNA species, being most abundant in mRNAs. Studies on enzymes or factors that catalyze, recognize, and remove m6A have revealed its comprehensive roles in almost every aspect of mRNA metabolism, as well as in a variety of physiological processes. This review describes the current understanding of the m6A modification, particularly the functions of its writers, erasers, readers in RNA metabolism, with an emphasis on its role in regulating the isoform dosage of mRNAs.
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Xio is a component of the Drosophila sex determination pathway and RNA N6-methyladenosine methyltransferase complex. Proc Natl Acad Sci U S A 2018; 115:3674-3679. [PMID: 29555755 DOI: 10.1073/pnas.1720945115] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
N6-methyladenosine (m6A), the most abundant chemical modification in eukaryotic mRNA, has been implicated in Drosophila sex determination by modifying Sex-lethal (Sxl) pre-mRNA and facilitating its alternative splicing. Here, we identify a sex determination gene, CG7358, and rename it xio according to its loss-of-function female-to-male transformation phenotype. xio encodes a conserved ubiquitous nuclear protein of unknown function. We show that Xio colocalizes and interacts with all previously known m6A writer complex subunits (METTL3, METTL14, Fl(2)d/WTAP, Vir/KIAA1429, and Nito/Rbm15) and that loss of xio is associated with phenotypes that resemble other m6A factors, such as sexual transformations, Sxl splicing defect, held-out wings, flightless flies, and reduction of m6A levels. Thus, Xio encodes a member of the m6A methyltransferase complex involved in mRNA modification. Since its ortholog ZC3H13 (or KIAA0853) also associates with several m6A writer factors, the function of Xio in the m6A pathway is likely evolutionarily conserved.
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Rambout X, Dequiedt F, Maquat LE. Beyond Transcription: Roles of Transcription Factors in Pre-mRNA Splicing. Chem Rev 2017; 118:4339-4364. [PMID: 29251915 DOI: 10.1021/acs.chemrev.7b00470] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Whereas individual steps of protein-coding gene expression in eukaryotes can be studied in isolation in vitro, it has become clear that these steps are intimately connected within cells. Connections not only ensure quality control but also fine-tune the gene expression process, which must adapt to environmental changes while remaining robust. In this review, we systematically present proven and potential mechanisms by which sequence-specific DNA-binding transcription factors can alter gene expression beyond transcription initiation and regulate pre-mRNA splicing, and thereby mRNA isoform production, by (i) influencing transcription elongation rates, (ii) binding to pre-mRNA to recruit splicing factors, and/or (iii) blocking the association of splicing factors with pre-mRNA. We propose various mechanistic models throughout the review, in some cases without explicit supportive evidence, in hopes of providing fertile ground for future studies.
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15
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Bartosovic M, Molares HC, Gregorova P, Hrossova D, Kudla G, Vanacova S. N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3'-end processing. Nucleic Acids Res 2017; 45:11356-11370. [PMID: 28977517 PMCID: PMC5737695 DOI: 10.1093/nar/gkx778] [Citation(s) in RCA: 288] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 08/26/2017] [Indexed: 12/16/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant base modification found in messenger RNAs (mRNAs). The discovery of FTO as the first m6A mRNA demethylase established the concept of reversible RNA modification. Here, we present a comprehensive transcriptome-wide analysis of RNA demethylation and uncover FTO as a potent regulator of nuclear mRNA processing events such as alternative splicing and 3΄ end mRNA processing. We show that FTO binds preferentially to pre-mRNAs in intronic regions, in the proximity of alternatively spliced (AS) exons and poly(A) sites. FTO knockout (KO) results in substantial changes in pre-mRNA splicing with prevalence of exon skipping events. The alternative splicing effects of FTO KO anti-correlate with METTL3 knockdown suggesting the involvement of m6A. Besides, deletion of intronic region that contains m6A-linked DRACH motifs partially rescues the FTO KO phenotype in a reporter system. All together, we demonstrate that the splicing effects of FTO are dependent on the catalytic activity in vivo and are mediated by m6A. Our results reveal for the first time the dynamic connection between FTO RNA binding and demethylation activity that influences several mRNA processing events.
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Affiliation(s)
- Marek Bartosovic
- CEITEC-Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
| | - Helena Covelo Molares
- CEITEC-Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
| | - Pavlina Gregorova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
| | - Dominika Hrossova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
| | - Grzegorz Kudla
- MRC Human Genetics Unit MRC IGMM, University of Edinburgh Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Stepanka Vanacova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
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Kan L, Grozhik AV, Vedanayagam J, Patil DP, Pang N, Lim KS, Huang YC, Joseph B, Lin CJ, Despic V, Guo J, Yan D, Kondo S, Deng WM, Dedon PC, Jaffrey SR, Lai EC. The m 6A pathway facilitates sex determination in Drosophila. Nat Commun 2017; 8:15737. [PMID: 28675155 PMCID: PMC5500889 DOI: 10.1038/ncomms15737] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/21/2017] [Indexed: 12/29/2022] Open
Abstract
The conserved modification N6-methyladenosine (m6A) modulates mRNA processing and activity. Here, we establish the Drosophila system to study the m6A pathway. We first apply miCLIP to map m6A across embryogenesis, characterize its m6A ‘writer’ complex, validate its YTH ‘readers’ CG6422 and YT521-B, and generate mutants in five m6A factors. While m6A factors with additional roles in splicing are lethal, m6A-specific mutants are viable but present certain developmental and behavioural defects. Notably, m6A facilitates the master female determinant Sxl, since multiple m6A components enhance female lethality in Sxl sensitized backgrounds. The m6A pathway regulates Sxl processing directly, since miCLIP data reveal Sxl as a major intronic m6A target, and female-specific Sxl splicing is compromised in multiple m6A pathway mutants. YT521-B is a dominant m6A effector for Sxl regulation, and YT521-B overexpression can induce female-specific Sxl splicing. Overall, our transcriptomic and genetic toolkit reveals in vivo biologic function for the Drosophila m6A pathway. N6-methyladenosine (m6A) is a conserved RNA modification that has recently emerged as an important regulator of messenger RNA processing and activity. Here, the authors provide evidence that m6A pathway facilitates female-specific splicing of Sxl, regulating sex determination in Drosophila.
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Affiliation(s)
- Lijuan Kan
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York City, New York 10065, USA
| | - Anya V Grozhik
- Department of Pharmacology, Weill Medical College, Cornell University, New York City, New York 10065, USA
| | - Jeffrey Vedanayagam
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York City, New York 10065, USA
| | - Deepak P Patil
- Department of Pharmacology, Weill Medical College, Cornell University, New York City, New York 10065, USA
| | - Nan Pang
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York City, New York 10065, USA
| | - Kok-Seong Lim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Yi-Chun Huang
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Brian Joseph
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York City, New York 10065, USA
| | - Ching-Jung Lin
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York City, New York 10065, USA
| | - Vladimir Despic
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York City, New York 10065, USA
| | - Jian Guo
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Yan
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Shu Kondo
- Invertebrate Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York City, New York 10065, USA
| | - Eric C Lai
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York City, New York 10065, USA
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17
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Lence T, Soller M, Roignant JY. A fly view on the roles and mechanisms of the m 6A mRNA modification and its players. RNA Biol 2017; 14:1232-1240. [PMID: 28353398 PMCID: PMC5699544 DOI: 10.1080/15476286.2017.1307484] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
RNA modifications are an emerging layer of posttranscriptional gene regulation in eukaryotes. N6-methyladenosine (m6A) is among the most abundant modifications in mRNAs (mRNAs) that was shown to influence many physiological processes from yeast to mammals. Like DNA methylation, m6A in mRNA is dynamically regulated. A conserved methyltransferase complex catalyzes the deposition of the methyl group on adenosine, which can be removed by specific classes of demethylases. Furthermore, YTH-domain containing proteins can recognize this modification to mediate m6A-dependent activities. Here we review the functions and mechanisms of the main m6A players with a particular focus on Drosophila melanogaster.
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Affiliation(s)
- Tina Lence
- a Laboratory of RNA Epigenetics , Institute of Molecular Biology (IMB) , Mainz , Germany
| | - Matthias Soller
- b School of Biosciences, College of Life and Environmental Sciences , University of Birmingham , Edgbaston, Birmingham , UK
| | - Jean-Yves Roignant
- a Laboratory of RNA Epigenetics , Institute of Molecular Biology (IMB) , Mainz , Germany
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18
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Swenson JM, Colmenares SU, Strom AR, Costes SV, Karpen GH. The composition and organization of Drosophila heterochromatin are heterogeneous and dynamic. eLife 2016; 5:e16096. [PMID: 27514026 PMCID: PMC4981497 DOI: 10.7554/elife.16096] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/06/2016] [Indexed: 12/13/2022] Open
Abstract
Heterochromatin is enriched for specific epigenetic factors including Heterochromatin Protein 1a (HP1a), and is essential for many organismal functions. To elucidate heterochromatin organization and regulation, we purified Drosophila melanogaster HP1a interactors, and performed a genome-wide RNAi screen to identify genes that impact HP1a levels or localization. The majority of the over four hundred putative HP1a interactors and regulators identified were previously unknown. We found that 13 of 16 tested candidates (83%) are required for gene silencing, providing a substantial increase in the number of identified components that impact heterochromatin properties. Surprisingly, image analysis revealed that although some HP1a interactors and regulators are broadly distributed within the heterochromatin domain, most localize to discrete subdomains that display dynamic localization patterns during the cell cycle. We conclude that heterochromatin composition and architecture is more spatially complex and dynamic than previously suggested, and propose that a network of subdomains regulates diverse heterochromatin functions.
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Affiliation(s)
- Joel M Swenson
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Serafin U Colmenares
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Amy R Strom
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Sylvain V Costes
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Gary H Karpen
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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19
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Abstract
N6-methyladenosine (m6A) is the most prevalent internal modification that occurs in the messenger RNA (mRNA) of most eukaryotes. In this review, Yue et al. summarize recent progress in the study of the m6A mRNA methylation machineries across eukaryotes and discuss their newly uncovered roles in post-transcriptional gene expression regulation. N6-methyladenosine (m6A) is the most prevalent and internal modification that occurs in the messenger RNAs (mRNA) of most eukaryotes, although its functional relevance remained a mystery for decades. This modification is installed by the m6A methylation “writers” and can be reversed by demethylases that serve as “erasers.” In this review, we mainly summarize recent progress in the study of the m6A mRNA methylation machineries across eukaryotes and discuss their newly uncovered biological functions. The broad roles of m6A in regulating cell fates and embryonic development highlight the existence of another layer of epigenetic regulation at the RNA level, where mRNA is subjected to chemical modifications that affect protein expression.
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Affiliation(s)
- Yanan Yue
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jianzhao Liu
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Chuan He
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, USA
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20
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Abstract
Sex-lethal (Sxl) encodes the master regulator of the sex determination pathway in Drosophila and acts by controlling sex identity in both soma and germ line. In females Sxl maintains its own expression by controlling the alternative splicing of its own mRNA. Here, we identify a novel sex determination gene, spenito (nito) that encodes a SPEN family protein. Loss of nito activity results in stem cell tumors in the female germ line as well as female-to-male somatic transformations. We show that Nito is a ubiquitous nuclear protein that controls the alternative splicing of the Sxl mRNA by interacting with Sxl protein and pre-mRNA, suggesting that it is directly involved in Sxl auto-regulation. Given that SPEN family proteins are frequently mutated in cancers, our results suggest that these factors might be implicated in tumorigenesis through splicing regulation.
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21
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Kaboord B, Smith S, Patel B, Meier S. Enrichment of low-abundant protein targets by immunoprecipitation upstream of mass spectrometry. Methods Mol Biol 2015; 1295:135-151. [PMID: 25820720 DOI: 10.1007/978-1-4939-2550-6_12] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Immunoprecipitation (IP) is commonly used upstream of mass spectrometry (MS) as an enrichment tool for low-abundant protein targets. However, several aspects of the classical IP procedure such as nonspecific protein binding to the isolation matrix, detergents or high salt concentrations in wash and elution buffers, and antibody chain contamination in elution fractions render it incompatible with downstream mass spectrometry analysis. Here, we discuss two IP workflows that are designed to minimize or eliminate these contaminants: the first employs biotinylated antibodies and streptavidin magnetic beads while the second method utilizes a traditional antibody that is oriented and cross-linked to Protein AG magnetic beads. Both modified magnetic supports have low background binding and both antibody immobilization strategies significantly reduce or eliminate antibody heavy and light chain contamination in the eluent, minimizing potential ion suppression effects and thereby maximizing detection of target antigens and interacting proteins.
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Affiliation(s)
- Barbara Kaboord
- Research & Development, Thermo Fisher Scientific, 3747 N. Meridian Rd., Rockford, IL, 61101, USA,
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22
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Anderson AM, Weasner BP, Weasner BM, Kumar JP. The Drosophila Wilms׳ Tumor 1-Associating Protein (WTAP) homolog is required for eye development. Dev Biol 2014; 390:170-80. [PMID: 24690230 DOI: 10.1016/j.ydbio.2014.03.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 03/04/2014] [Accepted: 03/19/2014] [Indexed: 11/17/2022]
Abstract
Sine Oculis (So), the founding member of the SIX family of homeobox transcription factors, binds to sequence specific DNA elements and regulates transcription of downstream target genes. It does so, in part, through the formation of distinct biochemical complexes with Eyes Absent (Eya) and Groucho (Gro). While these complexes play significant roles during development, they do not account for all So-dependent activities in Drosophila. It is thought that additional So-containing complexes make important contributions as well. This contention is supported by the identification of nearly two-dozen additional proteins that complex with So. However, very little is known about the roles that these additional complexes play in development. In this report we have used yeast two-hybrid screens and co-immunoprecipitation assays from Kc167 cells to identify a biochemical complex consisting of So and Fl(2)d, the Drosophila homolog of human Wilms׳ Tumor 1-Associating Protein (WTAP). We show that Fl(2)d protein is distributed throughout the entire eye-antennal imaginal disc and that loss-of-function mutations lead to perturbations in retinal development. The eye defects are manifested behind the morphogenetic furrow and result in part from increased levels of the pan-neuronal RNA binding protein Embryonic Lethal Abnormal Vision (Elav) and the RUNX class transcription factor Lozenge (Lz). We also provide evidence that So and Fl(2)d interact genetically in the developing eye. Wilms׳ tumor-1 (WT1), a binding partner of WTAP, is required for normal eye formation in mammals and loss-of-function mutations are associated with some versions of retinoblastoma. In contrast, WTAP and its homologs have not been implicated in eye development. To our knowledge, the results presented in this report are the first description of a role for WTAP in the retina of any seeing animal.
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Affiliation(s)
- Abigail M Anderson
- Department of Biology, Indiana University, Bloomington, IN 47405, United States
| | - Brandon P Weasner
- Department of Biology, Indiana University, Bloomington, IN 47405, United States
| | - Bonnie M Weasner
- Department of Biology, Indiana University, Bloomington, IN 47405, United States
| | - Justin P Kumar
- Department of Biology, Indiana University, Bloomington, IN 47405, United States.
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23
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Ping XL, Sun BF, Wang L, Xiao W, Yang X, Wang WJ, Adhikari S, Shi Y, Lv Y, Chen YS, Zhao X, Li A, Yang Y, Dahal U, Lou XM, Liu X, Huang J, Yuan WP, Zhu XF, Cheng T, Zhao YL, Wang X, Danielsen JMR, Liu F, Yang YG. Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase. Cell Res 2014; 24:177-89. [PMID: 24407421 PMCID: PMC3915904 DOI: 10.1038/cr.2014.3] [Citation(s) in RCA: 1624] [Impact Index Per Article: 162.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 12/03/2013] [Accepted: 12/04/2013] [Indexed: 12/21/2022] Open
Abstract
The methyltransferase like 3 (METTL3)-containing methyltransferase complex catalyzes the N6-methyladenosine (m6A) formation, a novel epitranscriptomic marker; however, the nature of this complex remains largely unknown. Here we report two new components of the human m6A methyltransferase complex, Wilms' tumor 1-associating protein (WTAP) and methyltransferase like 14 (METTL14). WTAP interacts with METTL3 and METTL14, and is required for their localization into nuclear speckles enriched with pre-mRNA processing factors and for catalytic activity of the m6A methyltransferase in vivo. The majority of RNAs bound by WTAP and METTL3 in vivo represent mRNAs containing the consensus m6A motif. In the absence of WTAP, the RNA-binding capability of METTL3 is strongly reduced, suggesting that WTAP may function to regulate recruitment of the m6A methyltransferase complex to mRNA targets. Furthermore, transcriptomic analyses in combination with photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) illustrate that WTAP and METTL3 regulate expression and alternative splicing of genes involved in transcription and RNA processing. Morpholino-mediated knockdown targeting WTAP and/or METTL3 in zebrafish embryos caused tissue differentiation defects and increased apoptosis. These findings provide strong evidence that WTAP may function as a regulatory subunit in the m6A methyltransferase complex and play a critical role in epitranscriptomic regulation of RNA metabolism.
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Affiliation(s)
- Xiao-Li Ping
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Bao-Fa Sun
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lu Wang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen Xiao
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xin Yang
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen-Jia Wang
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Samir Adhikari
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yue Shi
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Lv
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu-Sheng Chen
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xu Zhao
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ang Li
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Yang
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ujwal Dahal
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao-Min Lou
- Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xi Liu
- Center for Structural Biology, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jun Huang
- Life Sciences Institute, Zhejiang University, Zhejiang 310058, China
| | - Wei-Ping Yuan
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Tianjin 300041, China
| | - Xiao-Fan Zhu
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Tianjin 300041, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Tianjin 300041, China
| | - Yong-Liang Zhao
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinquan Wang
- Center for Structural Biology, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jannie M Rendtlew Danielsen
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- The Novo Nordisk Foundation Center for Protein Research, Ubiquitin Signalling Group, Faculty of Health Sciences, Copenhagen, Denmark
| | - Feng Liu
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun-Gui Yang
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
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24
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Horiuchi K, Kawamura T, Iwanari H, Ohashi R, Naito M, Kodama T, Hamakubo T. Identification of Wilms' tumor 1-associating protein complex and its role in alternative splicing and the cell cycle. J Biol Chem 2013; 288:33292-302. [PMID: 24100041 DOI: 10.1074/jbc.m113.500397] [Citation(s) in RCA: 250] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Wilms' tumor 1-associating protein (WTAP) is a putative splicing regulator that is thought to be required for cell cycle progression through the stabilization of cyclin A2 mRNA and mammalian early embryo development. To further understand how WTAP acts in the context of the cellular machinery, we identified its interacting proteins in human umbilical vein endothelial cells and HeLa cells using shotgun proteomics. Here we show that WTAP forms a novel protein complex including Hakai, Virilizer homolog, KIAA0853, RBM15, the arginine/serine-rich domain-containing proteins BCLAF1 and THRAP3, and certain general splicing regulators, most of which have reported roles in post-transcriptional regulation. The depletion of these respective components of the complex resulted in reduced cell proliferation along with G2/M accumulation. Double knockdown of the serine/arginine-rich (SR)-like proteins BCLAF1 and THRAP3 by siRNA resulted in a decrease in the nuclear speckle localization of WTAP, whereas the nuclear speckles were intact. Furthermore, we found that the WTAP complex regulates alternative splicing of the WTAP pre-mRNA by promoting the production of a truncated isoform, leading to a change in WTAP protein expression. Collectively, these findings show that the WTAP complex is a novel component of the RNA processing machinery, implying an important role in both posttranscriptional control and cell cycle regulation.
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Affiliation(s)
- Keiko Horiuchi
- From the Department of Quantitative Biology and Medicine and
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25
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The translation initiation factor eIF4E regulates the sex-specific expression of the master switch gene Sxl in Drosophila melanogaster. PLoS Genet 2011; 7:e1002185. [PMID: 21829374 PMCID: PMC3145617 DOI: 10.1371/journal.pgen.1002185] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2010] [Accepted: 05/20/2011] [Indexed: 11/27/2022] Open
Abstract
In female fruit flies, Sex-lethal (Sxl) turns off the X chromosome dosage compensation system by a mechanism involving a combination of alternative splicing and translational repression of the male specific lethal-2 (msl-2) mRNA. A genetic screen identified the translation initiation factor eif4e as a gene that acts together with Sxl to repress expression of the Msl-2 protein. However, eif4e is not required for Sxl mediated repression of msl-2 mRNA translation. Instead, eif4e functions as a co-factor in Sxl-dependent female-specific alternative splicing of msl-2 and also Sxl pre-mRNAs. Like other factors required for Sxl regulation of splicing, eif4e shows maternal-effect female-lethal interactions with Sxl. This female lethality can be enhanced by mutations in other co-factors that promote female-specific splicing and is caused by a failure to properly activate the Sxl-positive autoregulatory feedback loop in early embryos. In this feedback loop Sxl proteins promote their own synthesis by directing the female-specific alternative splicing of Sxl-Pm pre-mRNAs. Analysis of pre-mRNA splicing when eif4e activity is compromised demonstrates that Sxl-dependent female-specific splicing of both Sxl-Pm and msl-2 pre-mRNAs requires eif4e activity. Consistent with a direct involvement in Sxl-dependent alternative splicing, eIF4E is associated with unspliced Sxl-Pm pre-mRNAs and is found in complexes that contain early acting splicing factors—the U1/U2 snRNP protein Sans-fils (Snf), the U1 snRNP protein U1-70k, U2AF38, U2AF50, and the Wilms' Tumor 1 Associated Protein Fl(2)d—that have been directly implicated in Sxl splicing regulation. Gene expression in eukaryotes is a complex process that occurs in several discrete steps. Some of those steps are separated into different sub-cellular compartments and thus might be expected to occur independently of one another and involve entirely distinct factors. For example pre-mRNA splicing takes place in the nucleus where it is coupled with transcription, while mRNA translation requires export to the cytoplasm and ribosome loading. We describe studies on the fruit fly Drosophila which indicate that a cytoplasmic translation initiation factor, the cap binding protein eIF4E, plays a key role in alternative splicing in the nucleus. When eIF4E activity is compromised, we observe defects in sex-specific splicing of pre-mRNAs that are regulated by the sex determination master switch gene Sex-lethal. Our data argue that eIF4E likely plays a direct role in the regulation of alternative splicing by Sex-lethal.
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26
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Salz HK. Sex determination in insects: a binary decision based on alternative splicing. Curr Opin Genet Dev 2011; 21:395-400. [PMID: 21474300 DOI: 10.1016/j.gde.2011.03.001] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 03/11/2011] [Indexed: 12/22/2022]
Abstract
The gene regulatory networks that control sex determination vary between species. Despite these differences, comparative studies in insects have found that alternative splicing is reiteratively used in evolution to control expression of the key sex-determining genes. Sex determination is best understood in Drosophila where activation of the RNA binding protein-encoding gene Sex-lethal is the central female-determining event. Sex-lethal serves as a genetic switch because once activated it controls its own expression by a positive feedback splicing mechanism. Sex fate choice in is also maintained by self-sustaining positive feedback splicing mechanisms in other dipteran and hymenopteran insects, although different RNA binding protein-encoding genes function as the binary switch. Studies exploring the mechanisms of sex-specific splicing have revealed the extent to which sex determination is integrated with other developmental regulatory networks.
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Affiliation(s)
- Helen K Salz
- Department of Genetics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4955, USA.
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27
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Hartmann B, Castelo R, Miñana B, Peden E, Blanchette M, Rio DC, Singh R, Valcárcel J. Distinct regulatory programs establish widespread sex-specific alternative splicing in Drosophila melanogaster. RNA (NEW YORK, N.Y.) 2011; 17:453-468. [PMID: 21233220 PMCID: PMC3039145 DOI: 10.1261/rna.2460411] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 11/22/2010] [Indexed: 05/30/2023]
Abstract
In Drosophila melanogaster, female-specific expression of Sex-lethal (SXL) and Transformer (TRA) proteins controls sex-specific alternative splicing and/or translation of a handful of regulatory genes responsible for sexual differentiation and behavior. Recent findings in 2009 by Telonis-Scott et al. document widespread sex-biased alternative splicing in fruitflies, including instances of tissue-restricted sex-specific splicing. Here we report results arguing that some of these novel sex-specific splicing events are regulated by mechanisms distinct from those established by female-specific expression of SXL and TRA. Bioinformatic analysis of SXL/TRA binding sites, experimental analysis of sex-specific splicing in S2 and Kc cells lines and of the effects of SXL knockdown in Kc cells indicate that SXL-dependent and SXL-independent regulatory mechanisms coexist within the same cell. Additional determinants of sex-specific splicing can be provided by sex-specific differences in the expression of RNA binding proteins, including Hrp40/Squid. We report that sex-specific alternative splicing of the gene hrp40/squid leads to sex-specific differences in the levels of this hnRNP protein. The significant overlap between sex-regulated alternative splicing changes and those induced by knockdown of hrp40/squid and the presence of related sequence motifs enriched near subsets of Hrp40/Squid-regulated and sex-regulated splice sites indicate that this protein contributes to sex-specific splicing regulation. A significant fraction of sex-specific splicing differences are absent in germline-less tudor mutant flies. Intriguingly, these include alternative splicing events that are differentially spliced in tissues distant from the germline. Collectively, our results reveal that distinct genetic programs control widespread sex-specific splicing in Drosophila melanogaster.
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28
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Johnson ML, Nagengast AA, Salz HK. PPS, a large multidomain protein, functions with sex-lethal to regulate alternative splicing in Drosophila. PLoS Genet 2010; 6:e1000872. [PMID: 20221253 PMCID: PMC2832672 DOI: 10.1371/journal.pgen.1000872] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Accepted: 02/03/2010] [Indexed: 12/25/2022] Open
Abstract
Alternative splicing controls the expression of many genes, including the Drosophila sex determination gene Sex-lethal (Sxl). Sxl expression is controlled via a negative regulatory mechanism where inclusion of the translation-terminating male exon is blocked in females. Previous studies have shown that the mechanism leading to exon skipping is autoregulatory and requires the SXL protein to antagonize exon inclusion by interacting with core spliceosomal proteins, including the U1 snRNP protein Sans-fille (SNF). In studies begun by screening for proteins that interact with SNF, we identified PPS, a previously uncharacterized protein, as a novel component of the machinery required for Sxl male exon skipping. PPS encodes a large protein with four signature motifs, PHD, BRK, TFS2M, and SPOC, typically found in proteins involved in transcription. We demonstrate that PPS has a direct role in Sxl male exon skipping by showing first that loss of function mutations have phenotypes indicative of Sxl misregulation and second that the PPS protein forms a complex with SXL and the unspliced Sxl RNA. In addition, we mapped the recruitment of PPS, SXL, and SNF along the Sxl gene using chromatin immunoprecipitation (ChIP), which revealed that, like many other splicing factors, these proteins bind their RNA targets while in close proximity to the DNA. Interestingly, while SNF and SXL are specifically recruited to their predicted binding sites, PPS has a distinct pattern of accumulation along the Sxl gene, associating with a region that includes, but is not limited to, the SxlPm promoter. Together, these data indicate that PPS is different from other splicing factors involved in male-exon skipping and suggest, for the first time, a functional link between transcription and SXL-mediated alternative splicing. Loss of zygotic PPS function, however, is lethal to both sexes, indicating that its role may be of broad significance.
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Affiliation(s)
- Matthew L. Johnson
- Department of Genetics, Case Western Reserve University, School of Medicine, Cleveland, Ohio, United States of America
| | - Alexis A. Nagengast
- Department of Genetics, Case Western Reserve University, School of Medicine, Cleveland, Ohio, United States of America
| | - Helen K. Salz
- Department of Genetics, Case Western Reserve University, School of Medicine, Cleveland, Ohio, United States of America
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Abstract
One of the most important decisions in development is whether to be male or female. In Drosophila melanogaster, most cells make this choice independent of their neighbors such that diploid cells with one X chromosome (XY) are male and those with two X chromosomes (XX) are female. X-chromosome number is relayed through regulatory proteins that act together to activate Sex-lethal (Sxl) in XX animals. The resulting SXL female specific RNA binding protein modulates the expression of a set of downstream genes, ultimately leading to sexually dimorphic structures and behaviors. Despite the apparent simplicity of this mechanism, Sxl activity is controlled by a host of transcriptional and posttranscriptional mechanisms that tailor its function to specific developmental scenarios. This review describes recent advances in our understanding of Sxl regulation and function, highlighting work that challenges some of the textbook views about this classical (often cited, yet poorly understood) binary switch gene.
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Affiliation(s)
- Helen K Salz
- Department of Genetics, Case Western Reserve University, Cleveland, OH, USA.
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30
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Small TW, Pickering JG. Nuclear degradation of Wilms tumor 1-associating protein and survivin splice variant switching underlie IGF-1-mediated survival. J Biol Chem 2009; 284:24684-95. [PMID: 19605357 DOI: 10.1074/jbc.m109.034629] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
WTAP (Wilms tumor 1-associating protein) is a recently identified nuclear protein that is essential for mouse embryo development. The Drosophila homolog of WTAP, Fl(2)d, regulates pre-mRNA splicing; however, the role of WTAP in mammalian cells is uncertain. To elucidate a context for WTAP action, we screened growth and survival factors for their effects on WTAP expression in vascular smooth muscle cells (SMCs), a cell type previously found to express WTAP dynamically. This revealed that insulin-like growth factor-1 (IGF-1) uniquely reduced WTAP abundance. This decline in WTAP proved to be necessary for IGF-1 to confer its antiapoptotic properties, which were blocked by transducing the WTAP gene into SMCs. WTAP down-regulation by IGF-1 was mediated by an IGF-1 receptor-phosphatidylinositol 3-kinase-Akt signaling axis that directed WTAP degradation via a nuclear 26 S proteasome. Moreover, by promoting the degradation of WTAP, IGF-1 shifted the pre-mRNA splicing program for the survival factor, survivin, to reduce expression of survivin-2B, which is proapoptotic, and increase expression of survivin, which is antiapoptotic. Knockdown of survivin-2B rescued the ability of IGF-1 to promote survival when WTAP was overexpressed. These data uncover a novel regulatory cascade for human SMC survival based on adjusting the nuclear abundance of WTAP to define the splice variant balance among survivin isoforms.
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Affiliation(s)
- Theodore W Small
- Robarts Research Institute, University of Western Ontario, London, Ontario N6A 5K8, Canada
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31
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Zhong S, Li H, Bodi Z, Button J, Vespa L, Herzog M, Fray RG. MTA is an Arabidopsis messenger RNA adenosine methylase and interacts with a homolog of a sex-specific splicing factor. THE PLANT CELL 2008; 20:1278-88. [PMID: 18505803 PMCID: PMC2438467 DOI: 10.1105/tpc.108.058883] [Citation(s) in RCA: 451] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Revised: 04/23/2008] [Accepted: 05/12/2008] [Indexed: 05/18/2023]
Abstract
N6-Methyladenosine is a ubiquitous modification identified in the mRNA of numerous eukaryotes, where it is present within both coding and noncoding regions. However, this base modification does not alter the coding capacity, and its biological significance remains unclear. We show that Arabidopsis thaliana mRNA contains N6-methyladenosine at levels similar to those previously reported for animal cells. We further show that inactivation of the Arabidopsis ortholog of the yeast and human mRNA adenosine methylase (MTA) results in failure of the developing embryo to progress past the globular stage. We also demonstrate that the arrested seeds are deficient in mRNAs containing N6-methyladenosine. Expression of MTA is strongly associated with dividing tissues, particularly reproductive organs, shoot meristems, and emerging lateral roots. Finally, we show that MTA interacts in vitro and in vivo with At FIP37, a homolog of the Drosophila protein FEMALE LETHAL2D and of human WILMS' TUMOUR1-ASSOCIATING PROTEIN. The results reported here provide direct evidence for an essential function for N6-methyladenosine in a multicellular eukaryote, and the interaction with At FIP37 suggests possible RNA processing events that might be regulated or altered by this base modification.
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Affiliation(s)
- Silin Zhong
- Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
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32
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Camara N, Whitworth C, Van Doren M. The creation of sexual dimorphism in the Drosophila soma. Curr Top Dev Biol 2008; 83:65-107. [PMID: 19118664 DOI: 10.1016/s0070-2153(08)00403-1] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Animals have evolved a fascinating array of mechanisms for conducting sexual reproduction. These include producing the sex-specific gametes, as well as mechanisms for attracting a mate, courting a mate, and getting the gametes together. These processes require that males and females take on dramatically different forms (sexual dimorphism). Here, we will explore the problem of how sex is determined in Drosophila, and pay particular attention to how information about sexual identity is used to instruct males and females to develop differently. Along the way, we will highlight new work that challenges some of the traditional views about sex determination. In Drosophila, it is commonly thought that every cell decides its own sex based on its sex chromosome constitution (XX vs. XY). However, we now know that many cell types undergo nonautonomous sex determination, where they are told what sex to be through signals from surrounding cells, independent of their own chromosomal content. Further, it now appears that not all cells even "know" their sex, since key members of the sex determination pathway are not expressed in all cells. Thus, our understanding of how sex is determined, and how sexual identity is used to create sexual dimorphism, has changed considerably.
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Affiliation(s)
- Nicole Camara
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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