1
|
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.
Collapse
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
| |
Collapse
|
2
|
Irving OJ, Matthews L, Coulthard S, Neely RK, Grant MM, Albrecht T. Sterically Enhanced Control of Enzyme-Assisted DNA Assembly. Chembiochem 2023; 24:e202300361. [PMID: 37681318 DOI: 10.1002/cbic.202300361] [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: 05/12/2023] [Revised: 08/15/2023] [Accepted: 09/06/2023] [Indexed: 09/09/2023]
Abstract
Traditional methods for the assembly of functionalised DNA structures, involving enzyme restriction and modification, present difficulties when working with small DNA fragments (<100 bp), in part due to a lack of control over enzymatic action during the DNA modification process. This limits the design flexibility and range of accessible DNA structures. Here, we show that these limitations can be overcome by introducing chemical modifications into the DNA that spatially restrict enzymatic activity. This approach, sterically controlled nuclease enhanced (SCoNE) DNA assembly, thereby circumvents the size limitations of conventional Gibson assembly (GA) and allows the preparation of well-defined, functionalised DNA structures with multiple probes for specific analytes, such as IL-6, procalcitonin (PCT), and a biotin reporter group. Notably, when using the same starting materials, conventional GA under typical conditions fails. We demonstrate successful analyte capture based on standard and modified sandwich ELISA and also show how the inclusion of biotin probes provides additional functionality for product isolation.
Collapse
Affiliation(s)
- Oliver J Irving
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Lauren Matthews
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Steven Coulthard
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Robert K Neely
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Melissa M Grant
- School of Dentistry, Institute of Clinical Sciences, University of Birmingham and Birmingham Dental Hospital, Birmingham Community Healthcare Trust), 5 Mill Pool Way, Edgbaston, Birmingham, B5 7EG, UK
| | - Tim Albrecht
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| |
Collapse
|
3
|
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 cis- and trans-splicing of C. elegans mRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.16.558044. [PMID: 37745402 PMCID: PMC10516052 DOI: 10.1101/2023.09.16.558044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
pre-mRNA splicing is a critical feature of eukaryotic gene expression. Many eukaryotes use cis-splicing to remove intronic sequences from pre-mRNAs. In addition to cis-splicing, many organisms use trans-splicing to replace the 5' ends of mRNAs with a non-coding spliced-leader RNA. 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 m6A modification of U6 snRNA A43 by the RNA methyltransferase METT-10 is required for accurate and efficient cis- and trans-splicing of C. elegans pre-mRNAs. The absence of U6 snRNA m6A modification primarily leads to alternative splicing at 5' splice sites. Furthermore, weaker 5' splice site recognition by the unmodified U6 snRNA A43 affects splicing at 3' splice sites. U6 snRNA m6A43 and the splicing factor SNRNP27K function to recognise an overlapping set of 5' splice sites with an adenosine at +4 position. Finally, we show that U6 snRNA m6A43 is required for efficient SL trans-splicing at weak 3' trans-splice sites. We conclude that the U6 snRNA m6A modification is important for accurate and efficient cis- and trans-splicing in C. elegans.
Collapse
Affiliation(s)
- Aykut Shen
- School of Biological Sciences, University of East Anglia, NR4 7TJ, Norwich
| | - Katarzyna Hencel
- School of Biological Sciences, University of East Anglia, NR4 7TJ, Norwich
- These authors contributed equally
| | - Matthew T Parker
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
- These authors contributed equally
| | - 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
| | | | | | - 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
- 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
| |
Collapse
|
4
|
Zhang M, Nie J, Chen Y, Li X, Chen H. Connecting the Dots: N6-Methyladenosine (m 6 A) Modification in Spermatogenesis. Adv Biol (Weinh) 2023; 7:e2300068. [PMID: 37353958 DOI: 10.1002/adbi.202300068] [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: 02/09/2023] [Revised: 05/20/2023] [Indexed: 06/25/2023]
Abstract
N6-methyladenosine (m6 A) is the most common RNA modification found in eukaryotes and is involved in multiple biological processes, including neuronal development, tumorigenesis, and gametogenesis. It is well known that methylation-modifying enzymes (classified into writers, erasers, and readers) mediate catalysis, clearance, and recognition of m6 A. Recent studies suggest that these genes may be associated with spermatogenesis. Numerous studies have revealed the m6 A role during spermatogenesis. However, the expression patterns and relationships of these m6 A enzymes during various stages of spermatogenesis remain unknown. In this review, it is aimed to provide an overview of m6 A enzyme functions and elucidate their potential mechanisms and regulatory relationships at a specific phase during spermatogenesis, providing new insights into the m6 A modification underlying the spermatogenesis process.
Collapse
Affiliation(s)
- Mengya Zhang
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, 226000, China
| | - Junyu Nie
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, 226000, China
| | - Yufei Chen
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, 226000, China
| | - Xiaofeng Li
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Lianhua Road No. 1120, Futian District, Shenzhen, Guangdong Province, 518000, P. R. China
| | - Hao Chen
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, 226000, China
| |
Collapse
|
5
|
Wang F, Zhang J, Lin X, Yang L, Zhou Q, Mi X, Li Q, Wang S, Li D, Liu XM, Zhou J. METTL16 promotes translation and lung tumorigenesis by sequestering cytoplasmic eIF4E2. Cell Rep 2023; 42:112150. [PMID: 36840945 DOI: 10.1016/j.celrep.2023.112150] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/21/2022] [Accepted: 02/08/2023] [Indexed: 02/26/2023] Open
Abstract
N6-methyladenosine (m6A) plays crucial roles in regulating RNA metabolisms. METTL16 identified as a single-component methyltransferase catalyzes m6A formation in the nucleus; whether it regulates cytoplasmic RNA fate remains unknown. Here, we detected the dual localization of METTL16 in the nucleus and cytoplasm. METTL16 depletion attenuates protein synthesis, but the methyltransferase activity is not required for its translation-promoting function. Mechanistically, we identified an interactor of METTL16, eIF4E2, which represses translation by acting as a competitor of eIF4E. The METTL16-eIF4E2 interaction impedes the recruitment of eIF4E2 to 5' cap structure, promoting the cap recognition by eIF4E and selective protein synthesis. Depletion of METTL16 suppresses lung tumorigenesis by downregulating the translation of key oncogenes. Collectively, our study reports a role of METTL16 in modulating translation and provides a therapeutic target for lung cancer treatment.
Collapse
Affiliation(s)
- Fei Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Jun Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Xianrong Lin
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Lu Yang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Qi Zhou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Xue Mi
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Qiujie Li
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Shen Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Dawei Li
- Center for Translational Medicine, The Affiliated Zhangjiagang Hospital of Soochow University, 68 Jiyang West Road, 215600, Suzhou, China
| | - Xiao-Min Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China; Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 21009, China.
| | - Jun Zhou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu 210009, China; Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 21009, China.
| |
Collapse
|
6
|
Mermoud JE. The Role of the m 6A RNA Methyltransferase METTL16 in Gene Expression and SAM Homeostasis. Genes (Basel) 2022; 13:genes13122312. [PMID: 36553579 PMCID: PMC9778287 DOI: 10.3390/genes13122312] [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: 09/14/2022] [Revised: 11/26/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
The RNA methylation of adenosine at the N6-position (m6A) has attracted significant attention because of its abundance and dynamic nature. It accounts for more than 80% of all RNA modifications present in bacteria and eukaryotes and regulates crucial aspects of RNA biology and gene expression in numerous biological processes. The majority of m6A found in mammals is deposited by a multicomponent complex formed between methyltransferase-like (METTL) proteins METTL3 and METTL14. In the last few years, the list of m6A writers has grown, resulting in an expansion of our understanding of the importance of m6A and the methylation machinery. The characterization of the less familiar family member METTL16 has uncovered a new function of the m6A methylation apparatus, namely the fine-tuning of the cellular levels of the major methyl donor S-adenosylmethionine (SAM). METTL16 achieves this by adjusting the levels of the enzyme that synthesizes SAM in direct response to fluctuations in the SAM availability. This review summarizes recent progress made in understanding how METTL16 can sense and relay metabolic information and considers the wider implications. A brief survey highlights similarities and differences between METTL16 and the better-known METTL3/14 complex, followed by a discussion of the target specificity, modes of action and potential roles of METTL16.
Collapse
Affiliation(s)
- Jacqueline E Mermoud
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, 35043 Marburg, Germany
| |
Collapse
|
7
|
Sun B, Bhati KK, Song P, Edwards A, Petri L, Kruusvee V, Blaakmeer A, Dolde U, Rodrigues V, Straub D, Yang J, Jia G, Wenkel S. FIONA1-mediated methylation of the 3’UTR of FLC affects FLC transcript levels and flowering in Arabidopsis. PLoS Genet 2022; 18:e1010386. [PMID: 36166469 PMCID: PMC9543952 DOI: 10.1371/journal.pgen.1010386] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 10/07/2022] [Accepted: 08/19/2022] [Indexed: 12/02/2022] Open
Abstract
Adenosine bases of RNA can be transiently modified by the deposition of a methyl-group to form N6-methyladenosine (m6A). This adenosine-methylation is an ancient process and the enzymes involved are evolutionary highly conserved. A genetic screen designed to identify suppressors of late flowering transgenic Arabidopsis plants overexpressing the miP1a microProtein yielded a new allele of the FIONA1 (FIO1) m6A-methyltransferase. To characterize the early flowering phenotype of fio1 mutant plants we employed an integrative approach of mRNA-seq, Nanopore direct RNA-sequencing and meRIP-seq to identify differentially expressed transcripts as well as differentially methylated RNAs. We provide evidence that FIO1 is the elusive methyltransferase responsible for the 3’-end methylation of the FLOWERING LOCUS C (FLC) transcript. Furthermore, our genetic and biochemical data suggest that 3’-methylation stabilizes FLC mRNAs and non-methylated FLC is a target for rapid degradation. Plants constantly measure environmental parameters such as temperature, light-quality, -quantity and -duration, as well as other parameters to adjust their growth and development. The transition to flowering is a crucial transition during plant development because it impacts the number of fertile offspring a plant can produce. Thus, this transition is under tight control by various transcription factors and epigenetic mechanisms. In a genetic screen for early flowering mutants, we identified the gene encoding the FIONA1 methyltransferase to act as a repressor of flowering. Investigation of the changes of the transcriptome and m6A-RNA-methylome revealed a large number of differentially expressed genes and methylated RNAs. Among these RNAs is the also the mRNA of the floral repressor FLOWERING LOCUS C that shows loss of m6A methylation in the 3’UTR that causes destabilization of the FLC transcript.
Collapse
Affiliation(s)
- Bin Sun
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Kaushal Kumar Bhati
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Peizhe Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Ashleigh Edwards
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Louise Petri
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Valdeko Kruusvee
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Anko Blaakmeer
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Ulla Dolde
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Vandasue Rodrigues
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Daniel Straub
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
- Quantitative Biology Center (QBiC), University of Tübingen, Auf der Morgenstelle, Tübingen, Germany
| | - Junbo Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Stephan Wenkel
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
- NovoCrops Center, Frederiksberg, Denmark
- * E-mail:
| |
Collapse
|
8
|
Oerum S, Meynier V, Catala M, Tisné C. A comprehensive review of m6A/m6Am RNA methyltransferase structures. Nucleic Acids Res 2021; 49:7239-7255. [PMID: 34023900 PMCID: PMC8287941 DOI: 10.1093/nar/gkab378] [Citation(s) in RCA: 196] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
Gene expression is regulated at many levels including co- or post-transcriptionally, where chemical modifications are added to RNA on riboses and bases. Expression control via RNA modifications has been termed 'epitranscriptomics' to keep with the related 'epigenomics' for DNA modification. One such RNA modification is the N6-methylation found on adenosine (m6A) and 2'-O-methyladenosine (m6Am) in most types of RNA. The N6-methylation can affect the fold, stability, degradation and cellular interaction(s) of the modified RNA, implicating it in processes such as splicing, translation, export and decay. The multiple roles played by this modification explains why m6A misregulation is connected to multiple human cancers. The m6A/m6Am writer enzymes are RNA methyltransferases (MTases). Structures are available for functionally characterized m6A RNA MTases from human (m6A mRNA, m6A snRNA, m6A rRNA and m6Am mRNA MTases), zebrafish (m6Am mRNA MTase) and bacteria (m6A rRNA MTase). For each of these MTases, we describe their overall domain organization, the active site architecture and the substrate binding. We identify areas that remain to be investigated, propose yet unexplored routes for structural characterization of MTase:substrate complexes, and highlight common structural elements that should be described for future m6A/m6Am RNA MTase structures.
Collapse
Affiliation(s)
- Stephanie Oerum
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France
| | - Vincent Meynier
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France
| | - Marjorie Catala
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France
| | - Carine Tisné
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France
| |
Collapse
|
9
|
Satterwhite ER, Mansfield KD. RNA methyltransferase METTL16: Targets and function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1681. [PMID: 34227247 PMCID: PMC9286414 DOI: 10.1002/wrna.1681] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/12/2022]
Abstract
The N6-methyladenosine (m6A) RNA methyltransferase METTL16 is an emerging player in the RNA modification landscape of the human cell. Originally thought to be a ribosomal RNA methyltransferase, it has now been shown to bind and methylate the MAT2A messenger RNA (mRNA) and U6 small nuclear RNA (snRNA). It has also been shown to bind the MALAT1 long noncoding RNA and several other RNAs. METTL16's methyltransferase domain contains the Rossmann-like fold of class I methyltransferases and uses S-adenosylmethionine (SAM) as the methyl donor. It has an RNA methylation consensus sequence of UACAGARAA (modified A underlined), and structural requirements for its known RNA interactors. In addition to the methyltransferase domain, METTL16 protein has two other RNA binding domains, one of which resides in a vertebrate conserved region, and a putative nuclear localization signal. The role of METTL16 in the cell is still being explored, however evidence suggests it is essential for most cells. This is currently hypothesized to be due to its role in regulating the splicing of MAT2A mRNA in response to cellular SAM levels. However, one of the more pressing questions remaining is what role METTL16's methylation of U6 snRNA plays in splicing and potentially cellular survival. METTL16 also has several other putative coding and noncoding RNA interactors but the definitive methylation status of those RNAs and the role METTL16 plays in their life cycle is yet to be determined. Overall, METTL16 is an intriguing RNA binding protein and methyltransferase whose important functions in the cell are just beginning to be understood. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
Collapse
Affiliation(s)
- Emily R Satterwhite
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Kyle D Mansfield
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| |
Collapse
|
10
|
Gui Y, Yuan S. Epigenetic regulations in mammalian spermatogenesis: RNA-m 6A modification and beyond. Cell Mol Life Sci 2021; 78:4893-4905. [PMID: 33835194 PMCID: PMC11073063 DOI: 10.1007/s00018-021-03823-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/04/2021] [Accepted: 03/25/2021] [Indexed: 02/06/2023]
Abstract
Emerging evidence shows that m6A, one of the most abundant RNA modifications in mammals, is involved in the entire process of spermatogenesis, including mitosis, meiosis, and spermiogenesis. "Writers" catalyze m6A formation on stage-specific transcripts during male germline development, while "erasers" remove m6A modification to maintain a balance between methylation and demethylation. The different functions of RNA-m6A transcripts depend on their recognition by "readers". m6A modification mediates RNA metabolism, including mRNA splicing, translation, and degradation, as well as the maturity and biosynthesis of non-coding RNAs. Sperm RNA profiles are easily affected by environmental exposure and can even be inherited for several generations, similar to epigenetic inheritance. Here, we review and summarize the critical role of m6A in different developmental stages of male germ cells, to understand of the mechanisms and epigenetic regulation of m6A modifications. In addition, we also outline and discuss the important role of non-coding RNAs in spermatogenesis and RNA modifications in epigenetic inheritance.
Collapse
Affiliation(s)
- Yiqian Gui
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, 518057, China.
| |
Collapse
|
11
|
A single m 6A modification in U6 snRNA diversifies exon sequence at the 5' splice site. Nat Commun 2021; 12:3244. [PMID: 34050143 PMCID: PMC8163875 DOI: 10.1038/s41467-021-23457-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/29/2021] [Indexed: 11/09/2022] Open
Abstract
N6-methyladenosine (m6A) is a modification that plays pivotal roles in RNA metabolism and function, although its functions in spliceosomal U6 snRNA remain unknown. To elucidate its role, we conduct a large-scale transcriptome analysis of a Schizosaccharomyces pombe strain lacking this modification and found a global change of pre-mRNA splicing. The most significantly impacted introns are enriched for adenosine at the fourth position pairing the m6A in U6 snRNA, and exon sequences weakly recognized by U5 snRNA. This suggests cooperative recognition of 5' splice site by U6 and U5 snRNPs, and also a role of m6A facilitating efficient recognition of the splice sites weakly interacting with U5 snRNA, indicating that U6 snRNA m6A relaxes the 5' exon constraint and allows protein sequence diversity along with explosively increasing number of introns over the course of eukaryotic evolution.
Collapse
|
12
|
Mendel M, Delaney K, Pandey RR, Chen KM, Wenda JM, Vågbø CB, Steiner FA, Homolka D, Pillai RS. Splice site m 6A methylation prevents binding of U2AF35 to inhibit RNA splicing. Cell 2021; 184:3125-3142.e25. [PMID: 33930289 PMCID: PMC8208822 DOI: 10.1016/j.cell.2021.03.062] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 02/16/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023]
Abstract
The N6-methyladenosine (m6A) RNA modification is used widely to alter the fate of mRNAs. Here we demonstrate that the C. elegans writer METT-10 (the ortholog of mouse METTL16) deposits an m6A mark on the 3′ splice site (AG) of the S-adenosylmethionine (SAM) synthetase pre-mRNA, which inhibits its proper splicing and protein production. The mechanism is triggered by a rich diet and acts as an m6A-mediated switch to stop SAM production and regulate its homeostasis. Although the mammalian SAM synthetase pre-mRNA is not regulated via this mechanism, we show that splicing inhibition by 3′ splice site m6A is conserved in mammals. The modification functions by physically preventing the essential splicing factor U2AF35 from recognizing the 3′ splice site. We propose that use of splice-site m6A is an ancient mechanism for splicing regulation. m6A deposited at 3′ splice site by worm METT-10 inhibits splicing Methylation blocks 3′ splice site recognition by splicing factor U2AF35 Methylation and splicing inhibition is a response to change in worm diet Splicing inhibition by 3′ splice site m6A is conserved in mammals
Collapse
Affiliation(s)
- Mateusz Mendel
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Kamila Delaney
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Radha Raman Pandey
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Kuan-Ming Chen
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Joanna M Wenda
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Cathrine Broberg Vågbø
- Proteomics and Modomics Experimental Core (PROMEC), Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU) and St. Olavs Hospital Central Staff, Trondheim, Norway
| | - Florian A Steiner
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - David Homolka
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland.
| | - Ramesh S Pillai
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland.
| |
Collapse
|
13
|
Ruszkowska A. METTL16, Methyltransferase-Like Protein 16: Current Insights into Structure and Function. Int J Mol Sci 2021; 22:ijms22042176. [PMID: 33671635 PMCID: PMC7927073 DOI: 10.3390/ijms22042176] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/03/2021] [Accepted: 02/16/2021] [Indexed: 12/31/2022] Open
Abstract
Methyltransferase-like protein 16 (METTL16) is a human RNA methyltransferase that installs m6A marks on U6 small nuclear RNA (U6 snRNA) and S-adenosylmethionine (SAM) synthetase pre-mRNA. METTL16 also controls a significant portion of m6A epitranscriptome by regulating SAM homeostasis. Multiple molecular structures of the N-terminal methyltransferase domain of METTL16, including apo forms and complexes with S-adenosylhomocysteine (SAH) or RNA, provided the structural basis of METTL16 interaction with the coenzyme and substrates, as well as indicated autoinhibitory mechanism of the enzyme activity regulation. Very recent structural and functional studies of vertebrate-conserved regions (VCRs) indicated their crucial role in the interaction with U6 snRNA. METTL16 remains an object of intense studies, as it has been associated with numerous RNA classes, including mRNA, non-coding RNA, long non-coding RNA (lncRNA), and rRNA. Moreover, the interaction between METTL16 and oncogenic lncRNA MALAT1 indicates the existence of METTL16 features specifically recognizing RNA triple helices. Overall, the number of known human m6A methyltransferases has grown from one to five during the last five years. METTL16, CAPAM, and two rRNA methyltransferases, METTL5/TRMT112 and ZCCHC4, have joined the well-known METTL3/METTL14. This work summarizes current knowledge about METTL16 in the landscape of human m6A RNA methyltransferases.
Collapse
Affiliation(s)
- Agnieszka Ruszkowska
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| |
Collapse
|
14
|
Wang J, Wang WA, Zhang A, Liu HB. Molecular mechanism of methyltransferase-like protein family: Relationship with gastric cancer. Shijie Huaren Xiaohua Zazhi 2020; 28:428-434. [DOI: 10.11569/wcjd.v28.i11.428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Methyltransferase-like proteins (METTL) are part of a large protein family, which is characterized by the presence of an S-adenosylmethionine (SAM; a common substrate for methylation reactions) binding domain. Although members of this protein family have been shown or predicted as methyltransferases of RNA, DNA, or proteins, most methyltransferases are still poorly characterized. Identifying the complexes where these potential enzymes work can help to understand their function and substrate specificity. The METTL protein family is closely related to the occurrence and development of gastric cancer (GC), and its relationship with GC is of great importance in the diagnosis, treatment, and prognosis of GC. Here we give a systematic and comprehensive review of the mechanism of METTL protein family and its relationship with GC, with an aim to provide important resources for further research on these potential new methyltransferases and the diagnosis and treatment of GC.
Collapse
Affiliation(s)
- Jing Wang
- Gansu University of Chinese Medicine, Lanzhou 730000, Gansu Province, China
| | - Wen-An Wang
- Gansu University of Chinese Medicine, Lanzhou 730000, Gansu Province, China
| | - An Zhang
- Gansu University of Chinese Medicine, Lanzhou 730000, Gansu Province, China
| | - Hong-Bin Liu
- People's Liberation Army Joint Logistics Support Unit 940 Hospital, Lanzhou 730000, Gansu Province, China
| |
Collapse
|
15
|
Hubbard EJA, Schedl T. Biology of the Caenorhabditis elegans Germline Stem Cell System. Genetics 2019; 213:1145-1188. [PMID: 31796552 PMCID: PMC6893382 DOI: 10.1534/genetics.119.300238] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 09/09/2019] [Indexed: 12/14/2022] Open
Abstract
Stem cell systems regulate tissue development and maintenance. The germline stem cell system is essential for animal reproduction, controlling both the timing and number of progeny through its influence on gamete production. In this review, we first draw general comparisons to stem cell systems in other organisms, and then present our current understanding of the germline stem cell system in Caenorhabditis elegans In contrast to stereotypic somatic development and cell number stasis of adult somatic cells in C. elegans, the germline stem cell system has a variable division pattern, and the system differs between larval development, early adult peak reproduction and age-related decline. We discuss the cell and developmental biology of the stem cell system and the Notch regulated genetic network that controls the key decision between the stem cell fate and meiotic development, as it occurs under optimal laboratory conditions in adult and larval stages. We then discuss alterations of the stem cell system in response to environmental perturbations and aging. A recurring distinction is between processes that control stem cell fate and those that control cell cycle regulation. C. elegans is a powerful model for understanding germline stem cells and stem cell biology.
Collapse
Affiliation(s)
- E Jane Albert Hubbard
- Skirball Institute of Biomolecular Medicine, Departments of Cell Biology and Pathology, New York University School of Medicine, New York 10016
| | - Tim Schedl
- and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
| |
Collapse
|
16
|
Shima H, Matsumoto M, Ishigami Y, Ebina M, Muto A, Sato Y, Kumagai S, Ochiai K, Suzuki T, Igarashi K. S-Adenosylmethionine Synthesis Is Regulated by Selective N 6-Adenosine Methylation and mRNA Degradation Involving METTL16 and YTHDC1. Cell Rep 2018; 21:3354-3363. [PMID: 29262316 DOI: 10.1016/j.celrep.2017.11.092] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 10/18/2017] [Accepted: 11/28/2017] [Indexed: 11/19/2022] Open
Abstract
S-adenosylmethionine (SAM) is an important metabolite as a methyl-group donor in DNA and histone methylation, tuning regulation of gene expression. Appropriate intracellular SAM levels must be maintained, because methyltransferase reaction rates can be limited by SAM availability. In response to SAM depletion, MAT2A, which encodes a ubiquitous mammalian methionine adenosyltransferase isozyme, was upregulated through mRNA stabilization. SAM-depletion reduced N6-methyladenosine (m6A) in the 3' UTR of MAT2A. In vitro reactions using recombinant METTL16 revealed multiple, conserved methylation targets in the 3' UTR. Knockdown of METTL16 and the m6A reader YTHDC1 abolished SAM-responsive regulation of MAT2A. Mutations of the target adenine sites of METTL16 within the 3' UTR revealed that these m6As were redundantly required for regulation. MAT2A mRNA methylation by METTL16 is read by YTHDC1, and we suggest that this allows cells to monitor and maintain intracellular SAM levels.
Collapse
Affiliation(s)
- Hiroki Shima
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan; Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Mitsuyo Matsumoto
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan; Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Yuma Ishigami
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Masayuki Ebina
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Akihiko Muto
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Yuho Sato
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Sayaka Kumagai
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Kyoko Ochiai
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan; Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan; Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan.
| |
Collapse
|
17
|
Ruszkowska A, Ruszkowski M, Dauter Z, Brown JA. Structural insights into the RNA methyltransferase domain of METTL16. Sci Rep 2018; 8:5311. [PMID: 29593291 PMCID: PMC5871880 DOI: 10.1038/s41598-018-23608-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/16/2018] [Indexed: 12/30/2022] Open
Abstract
N6-methyladenosine (m6A) is an abundant modification in messenger RNA and noncoding RNAs that affects RNA metabolism. Methyltransferase-like protein 16 (METTL16) is a recently confirmed m6A RNA methyltransferase that methylates U6 spliceosomal RNA and interacts with the 3′-terminal RNA triple helix of MALAT1 (metastasis-associated lung adenocarcinoma transcript 1). Here, we present two X-ray crystal structures of the N-terminal methyltransferase domain (residues 1–291) of human METTL16 (METTL16_291): an apo structure at 1.9 Å resolution and a post-catalytic S-adenosylhomocysteine-bound complex at 2.1 Å resolution. The structures revealed a highly conserved Rossmann fold that is characteristic of Class I S-adenosylmethionine-dependent methyltransferases and a large, positively charged groove. This groove likely represents the RNA-binding site and it includes structural elements unique to METTL16. In-depth analysis of the active site led to a model of the methyl transfer reaction catalyzed by METTL16. In contrast to the major m6A methyltransferase heterodimer METTL3/METTL14, full-length METTL16 forms a homodimer and METTL16_291 exists as a monomer based on size-exclusion chromatography. A native gel-shift assay shows that METTL16 binds to the MALAT1 RNA triple helix, but monomeric METTL16_291 does not. Our results provide insights into the molecular structure of METTL16, which is distinct from METTL3/METTL14.
Collapse
Affiliation(s)
- Agnieszka Ruszkowska
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Milosz Ruszkowski
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL, 60439, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL, 60439, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA.
| |
Collapse
|
18
|
Pendleton KE, Chen B, Liu K, Hunter OV, Xie Y, Tu BP, Conrad NK. The U6 snRNA m 6A Methyltransferase METTL16 Regulates SAM Synthetase Intron Retention. Cell 2017; 169:824-835.e14. [PMID: 28525753 DOI: 10.1016/j.cell.2017.05.003] [Citation(s) in RCA: 692] [Impact Index Per Article: 98.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/16/2017] [Accepted: 04/28/2017] [Indexed: 12/15/2022]
Abstract
Maintenance of proper levels of the methyl donor S-adenosylmethionine (SAM) is critical for a wide variety of biological processes. We demonstrate that the N6-adenosine methyltransferase METTL16 regulates expression of human MAT2A, which encodes the SAM synthetase expressed in most cells. Upon SAM depletion by methionine starvation, cells induce MAT2A expression by enhanced splicing of a retained intron. Induction requires METTL16 and its methylation substrate, a vertebrate conserved hairpin (hp1) in the MAT2A 3' UTR. Increasing METTL16 occupancy on the MAT2A 3' UTR is sufficient to induce efficient splicing. We propose that, under SAM-limiting conditions, METTL16 occupancy on hp1 increases due to inefficient enzymatic turnover, which promotes MAT2A splicing. We further show that METTL16 is the long-unknown methyltransferase for the U6 spliceosomal small nuclear RNA (snRNA). These observations suggest that the conserved U6 snRNA methyltransferase evolved an additional function in vertebrates to regulate SAM homeostasis.
Collapse
Affiliation(s)
- Kathryn E Pendleton
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Beibei Chen
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kuanqing Liu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Olga V Hunter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang Xie
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Benjamin P Tu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nicholas K Conrad
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
19
|
Brown JA, Kinzig CG, DeGregorio SJ, Steitz JA. Methyltransferase-like protein 16 binds the 3'-terminal triple helix of MALAT1 long noncoding RNA. Proc Natl Acad Sci U S A 2016; 113:14013-14018. [PMID: 27872311 PMCID: PMC5150381 DOI: 10.1073/pnas.1614759113] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a cancer-promoting long noncoding RNA, accumulates in cells by using a 3'-triple-helical RNA stability element for nuclear expression (ENE). The ENE, a stem-loop structure containing a U-rich internal loop, interacts with a downstream A-rich tract (ENE+A) to form a blunt-ended triple helix composed of nine U•A-U triples interrupted by a C•G-C triple and C-G doublet. This unique structure prompted us to explore the possibility of protein binding. Native gel-shift assays revealed a shift in radiolabeled MALAT1 ENE+A RNA upon addition of HEK293T cell lysate. Competitive gel-shift assays suggested that protein binding depends not only on the triple-helical structure but also its nucleotide composition. Selection from the lysate using a biotinylated-RNA probe followed by mass spectrometry identified methyltransferase-like protein 16 (METTL16), a putative RNA methyltransferase, as an interacting protein of the MALAT1 ENE+A. Gel-shift assays confirmed the METTL16-MALAT1 ENE+A interaction in vitro: Binding was observed with recombinant METTL16, but diminished in lysate depleted of METTL16, and a supershift was detected after adding anti-METTL16 antibody. Importantly, RNA immunoprecipitation after in vivo UV cross-linking and an in situ proximity ligation assay for RNA-protein interactions confirmed an association between METTL16 and MALAT1 in cells. METTL16 is an abundant (∼5 × 105 molecules per cell) nuclear protein in HeLa cells. Its identification as a triple-stranded RNA binding protein supports the formation of RNA triple helices inside cells and suggests the existence of a class of triple-stranded RNA binding proteins, which may enable the discovery of additional cellular RNA triple helices.
Collapse
Affiliation(s)
- Jessica A Brown
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536
| | - Charles G Kinzig
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536
| | - Suzanne J DeGregorio
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536
| |
Collapse
|
20
|
Rastogi S, Borgo B, Pazdernik N, Fox P, Mardis ER, Kohara Y, Havranek J, Schedl T. Caenorhabditis elegans glp-4 Encodes a Valyl Aminoacyl tRNA Synthetase. G3 (BETHESDA, MD.) 2015; 5:2719-28. [PMID: 26464357 PMCID: PMC4683644 DOI: 10.1534/g3.115.021899] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 10/05/2015] [Indexed: 02/07/2023]
Abstract
Germline stem cell proliferation is necessary to populate the germline with sufficient numbers of cells for gametogenesis and for signaling the soma to control organismal properties such as aging. The Caenorhabditis elegans gene glp-4 was identified by the temperature-sensitive allele bn2 where mutants raised at the restrictive temperature produce adults that are essentially germ cell deficient, containing only a small number of stem cells arrested in the mitotic cycle but otherwise have a morphologically normal soma. We determined that glp-4 encodes a valyl aminoacyl transfer RNA synthetase (VARS-2) and that the probable null phenotype is early larval lethality. Phenotypic analysis indicates glp-4(bn2ts) is partial loss of function in the soma. Structural modeling suggests that bn2 Gly296Asp results in partial loss of function by a novel mechanism: aspartate 296 in the editing pocket induces inappropriate deacylation of correctly charged Val-tRNA(val). Intragenic suppressor mutations are predicted to displace aspartate 296 so that it is less able to catalyze inappropriate deacylation. Thus glp-4(bn2ts) likely causes reduced protein translation due to decreased levels of Val-tRNA(val). The germline, as a reproductive preservation mechanism during unfavorable conditions, signals the soma for organismal aging, stress and pathogen resistance. glp-4(bn2ts) mutants are widely used to generate germline deficient mutants for organismal studies, under the assumption that the soma is unaffected. As reduced translation has also been demonstrated to alter organismal properties, it is unclear whether changes in aging, stress resistance, etc. observed in glp-4(bn2ts) mutants are the result of germline deficiency or reduced translation.
Collapse
Affiliation(s)
- Suchita Rastogi
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110
| | - Ben Borgo
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110
| | - Nanette Pazdernik
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110
| | - Paul Fox
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110
| | - Elaine R Mardis
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110
| | - Yuji Kohara
- National Institute of Genetics, Mishima, 411-8540 Japan
| | - Jim Havranek
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110
| | - Tim Schedl
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110
| |
Collapse
|
21
|
Steinbaugh MJ, Narasimhan SD, Robida-Stubbs S, Moronetti Mazzeo LE, Dreyfuss JM, Hourihan JM, Raghavan P, Operaña TN, Esmaillie R, Blackwell TK. Lipid-mediated regulation of SKN-1/Nrf in response to germ cell absence. eLife 2015. [PMID: 26196144 PMCID: PMC4541496 DOI: 10.7554/elife.07836] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In Caenorhabditis elegans, ablation of germline stem cells (GSCs) extends lifespan, but also increases fat accumulation and alters lipid metabolism, raising the intriguing question of how these effects might be related. Here, we show that a lack of GSCs results in a broad transcriptional reprogramming in which the conserved detoxification regulator SKN-1/Nrf increases stress resistance, proteasome activity, and longevity. SKN-1 also activates diverse lipid metabolism genes and reduces fat storage, thereby alleviating the increased fat accumulation caused by GSC absence. Surprisingly, SKN-1 is activated by signals from this fat, which appears to derive from unconsumed yolk that was produced for reproduction. We conclude that SKN-1 plays a direct role in maintaining lipid homeostasis in which it is activated by lipids. This SKN-1 function may explain the importance of mammalian Nrf proteins in fatty liver disease and suggest that particular endogenous or dietary lipids might promote health through SKN-1/Nrf.
Collapse
Affiliation(s)
| | | | | | | | | | - John M Hourihan
- Department of Genetics and Harvard Stem Cell Institute, Harvard Medical School, Boston, United States
| | | | | | - Reza Esmaillie
- Research Division, Joslin Diabetes Center, Boston, United States
| | | |
Collapse
|
22
|
Wang X, Gupta P, Fairbanks J, Hansen D. Protein kinase CK2 both promotes robust proliferation and inhibits the proliferative fate in the C. elegans germ line. Dev Biol 2014; 392:26-41. [PMID: 24824786 DOI: 10.1016/j.ydbio.2014.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 04/02/2014] [Accepted: 05/02/2014] [Indexed: 11/18/2022]
Abstract
Stem cells are capable of both self-renewal (proliferation) and differentiation. Determining the regulatory mechanisms controlling the balance between stem cell proliferation and differentiation is not only an important biological question, but also holds the key for using stem cells as therapeutic agents. The Caenorhabditis elegans germ line has emerged as a valuable model to study the molecular mechanisms controlling stem cell behavior. In this study, we describe a large-scale RNAi screen that identified kin-10, which encodes the β subunit of protein kinase CK2, as a novel factor regulating stem cell proliferation in the C. elegans germ line. While a loss of kin-10 in an otherwise wild-type background results in a decrease in the number of proliferative cells, loss of kin-10 in sensitized genetic backgrounds results in a germline tumor. Therefore, kin-10 is not only necessary for robust proliferation, it also inhibits the proliferative fate. We found that kin-10's regulatory role in inhibiting the proliferative fate is carried out through the CK2 holoenzyme, rather than through a holoenzyme-independent function, and that it functions downstream of GLP-1/Notch signaling. We propose that a loss of kin-10 leads to a defect in CK2 phosphorylation of its downstream targets, resulting in abnormal activity of target protein(s) that are involved in the proliferative fate vs. differentiation decision. This eventually causes a shift towards the proliferative fate in the stem cell fate decision.
Collapse
Affiliation(s)
- Xin Wang
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
| | - Pratyush Gupta
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
| | - Jared Fairbanks
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
| | - Dave Hansen
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4.
| |
Collapse
|
23
|
Loss of Caenorhabditis elegans BRCA1 promotes genome stability during replication in smc-5 mutants. Genetics 2014; 196:985-99. [PMID: 24424777 PMCID: PMC3982690 DOI: 10.1534/genetics.113.158295] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
DNA damage by ultraviolet (UV) light poses a risk for mutagenesis and a potential hindrance for cell cycle progression. Cells cope with UV-induced DNA damage through two general strategies to repair the damaged nucleotides and to promote cell cycle progression in the presence of UV-damaged DNA. Defining the genetic pathways and understanding how they function together to enable effective tolerance to UV remains an important area of research. The structural maintenance of chromosomes (SMC) proteins form distinct complexes that maintain genome stability during chromosome segregation, homologous recombination, and DNA replication. Using a forward genetic screen, we identified two alleles of smc-5 that exacerbate UV sensitivity in Caenorhabditis elegans. Germ cells of smc-5-defective animals show reduced proliferation, sensitivity to perturbed replication, chromatin bridge formation, and accumulation of RAD-51 foci that indicate the activation of homologous recombination at DNA double-strand breaks. Mutations in the translesion synthesis polymerase polh-1 act synergistically with smc-5 mutations in provoking genome instability after UV-induced DNA damage. In contrast, the DNA damage accumulation and sensitivity of smc-5 mutant strains to replication impediments are suppressed by mutations in the C. elegans BRCA1/BARD1 homologs, brc-1 and brd-1. We propose that SMC-5/6 promotes replication fork stability and facilitates recombination-dependent repair when the BRC-1/BRD-1 complex initiates homologous recombination at stalled replication forks. Our data suggest that BRC-1/BRD-1 can both promote and antagonize genome stability depending on whether homologous recombination is initiated during DNA double-strand break repair or during replication stalling.
Collapse
|
24
|
Hansen D, Schedl T. Stem cell proliferation versus meiotic fate decision in Caenorhabditis elegans. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 757:71-99. [PMID: 22872475 PMCID: PMC3786863 DOI: 10.1007/978-1-4614-4015-4_4] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The C. elegans germ line has emerged as an important model for -understanding how a stem cell population is maintained throughout the life of the animal while still producing the gametes necessary for propagation of the species. The stem cell population in the adult hermaphrodite is relatively large, with stem cells giving rise to daughters that appear intrinsically equivalent; however, some of the daughters retain the proliferative fate while others enter meiotic prophase. While machinery exists for cells to progress through the mitotic cell cycle and machinery exists for cells to progress through meiotic prophase, central to understanding germ line development is identifying the genes and regulatory processes that determine whether the mitotic cell cycle or meiotic prophase machinery will be utilized; in other words, the genes that regulate the switch of germ cells from the proliferative stem cell fate to the meiotic development fate. Whether a germ cell self-renews or enters meiotic prophase is largely determined by its proximity to the distal tip cell (DTC), which is the somatic niche cell that caps the distal end of the gonad. Germ cells close to the DTC have high levels of GLP-1 Notch signaling, which promotes the proliferative fate, while cells further from the DTC have high activity levels of the GLD-1 and GLD-2 redundant RNA regulatory pathways, as well as a third uncharacterized pathway, each of which direct cells to enter meiotic prophase. Other factors and pathways modulate this core genetic pathway, or work in parallel to it, presumably to ensure that a tight balance is maintained between proliferation and meiotic entry.
Collapse
Affiliation(s)
- Dave Hansen
- Department of Biological Sciences, 2500 University Drive, University of Calgary, Calgary, Alberta, Canada
| | - Tim Schedl
- Department of Genetics, Campus Box 8232, Washington University School of Medicine, 4566 Scott Ave, St Louis MO
| |
Collapse
|
25
|
Rangarajan A, Schedl T, Yook K, Chan J, Haenel S, Otis L, Faelten S, DePellegrin-Connelly T, Isaacson R, Skrzypek MS, Marygold SJ, Stefancsik R, Cherry JM, Sternberg PW, Müller HM. Toward an interactive article: integrating journals and biological databases. BMC Bioinformatics 2011; 12:175. [PMID: 21595960 PMCID: PMC3213741 DOI: 10.1186/1471-2105-12-175] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 05/19/2011] [Indexed: 05/06/2023] Open
Abstract
Background Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five years and have resulted in the development of automated tools that can recognize entities within a document and link those entities to a relevant database. Unfortunately, automated tools cannot resolve ambiguities that arise from one term being used to signify entities that are quite distinct from one another. Instead, resolving these ambiguities requires some manual oversight. Finding the right balance between the speed and portability of automation and the accuracy and flexibility of manual effort is a crucial goal to making text markup a successful venture. Results We have established a journal article mark-up pipeline that links GENETICS journal articles and the model organism database (MOD) WormBase. This pipeline uses a lexicon built with entities from the database as a first step. The entity markup pipeline results in links from over nine classes of objects including genes, proteins, alleles, phenotypes and anatomical terms. New entities and ambiguities are discovered and resolved by a database curator through a manual quality control (QC) step, along with help from authors via a web form that is provided to them by the journal. New entities discovered through this pipeline are immediately sent to an appropriate curator at the database. Ambiguous entities that do not automatically resolve to one link are resolved by hand ensuring an accurate link. This pipeline has been extended to other databases, namely Saccharomyces Genome Database (SGD) and FlyBase, and has been implemented in marking up a paper with links to multiple databases. Conclusions Our semi-automated pipeline hyperlinks articles published in GENETICS to model organism databases such as WormBase. Our pipeline results in interactive articles that are data rich with high accuracy. The use of a manual quality control step sets this pipeline apart from other hyperlinking tools and results in benefits to authors, journals, readers and databases.
Collapse
Affiliation(s)
- Arun Rangarajan
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Abstract
Although now dogma, the idea that nonvertebrate organisms such as yeast, worms, and flies could inform, and in some cases even revolutionize, our understanding of oncogenesis in humans was not immediately obvious. Aided by the conservative nature of evolution and the persistence of a cohort of devoted researchers, the role of model organisms as a key tool in solving the cancer problem has, however, become widely accepted. In this review, we focus on the nematode Caenorhabditis elegans and its diverse and sometimes surprising contributions to our understanding of the tumorigenic process. Specifically, we discuss findings in the worm that address a well-defined set of processes known to be deregulated in cancer cells including cell cycle progression, growth factor signaling, terminal differentiation, apoptosis, the maintenance of genome stability, and developmental mechanisms relevant to invasion and metastasis.
Collapse
Affiliation(s)
- Natalia V. Kirienko
- University of Wyoming, College of Agriculture, Department of Molecular Biology, Dept 3944, 1000 E. University Avenue, Laramie, WY 82071
| | - Kumaran Mani
- University of Wyoming, College of Agriculture, Department of Molecular Biology, Dept 3944, 1000 E. University Avenue, Laramie, WY 82071
| | - David S. Fay
- University of Wyoming, College of Agriculture, Department of Molecular Biology, Dept 3944, 1000 E. University Avenue, Laramie, WY 82071
| |
Collapse
|
27
|
Korta DZ, Hubbard EJA. Soma-germline interactions that influence germline proliferation in Caenorhabditis elegans. Dev Dyn 2010; 239:1449-59. [PMID: 20225254 PMCID: PMC3323287 DOI: 10.1002/dvdy.22268] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Caenorhabditis elegans boasts a short lifecycle and high fecundity, two features that make it an attractive and powerful genetic model organism. Several recent studies indicate that germline proliferation, a prerequisite to optimal fecundity, is tightly controlled over the course of development. Cell proliferation control includes regulation of competence to proliferate, a poorly understood aspect of cell fate specification, as well as cell-cycle control. Furthermore, dynamic regulation of cell proliferation occurs in response to multiple external signals. The C. elegans germ line is proving a valuable model for linking genetic, developmental, systemic, and environmental control of cell proliferation. Here, we consider recent studies that contribute to our understanding of germ cell proliferation in C. elegans. We focus primarily on somatic control of germline proliferation, how it differs at different life stages, and how it can be altered in the context of the life cycle and changes in environmental status.
Collapse
Affiliation(s)
- Dorota Z. Korta
- Developmental Genetics Program, Department of Pathology, Helen and Martin Kimmel Center for Stem Cell Biology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York
| | - E. Jane Albert Hubbard
- Developmental Genetics Program, Department of Pathology, Helen and Martin Kimmel Center for Stem Cell Biology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York
| |
Collapse
|
28
|
Michaelson D, Korta DZ, Capua Y, Hubbard EJA. Insulin signaling promotes germline proliferation in C. elegans. Development 2010; 137:671-80. [PMID: 20110332 DOI: 10.1242/dev.042523] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cell proliferation must be coordinated with cell fate specification during development, yet interactions among pathways that control these two critical aspects of development are not well understood. The coordination of cell fate specification and proliferation is particularly crucial during early germline development, when it impacts the establishment of stem/progenitor cell populations and ultimately the production of gametes. In C. elegans, insulin/IGF-like receptor (IIR) signaling has been implicated in fertility, but the basis for the fertility defect had not been previously characterized. We found that IIR signaling is required for robust larval germline proliferation, separate from its well-characterized role in preventing dauer entry. IIR signaling stimulates the larval germline cell cycle. This activity is distinct from Notch signaling, occurs in a predominantly germline-autonomous manner, and responds to somatic activity of ins-3 and ins-33, genes that encode putative insulin-like ligands. IIR signaling in this role acts through the canonical PI3K pathway, inhibiting DAF-16/FOXO. However, signaling from these ligands does not inhibit daf-16 in neurons nor in the intestine, two tissues previously implicated in other IIR roles. Our data are consistent with a model in which: (1) under replete reproductive conditions, the larval germline responds to insulin signaling to ensure robust germline proliferation that builds up the germline stem cell population; and (2) distinct insulin-like ligands contribute to different phenotypes by acting on IIR signaling in different tissues.
Collapse
Affiliation(s)
- David Michaelson
- Developmental Genetics Program, Helen and Martin Kimmel Center for Stem Cell Biology, Skirball Institute of Biomolecular Medicine, Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | | | | | | |
Collapse
|
29
|
Dorsett M, Schedl T. A role for dynein in the inhibition of germ cell proliferative fate. Mol Cell Biol 2009; 29:6128-39. [PMID: 19752194 PMCID: PMC2772574 DOI: 10.1128/mcb.00815-09] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Revised: 07/24/2009] [Accepted: 09/08/2009] [Indexed: 01/30/2023] Open
Abstract
During normal development as well as in diseased states such as cancer, extracellular "niches" often provide cues to proximal cells and activate intracellular pathways. Activation of such signaling pathways in turn instructs cellular proliferation and differentiation. In the Caenorhabditis elegans gonad, GLP-1/Notch signaling instructs germ line stem cells to self-renew through mitotic cell division. As germ cells progressively move out of the niche, they differentiate by entering meiosis and eventually form gametes. In this model system, we uncovered an unexpected role for the dynein motor complex in promoting normal differentiation of proliferating germ cells. We demonstrate that dynein light chain 1 (DLC-1) and its partner, dynein heavy chain 1, inhibit the proliferative cell fate, in part through regulation of METT-10, a conserved putative methyltransferase. We show that DLC-1 physically interacts with METT-10 and promotes both its overall levels and nuclear accumulation. Our results add a new dimension to the processes controlled by the dynein motor complex, demonstrating that dynein can act as an antiproliferative factor.
Collapse
Affiliation(s)
- Maia Dorsett
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, 63110
| | - Tim Schedl
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, 63110
| |
Collapse
|