1
|
Fu J, Cui X, Zhang X, Cheng M, Li X, Guo Z, Cui X. The Role of m6A Ribonucleic Acid Modification in the Occurrence of Atherosclerosis. Front Genet 2021; 12:733871. [PMID: 34603394 PMCID: PMC8481608 DOI: 10.3389/fgene.2021.733871] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/02/2021] [Indexed: 12/29/2022] Open
Abstract
The N6-methyladenosine (m6A) modification is the most abundant epitranscriptomic modification in eukaryotic messenger RNA (mRNA). The m6A modification process is jointly regulated by various enzymes and proteins, such as methyltransferases, demethylases and related m6A-binding proteins. The process is dynamic and reversible, and it plays an essential role in mRNA metabolism and various biological activities. Recently, an increasing number of researchers have confirmed that the onset and development of many diseases are closely associated with the molecular biological mechanism of m6A RNA methylation. This study focuses on the relationship between m6A RNA modification and atherosclerosis (AS). It thoroughly summarizes the mechanisms and processes of m6A RNA modification in AS-related cells and the relationships between m6A RNA modification and AS risk factors, and it provides a reference for exploring new targets for the early diagnosis and treatment of AS.
Collapse
Affiliation(s)
- Jie Fu
- School of Clinical Medicine, Weifang Medical University, Weifang, China.,School of Basic Medicine Sciences, Weifang Medical University, Weifang, China
| | - Xinghui Cui
- School of Clinical Medicine, Weifang Medical University, Weifang, China.,School of Basic Medicine Sciences, Weifang Medical University, Weifang, China
| | - Xiaoyun Zhang
- School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Min Cheng
- School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Xiaoxia Li
- Institute of Stem Cell and Regenerative Medicine, Department of Basic Medicine, Qingdao University Medical College, Qingdao, China
| | - Zhiliang Guo
- The 80th Group Army Hospital of Chinese People' Liberation Army, Weifang, China
| | - Xiaodong Cui
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, China
| |
Collapse
|
2
|
Nakagawa N, Sonohara F, Tanaka K, Sunagawa Y, Inokawa Y, Takami H, Hayashi M, Yamada S, Kanda M, Tanaka C, Nakayama G, Koike M, Kodera Y. Novel prognostic implications of YTH domain family 2 in resected hepatocellular carcinoma. Oncol Lett 2021; 22:538. [PMID: 34084217 PMCID: PMC8161462 DOI: 10.3892/ol.2021.12799] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/04/2021] [Indexed: 02/06/2023] Open
Abstract
N6-methyladenosine (m6A), the most abundant internal RNA modification, serves a critical role in cancer development. However, the clinical implications of m6A in hepatocellular carcinoma (HCC) remain unclear. The present study sought to reveal the potential roles of m6A readers, which recognize m6A, in HCC. A total of 177 HCC and paired non-cancerous liver tissues from patients who underwent hepatectomy were analysed using quantitative PCR for the expression of m6A readers: YT521-B homology domain family 1 (YTHDF1) and YT521-B homology domain family 2 (YTHDF2). The expression levels of both YTHDF1 and YTHDF2 were not significantly different between tumour and non-cancerous tissues (P=0.93 and P=0.7, respectively). Analysis of the association between clinical features and m6A reader expression revealed that YTHDF1 expression was associated with formation of capsule (P=0.02), whereas low YTHDF2 expression was associated with septal formation (P=0.02). Furthermore, high YTHDF1 expression and high YTHDF2 expression were significantly associated with shorter recurrence-free survival (RFS) [YTHDF1: Mean survival time (MST), 34.0 vs. 19.0 months, P=0.014; YTHDF2: MST, 30.1 vs. 12.9 months, P=0.0032], whereas YTHDF1 and YTHDF2 expression was not significantly associated with overall survival (OS) (YTHDF1: MST, 99.4 vs. 70.2 months, P=0.74; YTHDF2: MST, 98.4 vs. 64.1 months, P=0.28). According to multivariate analysis, serosal invasion [hazard ratio (HR), 2.39; 95% CI 1.30–4.42; P=0.005), portal vein or hepatic vein invasion (HR, 2.82; 95% CI 1.26–6.28; P=0.01) and YTHDF2 expression in HCC tissues (HR, 1.85; 95% CI 1.09–3.15; P=0.02) were identified as significant independent prognostic factors for RFS. α-fetoprotein (HR, 1.79; 95% CI 1.10–2.92; P=0.02), serosal invasion (HR, 1.99; 95% CI 1.17–3.34; P=0.01) and portal vein or hepatic vein invasion (HR, 3.02; 95% CI 1.38–6.61; P=0.006) were identified as significant independent prognostic factors for OS. In conclusion, the present study revealed that high YTHDF2 expression, an m6A reader, in HCC tissues was associated with cancer recurrence.
Collapse
Affiliation(s)
- Nobuhiko Nakagawa
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Fuminori Sonohara
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Katsuhito Tanaka
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Yuki Sunagawa
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Yoshikuni Inokawa
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Hideki Takami
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Masamichi Hayashi
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Suguru Yamada
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Mitsuro Kanda
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Chie Tanaka
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Goro Nakayama
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Masahiko Koike
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Yasuhiro Kodera
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| |
Collapse
|
3
|
Xu J, Cai Y, Ma Z, Jiang B, Liu W, Cheng J, Guo N, Wang Z, Sealy JE, Song C, Wang X, Li Y. The RNA helicase DDX5 promotes viral infection via regulating N6-methyladenosine levels on the DHX58 and NFκB transcripts to dampen antiviral innate immunity. PLoS Pathog 2021; 17:e1009530. [PMID: 33909701 PMCID: PMC8081163 DOI: 10.1371/journal.ppat.1009530] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/02/2021] [Indexed: 02/06/2023] Open
Abstract
Multi-functional DEAD-box helicase 5 (DDX5), which is important in transcriptional regulation, is hijacked by diverse viruses to facilitate viral replication. However, its regulatory effect in antiviral innate immunity remains unclear. We found that DDX5 interacts with the N6-methyladenosine (m6A) writer METTL3 to regulate methylation of mRNA through affecting the m6A writer METTL3–METTL14 heterodimer complex. Meanwhile, DDX5 promoted the m6A modification and nuclear export of transcripts DHX58, p65, and IKKγ by binding conserved UGCUGCAG element in innate response after viral infection. Stable IKKγ and p65 transcripts underwent YTHDF2-dependent mRNA decay, whereas DHX58 translation was promoted, resulting in inhibited antiviral innate response by DDX5 via blocking the p65 pathway and activating the DHX58-TBK1 pathway after infection with RNA virus. Furthermore, we found that DDX5 suppresses antiviral innate immunity in vivo. Our findings reveal that DDX5 serves as a negative regulator of innate immunity by promoting RNA methylation of antiviral transcripts and consequently facilitating viral propagation. DEAD-box helicase 5 (DDX5) greatly contributes to cancer development and facilitation of viral propagation. However, how DDX5 manipulates host cell processes to facilitate replication remains poorly understood. In this study, we found DDX5 is a negative antiviral regulator through manipulating N6-methyladenosine (m6A) of transcripts in innate immunity. Firstly, DDX5 recruited the RNA m6A “writer” METTL3 to control the m6A writer complex, then specifically promoted m6A modification and nuclear export of DDX5 binding transcripts by binding conserved UGCUGCAG element in innate immune response, ultimately, leading to RNA decay of antiviral transcripts in a YTHDF2-dependent manner. Consequently, DDX5 played vital roles in cellular RNA metabolisms to negatively regulate innate immune response to viral infection. It is the first time to unravel DDX5 as an important component that mediates modification of N6-methyladenosine of mRNA in regulating innate immunity.
Collapse
Affiliation(s)
- Jian Xu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, P. R. China
| | - Yunhong Cai
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, P. R. China
| | - ZhenBang Ma
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, P. R. China
| | - Bo Jiang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, P. R. China
| | - Wenxiao Liu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, P. R. China
| | - Jing Cheng
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, P. R. China
| | - Nannan Guo
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, P. R. China
| | - Zishu Wang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, P. R. China
| | - Joshua E. Sealy
- The Pirbright Institute, Ash Rd, Pirbright, Woking, United Kingdom
| | - Cuiping Song
- China Animal Health and Epidemiology Center, Qingdao, Shandong, P. R. China
| | - Xiaojia Wang
- College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
| | - Yongqing Li
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, P. R. China
- * E-mail:
| |
Collapse
|
4
|
The Butterfly Effect of RNA Alterations on Transcriptomic Equilibrium. Cells 2019; 8:cells8121634. [PMID: 31847302 PMCID: PMC6953095 DOI: 10.3390/cells8121634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 12/17/2022] Open
Abstract
: Post-transcriptional regulation plays a key role in modulating gene expression, and the perturbation of transcriptomic equilibrium has been shown to drive the development of multiple diseases including cancer. Recent studies have revealed the existence of multiple post-transcriptional processes that coordinatively regulate the expression and function of each RNA transcript. In this review, we summarize the latest research describing various mechanisms by which small alterations in RNA processing or function can potentially reshape the transcriptomic landscape, and the impact that this may have on cancer development.
Collapse
|
5
|
Leonardi A, Evke S, Lee M, Melendez JA, Begley TJ. Epitranscriptomic systems regulate the translation of reactive oxygen species detoxifying and disease linked selenoproteins. Free Radic Biol Med 2019; 143:573-593. [PMID: 31476365 PMCID: PMC7650020 DOI: 10.1016/j.freeradbiomed.2019.08.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 02/07/2023]
Abstract
Here we highlight the role of epitranscriptomic systems in post-transcriptional regulation, with a specific focus on RNA modifying writers required for the incorporation of the 21st amino acid selenocysteine during translation, and the pathologies linked to epitranscriptomic and selenoprotein defects. Epitranscriptomic marks in the form of enzyme-catalyzed modifications to RNA have been shown to be important signals regulating translation, with defects linked to altered development, intellectual impairment, and cancer. Modifications to rRNA, mRNA and tRNA can affect their structure and function, while the levels of these dynamic tRNA-specific epitranscriptomic marks are stress-regulated to control translation. The tRNA for selenocysteine contains five distinct epitranscriptomic marks and the ALKBH8 writer for the wobble uridine (U) has been shown to be vital for the translation of the glutathione peroxidase (GPX) and thioredoxin reductase (TRXR) family of selenoproteins. The reactive oxygen species (ROS) detoxifying selenocysteine containing proteins are a prime examples of how specialized translation can be regulated by specific tRNA modifications working in conjunction with distinct codon usage patterns, RNA binding proteins and specific 3' untranslated region (UTR) signals. We highlight the important role of selenoproteins in detoxifying ROS and provide details on how epitranscriptomic marks and selenoproteins can play key roles in and maintaining mitochondrial function and preventing disease.
Collapse
Affiliation(s)
- Andrea Leonardi
- Colleges of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY, USA
| | - Sara Evke
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA
| | - May Lee
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA
| | - J Andres Melendez
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA.
| | - Thomas J Begley
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA; RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
| |
Collapse
|
6
|
Heck AM, Wilusz CJ. Small changes, big implications: The impact of m 6A RNA methylation on gene expression in pluripotency and development. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2019; 1862:194402. [PMID: 31325527 PMCID: PMC6742438 DOI: 10.1016/j.bbagrm.2019.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/21/2019] [Accepted: 07/12/2019] [Indexed: 12/20/2022]
Abstract
In order to maintain a state of self-renewal, yet retain the ability to rapidly differentiate in response to external signals, pluripotent cells exert tight control over gene expression at many levels. Recent studies have suggested that N6-methyladenosine (m6A) RNA methylation, one of the most abundant post-transcriptional modifications, is important for both pluripotency and differentiation. In this review, we summarize the current state of the m6A field, with emphasis on the impact of writers, erasers and readers of m6A on RNA metabolism and stem cell biology.
Collapse
Affiliation(s)
- Adam M Heck
- Program in Cell & Molecular Biology, and Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO 80525, United States of America
| | - Carol J Wilusz
- Program in Cell & Molecular Biology, and Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO 80525, United States of America.
| |
Collapse
|
7
|
Lesbirel S, Wilson SA. The m 6A‑methylase complex and mRNA export. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2019; 1862:319-328. [PMID: 30290229 PMCID: PMC6414750 DOI: 10.1016/j.bbagrm.2018.09.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 09/26/2018] [Accepted: 09/28/2018] [Indexed: 11/21/2022]
Abstract
During synthesis, mRNA undergoes a number of modifications such as capping, splicing and polyadenylation. These processes are coupled with the orderly deposition of the TREX complex on the mRNA and subsequent recruitment of the NXF1-P15 heterodimer which stimulates the nuclear export of mature mRNAs. mRNAs also undergo a number of internal modifications, the most common of which is the N6‑methyladenosine (m6A) modification. In this review we discuss the recent evidence of coupling between the m6A modification, RNA processing and export.
Collapse
Affiliation(s)
- Simon Lesbirel
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield S10 2TN, UK
| | - Stuart A Wilson
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield S10 2TN, UK.
| |
Collapse
|
8
|
Covelo-Molares H, Bartosovic M, Vanacova S. RNA methylation in nuclear pre-mRNA processing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1489. [PMID: 29921017 PMCID: PMC6221173 DOI: 10.1002/wrna.1489] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 01/09/2023]
Abstract
Eukaryotic RNA can carry more than 100 different types of chemical modifications. Early studies have been focused on modifications of highly abundant RNA, such as ribosomal RNA and transfer RNA, but recent technical advances have made it possible to also study messenger RNA (mRNA). Subsequently, mRNA modifications, namely methylation, have emerged as key players in eukaryotic gene expression regulation. The most abundant and widely studied internal mRNA modification is N6‐methyladenosine (m6A), but the list of mRNA chemical modifications continues to grow as fast as interest in this field. Over the past decade, transcriptome‐wide studies combined with advanced biochemistry and the discovery of methylation writers, readers, and erasers revealed roles for mRNA methylation in the regulation of nearly every aspect of the mRNA life cycle and in diverse cellular, developmental, and disease processes. Although large parts of mRNA function are linked to its cytoplasmic stability and regulation of its translation, a number of studies have begun to provide evidence for methylation‐regulated nuclear processes. In this review, we summarize the recent advances in RNA methylation research and highlight how these new findings have contributed to our understanding of methylation‐dependent RNA processing in the nucleus. This article is categorized under:
RNA Processing > RNA Editing and Modification RNA Processing > Splicing Regulation/Alternative Splicing RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications
Collapse
|
9
|
Kasowitz SD, Ma J, Anderson SJ, Leu NA, Xu Y, Gregory BD, Schultz RM, Wang PJ. Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development. PLoS Genet 2018; 14:e1007412. [PMID: 29799838 PMCID: PMC5991768 DOI: 10.1371/journal.pgen.1007412] [Citation(s) in RCA: 357] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/07/2018] [Accepted: 05/14/2018] [Indexed: 12/31/2022] Open
Abstract
The N6-methyladenosine (m6A) modification is the most prevalent internal RNA modification in eukaryotes. The majority of m6A sites are found in the last exon and 3' UTRs. Here we show that the nuclear m6A reader YTHDC1 is essential for embryo viability and germline development in mouse. Specifically, YTHDC1 is required for spermatogonial development in males and for oocyte growth and maturation in females; Ythdc1-deficient oocytes are blocked at the primary follicle stage. Strikingly, loss of YTHDC1 leads to extensive alternative polyadenylation in oocytes, altering 3' UTR length. Furthermore, YTHDC1 deficiency causes massive alternative splicing defects in oocytes. The majority of splicing defects in mutant oocytes are rescued by introducing wild-type, but not m6A-binding-deficient, YTHDC1. YTHDC1 is associated with the pre-mRNA 3' end processing factors CPSF6, SRSF3, and SRSF7. Thus, YTHDC1 plays a critical role in processing of pre-mRNA transcripts in the oocyte nucleus and may have similar non-redundant roles throughout fetal development.
Collapse
Affiliation(s)
- Seth D. Kasowitz
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States of America
| | - Jun Ma
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States of America
- Department of Biology, University of Pennsylvania, Philadelphia, United States of America
| | - Stephen J. Anderson
- Department of Biology, University of Pennsylvania, Philadelphia, United States of America
| | - N. Adrian Leu
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States of America
| | - Yang Xu
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States of America
| | - Brian D. Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, United States of America
| | - Richard M. Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, United States of America
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, United States of America
| | - P. Jeremy Wang
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States of America
| |
Collapse
|
10
|
Abstract
RNA contains over 150 types of chemical modifications. Although many of these chemical modifications were discovered several decades ago, their functions were not immediately apparent. Discoveries of RNA demethylases, along with advances in mass spectrometry and high-throughput sequencing techniques, have caused research into RNA modifications to progress at an accelerated rate. Post-transcriptional RNA modifications make up an epitranscriptome that extensively regulates gene expression and biological processes. Here, we present an overview of recent advances in the field that are shaping our understanding of chemical modifications, their impact on development and disease, and the dynamic mechanisms through which they regulate gene expression.
Collapse
Affiliation(s)
- Phillip J Hsu
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA.,Medical Scientist Training Program and Committee on Immunology, The University of Chicago, Chicago, IL, 60637, USA
| | - Hailing Shi
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA. .,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.
| |
Collapse
|
11
|
Roundtree IA, Luo GZ, Zhang Z, Wang X, Zhou T, Cui Y, Sha J, Huang X, Guerrero L, Xie P, He E, Shen B, He C. YTHDC1 mediates nuclear export of N 6-methyladenosine methylated mRNAs. eLife 2017; 6:31311. [PMID: 28984244 PMCID: PMC5648532 DOI: 10.7554/elife.31311] [Citation(s) in RCA: 772] [Impact Index Per Article: 110.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/04/2017] [Indexed: 12/11/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification of eukaryotic messenger RNA (mRNA) and plays critical roles in RNA biology. The function of this modification is mediated by m6A-selective ‘reader’ proteins of the YTH family, which incorporate m6A-modified mRNAs into pathways of RNA metabolism. Here, we show that the m6A-binding protein YTHDC1 mediates export of methylated mRNA from the nucleus to the cytoplasm in HeLa cells. Knockdown of YTHDC1 results in an extended residence time for nuclear m6A-containing mRNA, with an accumulation of transcripts in the nucleus and accompanying depletion within the cytoplasm. YTHDC1 interacts with the splicing factor and nuclear export adaptor protein SRSF3, and facilitates RNA binding to both SRSF3 and NXF1. This role for YTHDC1 expands the potential utility of chemical modification of mRNA, and supports an emerging paradigm of m6A as a distinct biochemical entity for selective processing and metabolism of mammalian mRNAs.
Collapse
Affiliation(s)
- Ian A Roundtree
- Department of Chemistry, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Chicago, United States.,Howard Hughes Medical Institute, University of Chicago, Chicago, United States.,University of Chicago Medical Scientist Training Program, Chicago, United States
| | - Guan-Zheng Luo
- Department of Chemistry, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Chicago, United States.,Howard Hughes Medical Institute, University of Chicago, Chicago, United States
| | - Zijie Zhang
- Department of Chemistry, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Chicago, United States.,Howard Hughes Medical Institute, University of Chicago, Chicago, United States
| | - Xiao Wang
- Department of Chemistry, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Chicago, United States.,Howard Hughes Medical Institute, University of Chicago, Chicago, United States
| | - Tao Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yiquang Cui
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Jiahao Sha
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Laura Guerrero
- Department of Chemistry, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Chicago, United States.,Howard Hughes Medical Institute, University of Chicago, Chicago, United States
| | - Phil Xie
- Department of Chemistry, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Chicago, United States.,Howard Hughes Medical Institute, University of Chicago, Chicago, United States
| | - Emily He
- Department of Chemistry, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Chicago, United States.,Howard Hughes Medical Institute, University of Chicago, Chicago, United States
| | - Bin Shen
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Chuan He
- Department of Chemistry, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Chicago, United States.,Howard Hughes Medical Institute, University of Chicago, Chicago, United States
| |
Collapse
|
12
|
Roundtree IA, Evans ME, Pan T, He C. Dynamic RNA Modifications in Gene Expression Regulation. Cell 2017; 169:1187-1200. [PMID: 28622506 PMCID: PMC5657247 DOI: 10.1016/j.cell.2017.05.045] [Citation(s) in RCA: 2041] [Impact Index Per Article: 291.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/08/2017] [Accepted: 05/26/2017] [Indexed: 12/14/2022]
Abstract
Over 100 types of chemical modifications have been identified in cellular RNAs. While the 5' cap modification and the poly(A) tail of eukaryotic mRNA play key roles in regulation, internal modifications are gaining attention for their roles in mRNA metabolism. The most abundant internal mRNA modification is N6-methyladenosine (m6A), and identification of proteins that install, recognize, and remove this and other marks have revealed roles for mRNA modification in nearly every aspect of the mRNA life cycle, as well as in various cellular, developmental, and disease processes. Abundant noncoding RNAs such as tRNAs, rRNAs, and spliceosomal RNAs are also heavily modified and depend on the modifications for their biogenesis and function. Our understanding of the biological contributions of these different chemical modifications is beginning to take shape, but it's clear that in both coding and noncoding RNAs, dynamic modifications represent a new layer of control of genetic information.
Collapse
Affiliation(s)
- Ian A Roundtree
- Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA; Medical Scientist Training Program, The University of Chicago, 924 East 57(th) Street, Chicago, IL 60637, USA
| | - Molly E Evans
- Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA.
| | - Chuan He
- Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA; Department of Chemistry, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA.
| |
Collapse
|
13
|
Wan Y, Tang K, Zhang D, Xie S, Zhu X, Wang Z, Lang Z. Transcriptome-wide high-throughput deep m(6)A-seq reveals unique differential m(6)A methylation patterns between three organs in Arabidopsis thaliana. Genome Biol 2015; 16:272. [PMID: 26667818 PMCID: PMC4714525 DOI: 10.1186/s13059-015-0839-2] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 11/18/2015] [Indexed: 12/25/2022] Open
Abstract
Background m6A is a ubiquitous RNA modification in eukaryotes. Transcriptome-wide m6A patterns in Arabidopsis have been assayed recently. However, differential m6A patterns between organs have not been well characterized. Results Over two-third of the transcripts in Arabidopsis are modified by m6A. In contrast to a recent observation of m6A enrichment in 5′ mRNA, we find that m6A is distributed predominantly near stop codons. Interestingly, 85 % of the modified transcripts show high m6A methylation extent compared to their transcript level. The 290 highly methylated transcripts are mainly associated with transporters, stress responses, redox, regulation factors, and some non-coding RNAs. On average, the proportion of transcripts showing differential methylation between two plant organs is higher than that showing differential transcript levels. The transcripts with extensively higher m6A methylation in an organ are associated with the unique biological processes of this organ, suggesting that m6A may be another important contributor to organ differentiation in Arabidopsis. Highly expressed genes are relatively less methylated and vice versa, and different RNAs have distinct m6A patterns, which hint at mRNA fate. Intriguingly, most of the transposable element transcripts maintained a fragmented form with a relatively low transcript level and high m6A methylation in the cells. Conclusions This is the first study to comprehensively analyze m6A patterns in a variety of RNAs, the relationship between transcript level and m6A methylation extent, and differential m6A patterns across organs in Arabidopsis. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0839-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yizhen Wan
- State Key Lab Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China. .,Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.
| | - Kai Tang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Dayong Zhang
- Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Shaojun Xie
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.,Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiaohong Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.,Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zegang Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Zhaobo Lang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA. .,Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| |
Collapse
|
14
|
Ke S, Alemu EA, Mertens C, Gantman EC, Fak JJ, Mele A, Haripal B, Zucker-Scharff I, Moore MJ, Park CY, Vågbø CB, Kusśnierczyk A, Klungland A, Darnell JE, Darnell RB. A majority of m6A residues are in the last exons, allowing the potential for 3' UTR regulation. Genes Dev 2015; 29:2037-53. [PMID: 26404942 PMCID: PMC4604345 DOI: 10.1101/gad.269415.115] [Citation(s) in RCA: 585] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 09/01/2015] [Indexed: 12/13/2022]
Abstract
Ke et al. found that >70% of m6A residues are present in the 3′-most (last) exons, with a sharp rise within 150–400 nucleotides of the start of the last exon. This report also suggests a role of m6A modification in regulating proximal alternative polyA choice. We adapted UV CLIP (cross-linking immunoprecipitation) to accurately locate tens of thousands of m6A residues in mammalian mRNA with single-nucleotide resolution. More than 70% of these residues are present in the 3′-most (last) exons, with a very sharp rise (sixfold) within 150–400 nucleotides of the start of the last exon. Two-thirds of last exon m6A and >40% of all m6A in mRNA are present in 3′ untranslated regions (UTRs); contrary to earlier suggestions, there is no preference for location of m6A sites around stop codons. Moreover, m6A is significantly higher in noncoding last exons than in next-to-last exons harboring stop codons. We found that m6A density peaks early in the 3′ UTR and that, among transcripts with alternative polyA (APA) usage in both the brain and the liver, brain transcripts preferentially use distal polyA sites, as reported, and also show higher proximal m6A density in the last exons. Furthermore, when we reduced m6A methylation by knocking down components of the methylase complex and then examined 661 transcripts with proximal m6A peaks in last exons, we identified a set of 111 transcripts with altered (approximately two-thirds increased proximal) APA use. Taken together, these observations suggest a role of m6A modification in regulating proximal alternative polyA choice.
Collapse
Affiliation(s)
- Shengdong Ke
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Endalkachew A Alemu
- Department of Microbiology, Division of Diagnostics and Intervention, Institute of Clinical Medicine, Oslo University Hospital, Rikshospitalet, NO-0027, Oslo, Norway; Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, 0316 Oslo, Norway
| | - Claudia Mertens
- Laboratory of Molecular Cell Biology, The Rockefeller University, New York, New York 10065, USA
| | - Emily Conn Gantman
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA; New York Genome Center, New York, New York 10013, USA
| | - John J Fak
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Aldo Mele
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Bhagwattie Haripal
- Laboratory of Molecular Cell Biology, The Rockefeller University, New York, New York 10065, USA
| | - Ilana Zucker-Scharff
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Michael J Moore
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Christopher Y Park
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA; New York Genome Center, New York, New York 10013, USA
| | - Cathrine Broberg Vågbø
- Proteomics and Metabolomics Core Facility, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7489 Trondheim, Norway
| | - Anna Kusśnierczyk
- Proteomics and Metabolomics Core Facility, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7489 Trondheim, Norway
| | - Arne Klungland
- Department of Microbiology, Division of Diagnostics and Intervention, Institute of Clinical Medicine, Oslo University Hospital, Rikshospitalet, NO-0027, Oslo, Norway; Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, 0316 Oslo, Norway
| | - James E Darnell
- Laboratory of Molecular Cell Biology, The Rockefeller University, New York, New York 10065, USA
| | - Robert B Darnell
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA; New York Genome Center, New York, New York 10013, USA
| |
Collapse
|
15
|
Alarcón CR, Lee H, Goodarzi H, Halberg N, Tavazoie SF. N6-methyladenosine marks primary microRNAs for processing. Nature 2015; 519:482-5. [PMID: 25799998 DOI: 10.1038/nature14281] [Citation(s) in RCA: 964] [Impact Index Per Article: 107.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 02/02/2015] [Indexed: 12/21/2022]
Abstract
The first step in the biogenesis of microRNAs is the processing of primary microRNAs (pri-miRNAs) by the microprocessor complex, composed of the RNA-binding protein DGCR8 and the type III RNase DROSHA. This initial event requires recognition of the junction between the stem and the flanking single-stranded RNA of the pri-miRNA hairpin by DGCR8 followed by recruitment of DROSHA, which cleaves the RNA duplex to yield the pre-miRNA product. While the mechanisms underlying pri-miRNA processing have been determined, the mechanism by which DGCR8 recognizes and binds pri-miRNAs, as opposed to other secondary structures present in transcripts, is not understood. Here we find in mammalian cells that methyltransferase-like 3 (METTL3) methylates pri-miRNAs, marking them for recognition and processing by DGCR8. Consistent with this, METTL3 depletion reduced the binding of DGCR8 to pri-miRNAs and resulted in the global reduction of mature miRNAs and concomitant accumulation of unprocessed pri-miRNAs. In vitro processing reactions confirmed the sufficiency of the N(6)-methyladenosine (m(6)A) mark in promoting pri-miRNA processing. Finally, gain-of-function experiments revealed that METTL3 is sufficient to enhance miRNA maturation in a global and non-cell-type-specific manner. Our findings reveal that the m(6)A mark acts as a key post-transcriptional modification that promotes the initiation of miRNA biogenesis.
Collapse
Affiliation(s)
- Claudio R Alarcón
- Laboratory of Systems Cancer Biology, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Hyeseung Lee
- Laboratory of Systems Cancer Biology, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Hani Goodarzi
- Laboratory of Systems Cancer Biology, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Nils Halberg
- Laboratory of Systems Cancer Biology, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| |
Collapse
|
16
|
Multiplicity of 5' cap structures present on short RNAs. PLoS One 2014; 9:e102895. [PMID: 25079783 PMCID: PMC4117478 DOI: 10.1371/journal.pone.0102895] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 06/24/2014] [Indexed: 12/18/2022] Open
Abstract
Most RNA molecules are co- or post-transcriptionally modified to alter their chemical and functional properties to assist in their ultimate biological function. Among these modifications, the addition of 5′ cap structure has been found to regulate turnover and localization. Here we report a study of the cap structure of human short (<200 nt) RNAs (sRNAs), using sequencing of cDNA libraries prepared by enzymatic pretreatment of the sRNAs with cap sensitive-specificity, thin layer chromatographic (TLC) analyses of isolated cap structures and mass spectrometric analyses for validation of TLC analyses. Processed versions of snoRNAs and tRNAs sequences of less than 50 nt were observed in capped sRNA libraries, indicating additional processing and recapping of these annotated sRNAs biotypes. We report for the first time 2,7 dimethylguanosine in human sRNAs cap structures and surprisingly we find multiple type 0 cap structures (mGpppC, 7mGpppG, GpppG, GpppA, and 7mGpppA) in RNA length fractions shorter than 50 nt. Finally, we find the presence of additional uncharacterized cap structures that wait determination by the creation of needed reference compounds to be used in TLC analyses. These studies suggest the existence of novel biochemical pathways leading to the processing of primary and sRNAs and the modifications of their RNA 5′ ends with a spectrum of chemical modifications.
Collapse
|
17
|
Merkestein M, McTaggart JS, Lee S, Kramer HB, McMurray F, Lafond M, Boutens L, Cox R, Ashcroft FM. Changes in gene expression associated with FTO overexpression in mice. PLoS One 2014; 9:e97162. [PMID: 24842286 PMCID: PMC4026227 DOI: 10.1371/journal.pone.0097162] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 04/14/2014] [Indexed: 01/24/2023] Open
Abstract
Single nucleotide polymorphisms in the first intron of the fat-mass-and-obesity-related gene FTO are associated with increased body weight and adiposity. Increased expression of FTO is likely underlying this obesity phenotype, as mice with two additional copies of Fto (FTO-4 mice) exhibit increased adiposity and are hyperphagic. FTO is a demethylase of single stranded DNA and RNA, and one of its targets is the m6A modification in RNA, which might play a role in the regulation of gene expression. In this study, we aimed to examine the changes in gene expression that occur in FTO-4 mice in order to gain more insight into the underlying mechanisms by which FTO influences body weight and adiposity. Our results indicate an upregulation of anabolic pathways and a downregulation of catabolic pathways in FTO-4 mice. Interestingly, although genes involved in methylation were differentially regulated in skeletal muscle of FTO-4 mice, no effect of FTO overexpression on m6A methylation of total mRNA was detected.
Collapse
Affiliation(s)
- Myrte Merkestein
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
| | - James S. McTaggart
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
| | - Sheena Lee
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
| | - Holger B. Kramer
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
| | - Fiona McMurray
- Medical Research Council Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Harwell, Oxford, United Kingdom
| | - Mathilde Lafond
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
| | - Lily Boutens
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
| | - Roger Cox
- Medical Research Council Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Harwell, Oxford, United Kingdom
| | - Frances M. Ashcroft
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
- * E-mail:
| |
Collapse
|
18
|
Harcourt EM, Ehrenschwender T, Batista PJ, Chang HY, Kool ET. Identification of a selective polymerase enables detection of N(6)-methyladenosine in RNA. J Am Chem Soc 2013; 135:19079-82. [PMID: 24328136 DOI: 10.1021/ja4105792] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
N(6)-methyladenosine (m(6)A) is the most abundant mRNA modification and has important links to human health. While recent studies have successfully identified thousands of mammalian RNA transcripts containing the modification, it is extremely difficult to identify the exact location of any specific m(6)A. Here we have identified a polymerase with reverse transcriptase activity (from Thermus thermophilus) that is selective by up to 18-fold for incorporation of thymidine opposite unmodified A over m(6)A. We show that the enzyme can be used to locate and quantify m(6)A in synthetic RNAs by analysis of pausing bands, and have used the enzyme in tandem with a nonselective polymerase to locate the presence and position of m(6)A in high-abundance cellular RNAs. By this approach we demonstrate that the long-undetermined position of m(6)A in mammalian 28S rRNA is nucleotide 4190.
Collapse
Affiliation(s)
- Emily M Harcourt
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | | | | | | | | |
Collapse
|
19
|
Niu Y, Zhao X, Wu YS, Li MM, Wang XJ, Yang YG. N6-methyl-adenosine (m6A) in RNA: an old modification with a novel epigenetic function. GENOMICS PROTEOMICS & BIOINFORMATICS 2012; 11:8-17. [PMID: 23453015 PMCID: PMC4357660 DOI: 10.1016/j.gpb.2012.12.002] [Citation(s) in RCA: 318] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 12/10/2012] [Accepted: 12/11/2012] [Indexed: 12/02/2022]
Abstract
N6-methyl-adenosine (m6A) is one of the most common and abundant modifications on RNA molecules present in eukaryotes. However, the biological significance of m6A methylation remains largely unknown. Several independent lines of evidence suggest that the dynamic regulation of m6A may have a profound impact on gene expression regulation. The m6A modification is catalyzed by an unidentified methyltransferase complex containing at least one subunit methyltransferase like 3 (METTL3). m6A modification on messenger RNAs (mRNAs) mainly occurs in the exonic regions and 3′-untranslated region (3′-UTR) as revealed by high-throughput m6A-seq. One significant advance in m6A research is the recent discovery of the first two m6A RNA demethylases fat mass and obesity-associated (FTO) gene and ALKBH5, which catalyze m6A demethylation in an α-ketoglutarate (α-KG)- and Fe2+-dependent manner. Recent studies in model organisms demonstrate that METTL3, FTO and ALKBH5 play important roles in many biological processes, ranging from development and metabolism to fertility. Moreover, perturbation of activities of these enzymes leads to the disturbed expression of thousands of genes at the cellular level, implicating a regulatory role of m6A in RNA metabolism. Given the vital roles of DNA and histone methylations in epigenetic regulation of basic life processes in mammals, the dynamic and reversible chemical m6A modification on RNA may also serve as a novel epigenetic marker of profound biological significances.
Collapse
Affiliation(s)
- Yamei Niu
- Disease Genomics and Individualized Medicine Laboratory, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | | | | | | | | | | |
Collapse
|
20
|
Jia G, Fu Y, He C. Reversible RNA adenosine methylation in biological regulation. Trends Genet 2012; 29:108-15. [PMID: 23218460 DOI: 10.1016/j.tig.2012.11.003] [Citation(s) in RCA: 289] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 11/01/2012] [Accepted: 11/05/2012] [Indexed: 01/20/2023]
Abstract
N(6)-methyladenosine (m(6)A) is a ubiquitous modification in mRNA and other RNAs across most eukaryotes. For many years, however, the exact functions of m(6)A were not clearly understood. The discovery that the fat mass and obesity-associated protein (FTO) is an m(6)A demethylase indicates that this modification is reversible and dynamically regulated, suggesting that it has regulatory roles. In addition, it has been shown that m(6)A affects cell fate decisions in yeast and plant development. Recent affinity-based m(6)A profiling in mouse and human cells further showed that this modification is a widespread mark in coding and noncoding RNA (ncRNA) transcripts and is likely dynamically regulated throughout developmental processes. Therefore, reversible RNA methylation, analogous to reversible DNA and histone modifications, may affect gene expression and cell fate decisions by modulating multiple RNA-related cellular pathways, which potentially provides rapid responses to various cellular and environmental signals, including energy and nutrient availability in mammals.
Collapse
Affiliation(s)
- Guifang Jia
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | | | | |
Collapse
|
21
|
Zheng G, Dahl JA, Niu Y, Fedorcsak P, Huang CM, Li CJ, Vågbø CB, Shi Y, Wang WL, Song SH, Lu Z, Bosmans RPG, Dai Q, Hao YJ, Yang X, Zhao WM, Tong WM, Wang XJ, Bogdan F, Furu K, Fu Y, Jia G, Zhao X, Liu J, Krokan HE, Klungland A, Yang YG, He C. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol Cell 2012. [PMID: 23177736 DOI: 10.1016/j.molcel.2012.10.015] [Citation(s) in RCA: 2360] [Impact Index Per Article: 196.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
N(6)-methyladenosine (m(6)A) is the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Here we report ALKBH5 as another mammalian demethylase that oxidatively reverses m(6)A in mRNA in vitro and in vivo. This demethylation activity of ALKBH5 significantly affects mRNA export and RNA metabolism as well as the assembly of mRNA processing factors in nuclear speckles. Alkbh5-deficient male mice have increased m(6)A in mRNA and are characterized by impaired fertility resulting from apoptosis that affects meiotic metaphase-stage spermatocytes. In accordance with this defect, we have identified in mouse testes 1,551 differentially expressed genes that cover broad functional categories and include spermatogenesis-related mRNAs involved in the p53 functional interaction network. The discovery of this RNA demethylase strongly suggests that the reversible m(6)A modification has fundamental and broad functions in mammalian cells.
Collapse
Affiliation(s)
- Guanqun Zheng
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Dominissini D, Moshitch-Moshkovitz S, Schwartz S, Salmon-Divon M, Ungar L, Osenberg S, Cesarkas K, Jacob-Hirsch J, Amariglio N, Kupiec M, Sorek R, Rechavi G. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 2012; 485:201-6. [PMID: 22575960 DOI: 10.1038/nature11112] [Citation(s) in RCA: 3242] [Impact Index Per Article: 270.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2011] [Accepted: 04/11/2012] [Indexed: 12/22/2022]
Abstract
An extensive repertoire of modifications is known to underlie the versatile coding, structural and catalytic functions of RNA, but it remains largely uncharted territory. Although biochemical studies indicate that N(6)-methyladenosine (m(6)A) is the most prevalent internal modification in messenger RNA, an in-depth study of its distribution and functions has been impeded by a lack of robust analytical methods. Here we present the human and mouse m(6)A modification landscape in a transcriptome-wide manner, using a novel approach, m(6)A-seq, based on antibody-mediated capture and massively parallel sequencing. We identify over 12,000 m(6)A sites characterized by a typical consensus in the transcripts of more than 7,000 human genes. Sites preferentially appear in two distinct landmarks--around stop codons and within long internal exons--and are highly conserved between human and mouse. Although most sites are well preserved across normal and cancerous tissues and in response to various stimuli, a subset of stimulus-dependent, dynamically modulated sites is identified. Silencing the m(6)A methyltransferase significantly affects gene expression and alternative splicing patterns, resulting in modulation of the p53 (also known as TP53) signalling pathway and apoptosis. Our findings therefore suggest that RNA decoration by m(6)A has a fundamental role in regulation of gene expression.
Collapse
Affiliation(s)
- Dan Dominissini
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Zamudio JR, Mittra B, Foldynová-Trantírková S, Zeiner GM, Lukes J, Bujnicki JM, Sturm NR, Campbell DA. The 2'-O-ribose methyltransferase for cap 1 of spliced leader RNA and U1 small nuclear RNA in Trypanosoma brucei. Mol Cell Biol 2007; 27:6084-92. [PMID: 17606627 PMCID: PMC1952150 DOI: 10.1128/mcb.00647-07] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
mRNA cap 1 2'-O-ribose methylation is a widespread modification that is implicated in processing, trafficking, and translational control in eukaryotic systems. The eukaryotic enzyme has yet to be identified. In kinetoplastid flagellates trans-splicing of spliced leader (SL) to polycistronic precursors conveys a hypermethylated cap 4, including a cap 0 m7G and seven additional methylations on the first 4 nucleotides, to all nuclear mRNAs. We report the first eukaryotic cap 1 2'-O-ribose methyltransferase, TbMTr1, a member of a conserved family of viral and eukaryotic enzymes. Recombinant TbMTr1 methylates the ribose of the first nucleotide of an m7G-capped substrate. Knockdowns and null mutants of TbMTr1 in Trypanosoma brucei grow normally, with loss of 2'-O-ribose methylation at cap 1 on substrate SL RNA and U1 small nuclear RNA. TbMTr1-null cells have an accumulation of cap 0 substrate without further methylation, while spliced mRNA is modified efficiently at position 4 in the absence of 2'-O-ribose methylation at position 1; downstream cap 4 methylations are independent of cap 1. Based on TbMTr1-green fluorescent protein localization, 2'-O-ribose methylation at position 1 occurs in the nucleus. Accumulation of 3'-extended SL RNA substrate indicates a delay in processing and suggests a synergistic role for cap 1 in maturation.
Collapse
Affiliation(s)
- Jesse R Zamudio
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, 609 Charles E. Young Drive East, University of California at Los Angeles, Los Angeles, CA 90095-1489, USA
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Clancy MJ, Shambaugh ME, Timpte CS, Bokar JA. Induction of sporulation in Saccharomyces cerevisiae leads to the formation of N6-methyladenosine in mRNA: a potential mechanism for the activity of the IME4 gene. Nucleic Acids Res 2002; 30:4509-18. [PMID: 12384598 PMCID: PMC137137 DOI: 10.1093/nar/gkf573] [Citation(s) in RCA: 227] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
N6-methyladenosine (m6A) is present at internal sites in mRNA isolated from all higher eukaryotes, but has not previously been detected in the mRNA of the yeast Saccharomyces cerevisiae. This nucleoside modification occurs only in a sequence- specific context that appears to be conserved across diverse species. The function of this modification is not fully established, but there is some indirect evidence that m6A may play a role in the efficiency of mRNA splicing, transport or translation. The S.cerevisiae gene IME4, which is important for induction of sporulation, is very similar to the human gene MT-A70, which has been shown to be a critical subunit of the human mRNA [N6-adenosine]-methyltransferase. This observation led to the hypothesis that yeast sporulation may be dependent upon methylation of yeast mRNA, mediated by Ime4p. In this study we show that induction of sporulation leads to the appearance of low levels of m6A in yeast mRNA and that this modification requires IME4. Moreover, single amino acid substitutions in the putative catalytic residues of Ime4p lead to severe sporulation defects in a strain whose sporulation ability is completely dependent on this protein. Collectively, these data suggest very strongly that the activation of sporulation by Ime4p is the result of its proposed methyltransferase activity and provide the most direct evidence to date of a physiologic role of m6A in a gene regulatory pathway.
Collapse
Affiliation(s)
- Mary J Clancy
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
| | | | | | | |
Collapse
|
25
|
Shimba S, Bokar JA, Rottman F, Reddy R. Accurate and efficient N-6-adenosine methylation in spliceosomal U6 small nuclear RNA by HeLa cell extract in vitro. Nucleic Acids Res 1995; 23:2421-6. [PMID: 7630720 PMCID: PMC307046 DOI: 10.1093/nar/23.13.2421] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Human U6 small nuclear RNA (U6 snRNA), an abundant snRNA required for splicing of pre-mRNAs, contains several post-transcriptional modifications including a single m6A (N-6-methyladenosine) at position 43. This A-43 residue is critical for the function of U6 snRNA in splicing of pre-mRNAs. Yeast and plant U6 snRNAs also contain m6A in the corresponding position showing that this modification is evolutionarily conserved. In this study, we show that upon incubation of an unmodified U6 RNA with HeLa cell extract, A-43 residue in human U6 snRNA was rapidly converted to m6A-43. This conversion was detectable as early as 3 min after incubation and was nearly complete in 60 min; no other A residue in U6 snRNA was converted to m6A. Deletion studies showed that the stem-loop structure near the 5' end of U6 snRNA is dispensable for m6A formation; however, the integrity of the 3' stem-loop was necessary for efficient m6A formation. These data show that a short stretch of primary sequence flanking the methylation site is not sufficient for U6 m6A methyltransferase recognition and the enzyme probably recognizes secondary and/or tertiary structural features in U6 snRNA. The enzyme that catalyzes m6A formation in U6 snRNA appears to be distinct from the prolactin mRNA methyltransferase which is also present in HeLa nuclear extracts.
Collapse
Affiliation(s)
- S Shimba
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | | |
Collapse
|
26
|
Narayan P, Ludwiczak RL, Goodwin EC, Rottman FM. Context effects on N6-adenosine methylation sites in prolactin mRNA. Nucleic Acids Res 1994; 22:419-26. [PMID: 8127679 PMCID: PMC523598 DOI: 10.1093/nar/22.3.419] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The methylation of internal adenosine residues in mRNA only occurs within GAC or AAC sequences. Although both of these sequence motifs are utilized, a general preference has been noted for the extended sequence RGACU. Not all RGACU sequences in an mRNA are methylated and the mechanisms that govern the selection of methylation sites in mRNA remain unclear. To address this problem we have examined the methylation of transcripts containing sequences of a natural mRNA, namely, bovine prolactin mRNA. In this mRNA, a specific AGACU sequence in the 3' untranslated region is the predominant site of methylation both in vivo and in vitro. The degree to which N6-adenosine methyltransferase recognizes the sequence context of the consensus methylation site was explored by mutational analysis of the nucleotides adjacent to the core sequence as well as the extended regions in which the core element was found. Our results indicate that efficient methylation depends on the extended five nucleotide consensus sequence but is strongly influenced by the context in which the consensus sequence occurs within the overall mRNA molecule. Furthermore, consensus methylation sites present in an RNA duplex are not recognized by the methyltransferase.
Collapse
Affiliation(s)
- P Narayan
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106
| | | | | | | |
Collapse
|
27
|
Tuck MT. Partial purification of a 6-methyladenine mRNA methyltransferase which modifies internal adenine residues. Biochem J 1992; 288 ( Pt 1):233-40. [PMID: 1445268 PMCID: PMC1132103 DOI: 10.1042/bj2880233] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Two forms of a 6-methyladenine mRNA methyltransferase have been partially purified using a T7 transcript coding for mouse dihydrofolate reductase as an RNA substrate. Both enzyme forms modify internal adenine residues within the RNA substrate. The enzymes were purified 357- and 37-fold respectively from nuclear salt extracts prepared from HeLa cells using DEAE-cellulose and phosphocellulose chromatography. The activity of the first form of the enzyme eluted from DEAE-cellulose (major form) was at least 3-fold greater than that of the second (minor form). H.p.l.c. analysis of the hydrolysed, methylated mRNA substrates demonstrated that both forms of the enzyme produced only 6-methyladenine. The two forms of the enzyme differed in their RNA substrate specificity as well as in the dependence for a 5' cap structure. The 6-methyladenine mRNA methyltransferase activity was found to be elevated in HeLa nuclei as compared with nuclear extracts from rat kidney and brain. Enzymic activity could not be detected in nuclei from either normal rat liver or regenerating rat liver. In the case of the HeLa cell, activity could only be detected in nuclear extracts, with a small amount in the ribosomal fraction. Other HeLa subcellular fractions were void of activity.
Collapse
Affiliation(s)
- M T Tuck
- Department of Chemistry, Ohio University, Athens 45701
| |
Collapse
|
28
|
Harper JE, Miceli SM, Roberts RJ, Manley JL. Sequence specificity of the human mRNA N6-adenosine methylase in vitro. Nucleic Acids Res 1990; 18:5735-41. [PMID: 2216767 PMCID: PMC332308 DOI: 10.1093/nar/18.19.5735] [Citation(s) in RCA: 179] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
N6-adenosine methylation is a frequent modification of mRNAs and their precursors, but little is known about the mechanism of the reaction or the function of the modification. To explore these questions, we developed conditions to examine N6-adenosine methylase activity in HeLa cell nuclear extracts. Transfer of the methyl group from S-[3H methyl]-adenosylmethionine to unlabeled random copolymer RNA substrates of varying ribonucleotide composition revealed a substrate specificity consistent with a previously deduced consensus sequence, Pu[G greater than A]AC[A/C/U]. 32-P labeled RNA substrates of defined sequence were used to examine the minimum sequence requirements for methylation. Each RNA was 20 nucleotides long, and contained either the core consensus sequence GGACU, or some variation of this sequence. RNAs containing GGACU, either in single or multiple copies, were good substrates for methylation, whereas RNAs containing single base substitutions within the GGACU sequence gave dramatically reduced methylation. These results demonstrate that the N6-adenosine methylase has a strict sequence specificity, and that there is no requirement for extended sequences or secondary structures for methylation. Recognition of this sequence does not require an RNA component, as micrococcal nuclease pretreatment of nuclear extracts actually increased methylation efficiency.
Collapse
Affiliation(s)
- J E Harper
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | | | | | | |
Collapse
|
29
|
Abstract
N6-methyladenosine (m6A) residues occur at internal positions in most cellular and viral RNAs; both heterogeneous nuclear RNA and mRNA are involved. This modification arises by enzymatic transfer of a methyl group from S-adenosylmethionine to the central adenosine residue in the canonical sequence G/AAC. Thus far, m6A has been mapped to specific locations in eucaryotic mRNA and viral genomic RNA. We have now examined an intron-specific sequence of a modified bovine prolactin precursor RNA for the presence of this methylated nucleotide by using both transfected-cell systems and a cell-free system capable of methylating mRNA transcripts in vitro. The results indicate the final intron-specific sequence (intron D) of a prolactin RNA molecule does indeed possess m6A residues. When mapped to specific T1 oligonucleotides, the predominant site of methylation was found to be within the consensus sequence AGm6ACU. The level of m6A at this site is nonstoichiometric; approximately 24% of the molecules are modified in vivo. Methylation was detected at markedly reduced levels at other consensus sites within the intron but not in T1 oligonucleotides which do not contain either AAC or GAC consensus sequences. In an attempt to correlate mRNA methylation with processing, stably transfected CHO cells expressing augmented levels of bovine prolactin were treated with neplanocin A, an inhibitor of methylation. Under these conditions, the relative steady-state levels of the intron-containing nuclear precursor increased four to six times that found in control cells.
Collapse
|
30
|
Carroll SM, Narayan P, Rottman FM. N6-methyladenosine residues in an intron-specific region of prolactin pre-mRNA. Mol Cell Biol 1990; 10:4456-65. [PMID: 2388614 PMCID: PMC361031 DOI: 10.1128/mcb.10.9.4456-4465.1990] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
N6-methyladenosine (m6A) residues occur at internal positions in most cellular and viral RNAs; both heterogeneous nuclear RNA and mRNA are involved. This modification arises by enzymatic transfer of a methyl group from S-adenosylmethionine to the central adenosine residue in the canonical sequence G/AAC. Thus far, m6A has been mapped to specific locations in eucaryotic mRNA and viral genomic RNA. We have now examined an intron-specific sequence of a modified bovine prolactin precursor RNA for the presence of this methylated nucleotide by using both transfected-cell systems and a cell-free system capable of methylating mRNA transcripts in vitro. The results indicate the final intron-specific sequence (intron D) of a prolactin RNA molecule does indeed possess m6A residues. When mapped to specific T1 oligonucleotides, the predominant site of methylation was found to be within the consensus sequence AGm6ACU. The level of m6A at this site is nonstoichiometric; approximately 24% of the molecules are modified in vivo. Methylation was detected at markedly reduced levels at other consensus sites within the intron but not in T1 oligonucleotides which do not contain either AAC or GAC consensus sequences. In an attempt to correlate mRNA methylation with processing, stably transfected CHO cells expressing augmented levels of bovine prolactin were treated with neplanocin A, an inhibitor of methylation. Under these conditions, the relative steady-state levels of the intron-containing nuclear precursor increased four to six times that found in control cells.
Collapse
Affiliation(s)
- S M Carroll
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106
| | | | | |
Collapse
|
31
|
Rana AP, Tuck MT. Analysis and in vitro localization of internal methylated adenine residues in dihydrofolate reductase mRNA. Nucleic Acids Res 1990; 18:4803-8. [PMID: 2395644 PMCID: PMC331949 DOI: 10.1093/nar/18.16.4803] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A T7 RNA transcript coding for mouse dihydrofolate reductase (DHFR) was utilized as a substrate for the N6-methyladenosine mRNA methyltransferase isolated from HeLa cell nuclei. This transcript acted as a 3 fold better substrate than either prolactin mRNA or a synthetic RNA substrate which contained multiple methylation consensus sequences. Formation of internal N6-methyladenine (m6A) residues in the DHFR transcript was shown to increase slightly by the absence of a 7-methylguanine-2'-O-methyl cap structure. Using T7 transcripts from different regions of the DHFR gene, the majority of the m6A residues were localized to the coding region and a segment of the transcript just 3' to the coding region. This data suggests that DHFR mRNA contains multiple methylation sites with most of these sites concentrated in the coding region of the transcript.
Collapse
Affiliation(s)
- A P Rana
- Department of Chemistry, Ohio University, Athens 45701
| | | |
Collapse
|
32
|
Clawson GA, MacDonald JR, Woo CH. Early hypomethylation of 2'-O-ribose moieties in hepatocyte cytoplasmic ribosomal RNA underlies the protein synthetic defect produced by CCl4. J Cell Biol 1987; 105:705-11. [PMID: 3114267 PMCID: PMC2114784 DOI: 10.1083/jcb.105.2.705] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Carbon tetrachloride (CCl4) treatment of rats produces an early defect in methylation of hepatocyte ribosomal RNA, which occurs concurrently with a defect in the protein synthetic capacity of isolated ribosomes. The CCl4-induced methylation defect is specific for the 2'-O-ribose position, and a corresponding proportional increase in m7G base methylation occurs in vivo. Undermethylated ribosomal subunits (rRNA) from CCl4-treated preparations can be methylated in vitro to a much greater extent than those from control preparations, and in vitro methylation restores their functional capacity. In vitro methylation of treated ribosomal subunits (which restores functional capacity) occurs at 2'-O-ribose positions (largely G residues). In contrast, in vitro methylation of control ribosomal subunits (which does not affect functional activity) represents base methylation as m7G, sites which are apparently methylated in treated preparations in vivo. Methylation/demethylation of 2'-O-ribose sites in rRNA exposed on the surface of cytoplasmic ribosomal subunits may represent an important cellular mechanism for controlling protein synthesis in quiescent hepatocytes, and it appears that CCl4 disrupts protein synthesis by inhibiting this 2'-O-ribose methylation.
Collapse
|
33
|
Abstract
Influenza virus mRNA is posttranscriptionally methylated at internal adenosine residues to form N6-methyladenosine (m6A). It has been previously shown that there is an average of three m6A residues per influenza virus mRNA (R. M. Krug, M. A. Morgan, and A. J. Shatkin, J. Virol. 20:45-53, 1976). To determine the distribution of m6A in the different influenza virus mRNAs, we purified six of the mRNAs by hybrid selection, digested them with nuclease, and determined their methylation patterns by high-pressure liquid chromatography. The amount of m6A in the different mRNAs varied from one in matrix to eight in hemagglutinin.
Collapse
|
34
|
Narayan P, Ayers DF, Rottman FM, Maroney PA, Nilsen TW. Unequal distribution of N6-methyladenosine in influenza virus mRNAs. Mol Cell Biol 1987; 7:1572-5. [PMID: 3600638 PMCID: PMC365250 DOI: 10.1128/mcb.7.4.1572-1575.1987] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Influenza virus mRNA is posttranscriptionally methylated at internal adenosine residues to form N6-methyladenosine (m6A). It has been previously shown that there is an average of three m6A residues per influenza virus mRNA (R. M. Krug, M. A. Morgan, and A. J. Shatkin, J. Virol. 20:45-53, 1976). To determine the distribution of m6A in the different influenza virus mRNAs, we purified six of the mRNAs by hybrid selection, digested them with nuclease, and determined their methylation patterns by high-pressure liquid chromatography. The amount of m6A in the different mRNAs varied from one in matrix to eight in hemagglutinin.
Collapse
|
35
|
Precise localization of m6A in Rous sarcoma virus RNA reveals clustering of methylation sites: implications for RNA processing. Mol Cell Biol 1986. [PMID: 3016525 DOI: 10.1128/mcb.5.9.2298] [Citation(s) in RCA: 129] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
N6-methyladenosine (m6A) residues are present as internal base modifications in most higher eucaryotic mRNAs; however, the biological function of this modification is not known. We describe a method for localizing and quantitating m6A within a large RNA molecule, the genomic RNA of Rous sarcoma virus. Specific fragments of 32P-labeled Rous sarcoma virus RNA were isolated by hybridization with complementary DNA restriction fragments spanning nucleotides 6185 to 8050. RNA was digested with RNase and finger-printed, and individual oligonucleotides were analyzed for the presence of m6A by paper electrophoresis and thin-layer chromatography. With this technique, seven sites of methylation in this region of the Rous sarcoma virus genome were localized at nucleotides 6394, 6447, 6507, 6718, 7414, 7424, and 8014. Further, m6A was observed at two additional sites whose nucleotide assignments remain ambiguous. A clustering of two or more m6A residues was seen at three positions within the RNA analyzed. Modification at certain sites was found to be heterogeneous, in that different molecules of RNA appeared to be methylated differently. Previous studies have determined that methylation occurs only in the sequences Gm6AC and Am6AC. We observed a high frequency of methylation at PuGm6ACU sequences. The possible involvement of m6A in RNA splicing events is discussed.
Collapse
|
36
|
Kane SE, Beemon K. Precise localization of m6A in Rous sarcoma virus RNA reveals clustering of methylation sites: implications for RNA processing. Mol Cell Biol 1985; 5:2298-306. [PMID: 3016525 PMCID: PMC366956 DOI: 10.1128/mcb.5.9.2298-2306.1985] [Citation(s) in RCA: 118] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
N6-methyladenosine (m6A) residues are present as internal base modifications in most higher eucaryotic mRNAs; however, the biological function of this modification is not known. We describe a method for localizing and quantitating m6A within a large RNA molecule, the genomic RNA of Rous sarcoma virus. Specific fragments of 32P-labeled Rous sarcoma virus RNA were isolated by hybridization with complementary DNA restriction fragments spanning nucleotides 6185 to 8050. RNA was digested with RNase and finger-printed, and individual oligonucleotides were analyzed for the presence of m6A by paper electrophoresis and thin-layer chromatography. With this technique, seven sites of methylation in this region of the Rous sarcoma virus genome were localized at nucleotides 6394, 6447, 6507, 6718, 7414, 7424, and 8014. Further, m6A was observed at two additional sites whose nucleotide assignments remain ambiguous. A clustering of two or more m6A residues was seen at three positions within the RNA analyzed. Modification at certain sites was found to be heterogeneous, in that different molecules of RNA appeared to be methylated differently. Previous studies have determined that methylation occurs only in the sequences Gm6AC and Am6AC. We observed a high frequency of methylation at PuGm6ACU sequences. The possible involvement of m6A in RNA splicing events is discussed.
Collapse
|
37
|
Horowitz S, Horowitz A, Nilsen TW, Munns TW, Rottman FM. Mapping of N6-methyladenosine residues in bovine prolactin mRNA. Proc Natl Acad Sci U S A 1984; 81:5667-71. [PMID: 6592581 PMCID: PMC391771 DOI: 10.1073/pnas.81.18.5667] [Citation(s) in RCA: 112] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
N6-Methyladenosine (m6A) residues, which are found internally in viral and cellular mRNA populations at the sequences Apm6ApC and Gpm6ApC, have been proposed to play a role in mRNA processing and transport. We have developed a sensitive approach to analyze the level and location of m6A in specific purified cellular mRNAs in an attempt to correlate m6A location with function. Polyadenylylated mRNA is hybridized to cDNA clones representing the full size mRNA under study or fragments of it, and the protected RNA is digested and labeled with polynucleotide kinase in vitro. After enrichment for m6A with anti-m6A antibody, the [32P]-pm6A is separated on TLC plates, and compared with the total amount of radiolabeled nucleotides. Using this combination of in vitro RNA labeling and antibody selection, we were able to detect m6A in purified stable mRNAs that cannot be readily labeled in cells with greater sensitivity than was possible by previous techniques. We applied this technique to bovine prolactin mRNA and showed that this mRNA contains m6A. Moreover, all of the m6A residues in this message are found within the 3' two-thirds of the molecule and are highly concentrated (61%) within a sequence of 108 nucleotides at the 3' noncoding region of the message. The nonrandom distribution of m6A in a specific cellular mRNA, as demonstrated for bovine prolactin, will have to be taken into account when designing a model for m6A function.
Collapse
|