351
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Arribas-Hernández L, Brodersen P. Occurrence and Functions of m 6A and Other Covalent Modifications in Plant mRNA. PLANT PHYSIOLOGY 2020; 182:79-96. [PMID: 31748418 PMCID: PMC6945878 DOI: 10.1104/pp.19.01156] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/13/2019] [Indexed: 05/07/2023]
Abstract
Posttranscriptional control of gene expression is indispensable for the execution of developmental programs and environmental adaptation. Among the many cellular mechanisms that regulate mRNA fate, covalent nucleotide modification has emerged as a major way of controlling the processing, localization, stability, and translatability of mRNAs. This powerful mechanism is conserved across eukaryotes and controls the cellular events that lead to development and growth. As in other eukaryotes, N 6-methylation of adenosine is the most abundant and best studied mRNA modification in flowering plants. It is essential for embryonic and postembryonic plant development and it affects growth rate and stress responses, including susceptibility to plant RNA viruses. Although the mRNA modification field is young, the intense interest triggered by its involvement in stem cell differentiation and cancer has led to rapid advances in understanding how mRNA modifications control gene expression in mammalian systems. An equivalent effort from plant molecular biologists has been lagging behind, but recent work in Arabidopsis (Arabidopsis thaliana) and other plant species is starting to give insights into how this essential layer of posttranscriptional regulation works in plants, and both similarities and differences with other eukaryotes are emerging. In this Update, we summarize, connect, and evaluate the experimental work that supports our current knowledge of the biochemistry, molecular mechanisms, and biological functions of mRNA modifications in plants. We devote particular attention to N 6-methylation of adenosine and attempt to place the knowledge gained from plant studies within the context of a more general framework derived from studies in other eukaryotes.
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Affiliation(s)
| | - Peter Brodersen
- University of Copenhagen, Department of Biology, DK-2200 Copenhagen N, Denmark
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352
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Flamand MN, Meyer KD. The epitranscriptome and synaptic plasticity. Curr Opin Neurobiol 2019; 59:41-48. [PMID: 31108373 PMCID: PMC6858947 DOI: 10.1016/j.conb.2019.04.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/18/2019] [Indexed: 12/22/2022]
Abstract
RNA modifications, collectively referred to as 'the epitranscriptome,' have recently emerged as a pervasive feature of cellular mRNAs which have diverse impacts on gene expression. In the last several years, technological advances improving our ability to identify mRNA modifications, coupled with the discovery of proteins that add and remove these marks, have substantially expanded our knowledge of how the epitranscriptome shapes gene expression. Efforts to uncover functional roles for mRNA modifications have begun to reveal important roles for some marks within the nervous system, and animal models have emerged which demonstrate severe neurodevelopmental and neurocognitive abnormalities resulting from the loss of mRNA modification machinery. Here, we review the recent advances in the field of neuroepitranscriptomics, with a particular emphasis on how modifications to mRNAs within the brain contribute to synaptic activity.
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Affiliation(s)
- Mathieu N Flamand
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, United States
| | - Kate D Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, United States.
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353
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Ma S, Chen C, Ji X, Liu J, Zhou Q, Wang G, Yuan W, Kan Q, Sun Z. The interplay between m6A RNA methylation and noncoding RNA in cancer. J Hematol Oncol 2019; 12:121. [PMID: 31757221 PMCID: PMC6874823 DOI: 10.1186/s13045-019-0805-7] [Citation(s) in RCA: 381] [Impact Index Per Article: 76.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/07/2019] [Indexed: 12/19/2022] Open
Abstract
N6-methyladenosine (m6A) methylation, one of the most common RNA modifications, has been reported to execute important functions that affect normal life activities and diseases. Most studies have suggested that m6A modification can affect the complexity of cancer progression by regulating biological functions related to cancer. M6A modification of noncoding RNAs regulates the cleavage, transport, stability, and degradation of noncoding RNAs themselves. It also regulates cell proliferation and metastasis, stem cell differentiation, and homeostasis in cancer by affecting the biological function of cells. Interestingly, noncoding RNAs also play significant roles in regulating these m6A modifications. Additionally, it is becoming increasingly clear that m6A and noncoding RNAs potentially contribute to the clinical application of cancer treatment. In this review, we summarize the effect of the interactions between m6A modifications and noncoding RNAs on the biological functions involved in cancer progression. In particular, we discuss the role of m6A and noncoding RNAs as possible potential biomarkers and therapeutic targets in the treatment of cancers.
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Affiliation(s)
- Shuai Ma
- Department of Anorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Chen Chen
- Department of Anorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Xiang Ji
- Department of Anorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Jinbo Liu
- Department of Anorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Quanbo Zhou
- Department of Anorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Guixian Wang
- Department of Anorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Weitang Yuan
- Department of Anorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Quancheng Kan
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Zhenqiang Sun
- Department of Anorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China. .,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China. .,Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
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354
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Hunt AG. mRNA 3′ end formation in plants: Novel connections to growth, development and environmental responses. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1575. [DOI: 10.1002/wrna.1575] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Arthur G. Hunt
- Department of Plant and Soil Sciences University of Kentucky Lexington Kentucky
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355
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Abstract
Similar to many other biological molecules, RNA is vulnerable to chemical insults from endogenous and exogenous sources. Noxious agents such as reactive oxygen species or alkylating chemicals have the potential to profoundly affect the chemical properties and hence the function of RNA molecules in the cell. Given the central role of RNA in many fundamental biological processes, including translation and splicing, changes to its chemical composition can have a detrimental impact on cellular fitness, with some evidence suggesting that RNA damage has roles in diseases such as neurodegenerative disorders. We are only just beginning to learn about how cells cope with RNA damage, with recent studies revealing the existence of quality-control processes that are capable of recognizing and degrading or repairing damaged RNA. Here, we begin by reviewing the most abundant types of chemical damage to RNA, including oxidation and alkylation. Focusing on mRNA damage, we then discuss how alterations to this species of RNA affect its function and how cells respond to these challenges to maintain proteostasis. Finally, we briefly discuss how chemical damage to noncoding RNAs such as rRNA, tRNA, small nuclear RNA, and small nucleolar RNA is likely to affect their function.
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Affiliation(s)
- Liewei L. Yan
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Hani S. Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, To whom correspondence should be addressed:
Dept. of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Dr., St. Louis, MO 63130. Tel.:
314-935-7662; Fax:
314-935-4432; E-mail:
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356
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Zaccara S, Ries RJ, Jaffrey SR. Reading, writing and erasing mRNA methylation. Nat Rev Mol Cell Biol 2019; 20:608-624. [PMID: 31520073 DOI: 10.1038/s41580-019-0168-5] [Citation(s) in RCA: 1334] [Impact Index Per Article: 266.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2019] [Indexed: 02/07/2023]
Abstract
RNA methylation to form N6-methyladenosine (m6A) in mRNA accounts for the most abundant mRNA internal modification and has emerged as a widespread regulatory mechanism that controls gene expression in diverse physiological processes. Transcriptome-wide m6A mapping has revealed the distribution and pattern of m6A in cellular RNAs, referred to as the epitranscriptome. These maps have revealed the specific mRNAs that are regulated by m6A, providing mechanistic links connecting m6A to cellular differentiation, cancer progression and other processes. The effects of m6A on mRNA are mediated by an expanding list of m6A readers and m6A writer-complex components, as well as potential erasers that currently have unclear relevance to m6A prevalence in the transcriptome. Here we review new and emerging methods to characterize and quantify the epitranscriptome, and we discuss new concepts - in some cases, controversies - regarding our understanding of the mechanisms and functions of m6A readers, writers and erasers.
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Affiliation(s)
- Sara Zaccara
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA
| | - Ryan J Ries
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA.
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357
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Chokkalla AK, Mehta SL, Kim T, Chelluboina B, Kim JY, Vemuganti R. Transient Focal Ischemia Significantly Alters the m 6A Epitranscriptomic Tagging of RNAs in the Brain. Stroke 2019; 50:2912-2921. [PMID: 31436138 PMCID: PMC6759411 DOI: 10.1161/strokeaha.119.026433] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background and Purpose- Adenosine in many types of RNAs can be converted to m6A (N6-methyladenosine) which is a highly dynamic epitranscriptomic modification that regulates RNA metabolism and function. Of all organs, the brain shows the highest abundance of m6A methylation of RNAs. As recent studies showed that m6A modification promotes cell survival after adverse conditions, we currently evaluated the effect of stroke on cerebral m6A methylation in mRNAs and lncRNAs. Methods- Adult C57BL/6J mice were subjected to transient middle cerebral artery occlusion. In the peri-infarct cortex, m6A levels were measured by dot blot analysis, and transcriptome-wide m6A changes were profiled using immunoprecipitated methylated RNAs with microarrays (44 122 mRNAs and 12 496 lncRNAs). Gene ontology analysis was conducted to understand the functional implications of m6A changes after stroke. Expression of m6A writers, readers, and erasers was also estimated in the ischemic brain. Results- Global m6A levels increased significantly at 12 hours and 24 hours of reperfusion compared with sham. While 139 transcripts (122 mRNAs and 17 lncRNAs) were hypermethylated, 8 transcripts (5 mRNAs and 3 lncRNAs) were hypomethylated (>5-fold compared with sham) in the ischemic brain at 12 hours reperfusion. Inflammation, apoptosis, and transcriptional regulation are the major biological processes modulated by the poststroke differentially m6A methylated mRNAs. The m6A writers were unaltered, but the m6A eraser (fat mass and obesity-associated protein) decreased significantly after stroke compared with sham. Conclusions- This is the first study to show that stroke alters the cerebral m6A epitranscriptome, which might have functional implications in poststroke pathophysiology. Visual Overview- An online visual overview is available for this article.
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Affiliation(s)
- Anil K Chokkalla
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin, Madison, WI, USA
| | - Suresh L. Mehta
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - TaeHee Kim
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Bharath Chelluboina
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Joo Yong Kim
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin, Madison, WI, USA
- William S. Middleton Memorial Veteran Administration Hospital, Madison, WI, USA
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358
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Gatsiou A, Stellos K. Dawn of Epitranscriptomic Medicine. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2019; 11:e001927. [PMID: 30354331 DOI: 10.1161/circgen.118.001927] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Medicine is at the crossroads of expanding disciplines. Prompt adaptation of medicine to each rapidly advancing research field, bridging bench to bedside, is a key step toward health improvement. Cardiovascular disease still ranks first among the mortality causes in the Western world, indicating a poor adaptation rate of cardiovascular medicine, albeit the gigantic scientific breakthroughs of this century. This urges the cardiovascular research field to explore novel concepts with promising prognostic and therapeutic potential. This review attempts to introduce the newly emerging field of epitranscriptome (or else known as RNA epigenetics) to cardiovascular researchers and clinicians summarizing its applications on health and disease. The traditionally perceived, intermediate carrier of genetic information or as contemporary revised as, occasionally, even the final product of gene expression, RNA, is dynamically subjected to >140 different kinds of chemical modifications determining its fate, which may profoundly impact the cellular responses and thus both health and disease course. Which are the most prevalent types of these RNA modifications, how are they catalyzed, how are they regulated, which role may they play in health and disease, and which are the implications for the cardiovascular medicine are few important questions that are discussed in the present review.
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Affiliation(s)
- Aikaterini Gatsiou
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany (A.G., K.S.).,Department of Cardiology, Center of Internal Medicine, Goethe University Frankfurt, Germany (A.G., K.S.).,German Center of Cardiovascular Research, Rhein-Main Partner Site, Frankfurt (A.G., K.S.)
| | - Konstantinos Stellos
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany (A.G., K.S.).,Department of Cardiology, Center of Internal Medicine, Goethe University Frankfurt, Germany (A.G., K.S.).,German Center of Cardiovascular Research, Rhein-Main Partner Site, Frankfurt (A.G., K.S.).,Cardiovascular Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom (K.S.).,Department of Cardiology, Freeman Hospital, Newcastle upon Tyne Hospitals National Health System Foundation Trust, United Kingdom (K.S.)
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359
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Malbec L, Zhang T, Chen YS, Zhang Y, Sun BF, Shi BY, Zhao YL, Yang Y, Yang YG. Dynamic methylome of internal mRNA N 7-methylguanosine and its regulatory role in translation. Cell Res 2019; 29:927-941. [PMID: 31520064 DOI: 10.1038/s41422-019-0230-z] [Citation(s) in RCA: 169] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 08/25/2019] [Indexed: 12/22/2022] Open
Abstract
Over 150 types of RNA modifications are identified in RNA molecules. Transcriptome profiling is one of the key steps in decoding the epitranscriptomic panorama of these chemical modifications and their potential functions. N7-methylguanosine (m7G) is one of the most abundant modifications present in tRNA, rRNA and mRNA 5'cap, and has critical roles in regulating RNA processing, metabolism and function. Besides its presence at the cap position in mRNAs, m7G is also identified in internal mRNA regions. However, its transcriptome-wide distribution and dynamic regulation within internal mRNA regions remain unknown. Here, we have established m7G individual-nucleotide-resolution cross-linking and immunoprecipitation with sequencing (m7G miCLIP-seq) to specifically detect internal mRNA m7G modification. Using this approach, we revealed that m7G is enriched at the 5'UTR region and AG-rich contexts, a feature that is well-conserved across different human/mouse cell lines and mouse tissues. Strikingly, the internal m7G modification is dynamically regulated under both H2O2 and heat shock treatments, with remarkable accumulations in the CDS and 3'UTR regions, and functions in promoting mRNA translation efficiency. Consistently, a PCNA 3'UTR minigene reporter harboring the native m7G modification site displays both enriched m7G modification and increased mRNA translation upon H2O2 treatment compared to the m7G site-mutated minigene reporter (G to A). Taken together, our findings unravel the dynamic profiles of internal mRNA m7G methylome and highlight m7G as a novel epitranscriptomic marker with regulatory roles in translation.
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Affiliation(s)
- Lionel Malbec
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ting Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu-Sheng Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bao-Fa Sun
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Bo-Yang Shi
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong-Liang Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Ying Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China. .,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408, China.
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China. .,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408, China.
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360
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361
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Li J, Yang X, Qi Z, Sang Y, Liu Y, Xu B, Liu W, Xu Z, Deng Y. The role of mRNA m 6A methylation in the nervous system. Cell Biosci 2019; 9:66. [PMID: 31452869 PMCID: PMC6701067 DOI: 10.1186/s13578-019-0330-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/14/2019] [Indexed: 11/21/2022] Open
Abstract
Epitranscriptomics, also known as “RNA epigenetics”, is a chemical modification for RNA regulation. Ribonucleic acid (RNA) methylation is considered to be a major discovery following the deoxyribonucleic acid (DNA) and histone methylation. Messenger RNA (mRNA) methylation modification accounts for more than 60% of all RNA modifications and N6-methyladenosine (m6A) is known as one of the most common type of eukaryotic mRNA methylation modifications in current. The m6A modification is a dynamic reversible modification, which can directly or indirectly affect biological processes, such as RNA degradation, translation and splicing, and can play important biological roles in vivo. This article introduces the mRNA m6A methylation modification enzymes and binding proteins, and reviews the research progress and related mechanisms of the role of mRNA m6A methylation in the nervous system from the aspects of neural stem cells, learning and memory, brain development, axon growth and glioblastoma.
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Affiliation(s)
- Jiashuo Li
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Xinxin Yang
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Zhipeng Qi
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Yanqi Sang
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Yanan Liu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Bin Xu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Wei Liu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Zhaofa Xu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Yu Deng
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
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362
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Gao Y, Pei G, Li D, Li R, Shao Y, Zhang QC, Li P. Multivalent m 6A motifs promote phase separation of YTHDF proteins. Cell Res 2019; 29:767-769. [PMID: 31388144 DOI: 10.1038/s41422-019-0210-3] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/14/2019] [Indexed: 11/09/2022] Open
Affiliation(s)
- Yifei Gao
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Gaofeng Pei
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Dongxue Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ru Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yanqiu Shao
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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363
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Transcriptome-wide dynamics of extensive m 6A mRNA methylation during Plasmodium falciparum blood-stage development. Nat Microbiol 2019; 4:2246-2259. [PMID: 31384004 DOI: 10.1038/s41564-019-0521-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 06/20/2019] [Indexed: 01/17/2023]
Abstract
Malaria pathogenesis results from the asexual replication of Plasmodium falciparum within human red blood cells, which relies on a precisely timed cascade of gene expression over a 48-h life cycle. Although substantial post-transcriptional regulation of this hardwired program has been observed, it remains unclear how these processes are mediated on a transcriptome-wide level. To this end, we identified mRNA modifications in the P. falciparum transcriptome and performed a comprehensive characterization of N6-methyladenosine (m6A) over the course of blood-stage development. Using mass spectrometry and m6A RNA sequencing, we demonstrate that m6A is highly developmentally regulated, exceeding m6A levels known in any other eukaryote. We characterize a distinct m6A writer complex and show that knockdown of the putative m6A methyltransferase, PfMT-A70, by CRISPR interference leads to increased levels of transcripts that normally contain m6A. In accordance, we find an inverse correlation between m6A methylation and mRNA stability or translational efficiency. We further identify two putative m6A-binding YTH proteins that are likely to be involved in the regulation of these processes across the parasite's life cycle. Our data demonstrate unique features of an extensive m6A mRNA methylation programme in malaria parasites and reveal its crucial role in dynamically fine-tuning the transcriptional cascade of a unicellular eukaryote.
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364
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Song H, Feng X, Zhang H, Luo Y, Huang J, Lin M, Jin J, Ding X, Wu S, Huang H, Yu T, Zhang M, Hong H, Yao S, Zhao Y, Zhang Z. METTL3 and ALKBH5 oppositely regulate m 6A modification of TFEB mRNA, which dictates the fate of hypoxia/reoxygenation-treated cardiomyocytes. Autophagy 2019; 15:1419-1437. [PMID: 30870073 PMCID: PMC6613905 DOI: 10.1080/15548627.2019.1586246] [Citation(s) in RCA: 317] [Impact Index Per Article: 63.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 01/25/2019] [Accepted: 02/07/2019] [Indexed: 01/19/2023] Open
Abstract
N6-methyladenosine (m6A) mRNA modifications play critical roles in various biological processes. However, no study addresses the role of m6A in macroautophagy/autophagy. Here, we show that m6A modifications are increased in H/R-treated cardiomyocytes and ischemia/reperfusion (I/R)-treated mice heart. We found that METTL3 (methyltransferase like 3) is the primary factor involved in aberrant m6A modification. Silencing METTL3 enhances autophagic flux and inhibits apoptosis in H/R-treated cardiomyocytes. However, overexpression of METTL3 or inhibition of the RNA demethylase ALKBH5 has an opposite effect, suggesting that METTL3 is a negative regulator of autophagy. Mechanistically, METTL3 methylates TFEB, a master regulator of lysosomal biogenesis and autophagy genes, at two m6A residues in the 3'-UTR, which promotes the association of the RNA-binding protein HNRNPD with TFEB pre-mRNA and subsequently decreases the expression levels of TFEB. Further experiments show that autophagic flux enhanced by METTL3 deficiency is TFEB dependent. In turn, TFEB regulates the expression levels of METTL3 and ALKBH5 in opposite directions: it induces ALKBH5 and inhibits METTL3. TFEB binds to the ALKBH5 promoter and activates its transcription. In contrast, inhibition of METTL3 by TFEB does not involve transcriptional repression but rather downregulation of mRNA stability, thereby establishing a negative feedback loop. Together, our work uncovers a critical link between METTL3-ALKBH5 and autophagy, providing insight into the functional importance of the reversible mRNA m6A methylation and its modulators in ischemic heart disease. Abbreviations: ACTB, actin beta; ALKBH5, alkB homolog 5, RNA demethylase; ANXA5, annexin A5; ATG, autophagy-related; BafA, bafilomycin A1; CASP3, caspase 3; ELAVL1, ELAV like RNA binding protein 1; FTO, FTO, alpha-ketoglutarate dependent dioxygenase; GFP, green fluorescent protein; GST, glutathione S-transferase; HNRNPD, heterogeneous nuclear ribonucleoprotein D; H/R, hypoxia/reoxygenation; I/R, ischemia/reperfusion; LAD, left anterior descending; m6A, N6-methyladenosine; MEFs, mouse embryo fibroblasts; Mer, mutated estrogen receptor domains; METTL3, methyltransferase like 3; METTL14, methyltransferase like 14; mRFP, monomeric red fluorescent protein; MTORC1, mechanistic target of rapamycin kinase complex 1; NMVCs, neonatal mouse ventricular cardiomyocytes; PCNA, proliferating cell nuclear antigen; PE, phosphatidylethanolamine; PI, propidium iodide; PTMs, post-translational modifications; PVDF, polyvinylidenedifluoride; RIP, RNA-immunoprecipitation; siRNA, small interfering RNA; SQSTM1, sequestosome 1; TFEB, transcription factor EB; TUBA: tublin alpha; WTAP, WT1 associated protein; YTHDF, YTH N6-methyladenosine RNA binding protein.
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Affiliation(s)
- Huiwen Song
- Longju Medical Research Center; Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi, China
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xing Feng
- Longju Medical Research Center; Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi, China
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Heng Zhang
- Department of Histology and Embryology, Xiang Ya School of Medicine, Central South University, Changsha, China
| | - Yunmei Luo
- Longju Medical Research Center; Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Juan Huang
- Longju Medical Research Center; Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Meihua Lin
- Research Center of Clinical Pharmacy, State Key Laboratory for Diagnosis and Treatment of Infectious Disease, First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Junfei Jin
- Laboratory of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Xue Ding
- Department of Cardiology; the First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Shujing Wu
- Department of Cardiology, The ChengGong Hospital Affiliated to Xiamen University, Xiamen, China
| | - He Huang
- Department of Histology and Embryology, Xiang Ya School of Medicine, Central South University, Changsha, China
- Digestive Cancer Laboratory, Second Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Tian Yu
- Department of Anesthesia, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Mukun Zhang
- Health Management Center, The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Hefei, China
| | - Haiou Hong
- Health Management Center, The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Hefei, China
| | - Shihua Yao
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yongxiang Zhao
- National Center for International Research of Biological Targeting Diagnosis and Therapy (Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research), Guangxi Medical University, Nanning, China
| | - Zhiyong Zhang
- Longju Medical Research Center; Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi, China
- Department of Surgery; Robert-Wood-Johnson Medical School University Hospital, Rutgers University, State University of New Jersey, New Brunswick, NJ USA
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365
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Ries RJ, Zaccara S, Klein P, Olarerin-George A, Namkoong S, Pickering BF, Patil DP, Kwak H, Lee JH, Jaffrey SR. m 6A enhances the phase separation potential of mRNA. Nature 2019; 571:424-428. [PMID: 31292544 PMCID: PMC6662915 DOI: 10.1038/s41586-019-1374-1] [Citation(s) in RCA: 449] [Impact Index Per Article: 89.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 06/13/2019] [Indexed: 12/11/2022]
Abstract
N6-methyladenosine (m6A) is the most prevalent modified nucleotide in mRNA1,2, with ~25% of mRNAs containing at least one m6A. Methylation of mRNA to form m6A is required for diverse cellular and physiological processes3. Although the presence of m6A in an mRNA can affect its fate in different ways, it is unclear how m6A directs this process and why the effects of m6A can vary in different cellular contexts. Here we show that the cytosolic m6A-binding proteins, YTHDF1–3, undergo liquid-liquid phase separation (LLPS) in vitro and in cells. This LLPS is markedly enhanced by mRNAs that contain multiple, but not single, m6A residues. Polymethylated mRNAs act as a multivalent scaffold for binding YTHDF proteins, juxtaposing their low-complexity domains, leading to phase separation. The resulting mRNA-YTHDF complexes then partition into different endogenous phase-separated compartments, such as P-bodies, stress granules, or neuronal RNA granules. m6A-mRNA is subject to compartment-specific regulation, including reduced mRNA stability and translation. These studies reveal that the number and distribution of m6A sites in cellular mRNAs can regulate and influence the composition of the phase-separated transcriptome. Additionally, these findings indicate that the cellular properties of m6A-modified mRNAs are governed by liquid-liquid phase separation principles.
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Affiliation(s)
- Ryan J Ries
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
| | - Sara Zaccara
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
| | - Pierre Klein
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
| | - Anthony Olarerin-George
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
| | - Sim Namkoong
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Brian F Pickering
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
| | - Deepak P Patil
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Jun Hee Lee
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA.
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366
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Williams GD, Gokhale NS, Horner SM. Regulation of Viral Infection by the RNA Modification N6-Methyladenosine. Annu Rev Virol 2019; 6:235-253. [PMID: 31283446 DOI: 10.1146/annurev-virology-092818-015559] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In recent years, the RNA modification N6-methyladenosine (m6A) has been found to play a role in the life cycles of numerous viruses and also in the cellular response to viral infection. m6A has emerged as a regulator of many fundamental aspects of RNA biology. Here, we highlight recent advances in techniques for the study of m6A, as well as advances in our understanding of the cellular machinery that controls the addition, removal, recognition, and functions of m6A. We then summarize the many newly discovered roles of m6A during viral infection, including how it regulates innate and adaptive immune responses to infection. Overall, the goals of this review are to summarize the roles of m6A on both cellular and viral RNAs and to describe future directions for uncovering new functions of m6A during infection.
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Affiliation(s)
- Graham D Williams
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA; , ,
| | - Nandan S Gokhale
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA; , ,
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA; , , .,Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
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367
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Yue H, Nie X, Yan Z, Weining S. N6-methyladenosine regulatory machinery in plants: composition, function and evolution. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1194-1208. [PMID: 31070865 PMCID: PMC6576107 DOI: 10.1111/pbi.13149] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 04/28/2019] [Accepted: 05/01/2019] [Indexed: 05/04/2023]
Abstract
N6-methyladenosine (m6A) RNA methylation, one of the most pivotal internal modifications of RNA, is a conserved post-transcriptional mechanism to enrich and regulate genetic information in eukaryotes. The scope and function of this modification in plants has been an intense focus of study, especially in model plant systems. The characterization of plant m6A writers, erasers and readers, as well as the elucidation of their functions, is currently one of the most fascinating hotspots in plant biology research. The functional analysis of m6A in plants will be booming in the foreseeable future, which could contribute to crop genetic improvement through epitranscriptome manipulation. In this review, we systematically analysed and summarized recent advances in the understanding of the structure and composition of plant m6A regulatory machinery, and the biological functions of m6A in plant growth, development and stress response. Finally, our analysis showed that the evolutionary relationships between m6A modification components were highly conserved across the plant kingdom.
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Affiliation(s)
- Hong Yue
- College of Life SciencesState Key Laboratory of Crop Stress Biology in Arid AreasNorthwest A&F UniversityYanglingShaanxiChina
| | - Xiaojun Nie
- College of Life SciencesState Key Laboratory of Crop Stress Biology in Arid AreasNorthwest A&F UniversityYanglingShaanxiChina
| | - Zhaogui Yan
- College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanHubeiChina
| | - Song Weining
- College of Life SciencesState Key Laboratory of Crop Stress Biology in Arid AreasNorthwest A&F UniversityYanglingShaanxiChina
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368
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Fazi F, Fatica A. Interplay Between N 6-Methyladenosine (m 6A) and Non-coding RNAs in Cell Development and Cancer. Front Cell Dev Biol 2019; 7:116. [PMID: 31316981 PMCID: PMC6611489 DOI: 10.3389/fcell.2019.00116] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/07/2019] [Indexed: 12/19/2022] Open
Abstract
RNA chemical modifications in coding and non-coding RNAs have been known for decades. They are generally installed by specific enzymes and, in some cases, can be read and erased by other specific proteins. The impact of RNA chemical modifications on gene expression regulation and the reversible nature of some of these modifications led to the birth of the word epitranscriptomics, in analogy with the changes that occur on DNA and histones. Among more than 100 different modifications identified so far, most of the epitranscriptomics studies focused on the N6-methyladenosine (m6A), which is the more abundant internal modification in protein coding RNAs. m6A can control several pathways of gene expression, including spicing, export, stability, and translation. In this review, we describe the interplay between m6A and non-coding RNAs, in particular microRNAs and lncRNAs, with examples of its role in gene expression regulation. Finally, we discuss its relevance in cell development and disease.
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Affiliation(s)
- Francesco Fazi
- Department of Anatomical, Histological, Forensic and Orthopedic Sciences, Section of Histology and Medical Embryology, Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Alessandro Fatica
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
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369
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Zhang C, Zhang M, Ge S, Huang W, Lin X, Gao J, Gong J, Shen L. Reduced m6A modification predicts malignant phenotypes and augmented Wnt/PI3K-Akt signaling in gastric cancer. Cancer Med 2019; 8:4766-4781. [PMID: 31243897 PMCID: PMC6712480 DOI: 10.1002/cam4.2360] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/14/2019] [Accepted: 05/29/2019] [Indexed: 12/13/2022] Open
Abstract
Background As the most abundant epigenetic modification on mRNAs and long non‐coding RNAs, N6‐methyladenosine (m6A) modification extensively exists in mammalian cells. Controlled by writers (methyltransferases), readers (signal transducers), and erasers (demethylases), m6A influences mRNA structure, maturation, and stability, thus negatively regulating protein expression in a post‐translational manner. Nevertheless, current understanding of m6A's roles in tumorigenesis, especially in gastric cancer (GC) remains to be unveiled. In this study, we assessed m6A's clinicopathological relevance to GC and explored the underlying mechanisms. Methods By referring to a proteomics‐based GC cohort we previously generated and the TCGA‐GC cohort, we merged expressions of canonical m6A writers (METTL3/METTL14), readers (YTHDF1/YTHDF2/YTHDF3), and erasers (ALKBH5/FTO), respectively, as W, R, and E signatures to represent m6A modification. We stratified patients according to these signatures to decipher m6A's associations with crucial mutations, prognosis, and clinical indexes. m6A's biological functions in GC were predicted by gene set enrichment analysis (GSEA) and validated by in vitro experiments. Results We discovered that W and R were potential tumor suppressive signatures, while E was a potential oncogenic signature in GC. According to W/R/E stratifications, patients with low m6A‐indications were accompanied with higher mutations of specific genes (CDH1, AR, GLI3, SETBP1, RHOA, MUC6, and TP53) and also demonstrated adverse clinical outcomes. GSEA suggested that reduced m6A was correlated with oncogenic signaling and phenotypes. Through in vitro experiments, we proved that m6A suppression (represented by METTL14 knockdown) promoted GC cell proliferation and invasiveness through activating Wnt and PI3K‐Akt signaling, while m6A elevation (represented by FTO knockdown) reversed these phenotypical and molecular changes. m6A may also be involved in interferon signaling and immune responses of GC. Conclusions Our work demonstrated that low‐m6A signatures predicted adverse clinicopathological features of GC, while the reduction of RNA m6A methylation activated oncogenic Wnt/PI3K‐Akt signaling and promoted malignant phenotypes of GC cells.
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Affiliation(s)
- Cheng Zhang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Mengqi Zhang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Sai Ge
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Wenwen Huang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiaoting Lin
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Jing Gao
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Jifang Gong
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Lin Shen
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
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370
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Chen J, Fang X, Zhong P, Song Z, Hu X. N6-methyladenosine modifications: interactions with novel RNA-binding proteins and roles in signal transduction. RNA Biol 2019; 16:991-1000. [PMID: 31107151 DOI: 10.1080/15476286.2019.1620060] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
RNA epigenetics has received a great deal of attention in recent years, and the reversible N6-methyladenosine (m6A) modification on messenger RNAs (mRNAs) has emerged as a widespread phenomenon. The vital roles of m6A in diverse biological processes are dependent on many RNA-binding proteins (RBPs) with 'reader' or 'nonreader' functions. Moreover, m6A effector proteins affect cellular processes, such as stem cell differentiation, tumor development and the immune response by controlling signal transduction. This review provides an overview of the interactions of m6A with various RBPs, including the 'reader' proteins (excluding the YT521-B homology (YTH) domain proteins and the heterogeneous nuclear ribonucleoproteins (hnRNPs)), and the functional 'nonreader' proteins, and this review focuses on their specific RNA-binding domains and their associations with other m6A effectors. Furthermore, we summarize key m6A-marked targets in distinct signaling pathways, leading to a better understanding of the cellular m6A machinery.
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Affiliation(s)
- Jiaxin Chen
- a Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province , Sir Run Shaw Hospital, Zhejiang University , Hangzhou , China
| | - Xiao Fang
- b Department of Anesthesiology and Key Laboratory of Biotherapy of Zhejiang Province , Sir Run Shaw Hospital, Zhejiang University , Hangzhou , China
| | - Pengcheng Zhong
- a Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province , Sir Run Shaw Hospital, Zhejiang University , Hangzhou , China
| | - Zhangfa Song
- c Department of Colorectal Surgery and Key Laboratory of Biotherapy of Zhejiang Province , Sir Run Shaw Hospital, Zhejiang University , Hangzhou , China
| | - Xiaotong Hu
- a Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province , Sir Run Shaw Hospital, Zhejiang University , Hangzhou , China
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371
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Zhuang M, Li X, Zhu J, Zhang J, Niu F, Liang F, Chen M, Li D, Han P, Ji SJ. The m6A reader YTHDF1 regulates axon guidance through translational control of Robo3.1 expression. Nucleic Acids Res 2019; 47:4765-4777. [PMID: 30843071 PMCID: PMC6511866 DOI: 10.1093/nar/gkz157] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 02/25/2019] [Accepted: 02/27/2019] [Indexed: 12/02/2022] Open
Abstract
N 6-Methyladenosine (m6A) is a dynamic mRNA modification which regulates protein expression in various posttranscriptional levels. Functional studies of m6A in nervous system have focused on its writers and erasers so far, whether and how m6A readers mediate m6A functions through recognizing and binding their target mRNA remains poorly understood. Here, we find that the expression of axon guidance receptor Robo3.1 which plays important roles in midline crossing of spinal commissural axons is regulated precisely at translational level. The m6A reader YTHDF1 binds to and positively regulates translation of m6A-modified Robo3.1 mRNA. Either mutation of m6A sites in Robo3.1 mRNA or YTHDF1 knockdown or knockout leads to dramatic reduction of Robo3.1 protein without affecting Robo3.1 mRNA level. Specific ablation of Ythdf1 in spinal commissural neurons results in pre-crossing axon guidance defects. Our findings identify a mechanism that YTHDF1-mediated translation of m6A-modified Robo3.1 mRNA controls pre-crossing axon guidance in spinal cord.
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Affiliation(s)
- Mengru Zhuang
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- SUSTech-HKUST Joint PhD Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Xinbei Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Junda Zhu
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jian Zhang
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Fugui Niu
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- SUSTech-HIT Joint Graduate Program, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Fanghao Liang
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- SUSTech-HIT Joint Graduate Program, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Mengxian Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Duo Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Peng Han
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Sheng-Jian Ji
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Institute of Neuroscience, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
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372
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Delaunay S, Frye M. RNA modifications regulating cell fate in cancer. Nat Cell Biol 2019; 21:552-559. [PMID: 31048770 DOI: 10.1038/s41556-019-0319-0] [Citation(s) in RCA: 217] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/26/2019] [Indexed: 02/02/2023]
Abstract
The deposition of chemical modifications into RNA is a crucial regulator of temporal and spatial gene expression programs during development. Accordingly, altered RNA modification patterns are widely linked to developmental diseases. Recently, the dysregulation of RNA modification pathways also emerged as a contributor to cancer. By modulating cell survival, differentiation, migration and drug resistance, RNA modifications add another regulatory layer of complexity to most aspects of tumourigenesis.
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Affiliation(s)
- Sylvain Delaunay
- Department of Genetics, University of Cambridge, Cambridge, UK
- German Cancer Center (DKFZ), Im Neuenheimer Feld, Heidelberg, Germany
| | - Michaela Frye
- Department of Genetics, University of Cambridge, Cambridge, UK.
- German Cancer Center (DKFZ), Im Neuenheimer Feld, Heidelberg, Germany.
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373
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Ianniello Z, Paiardini A, Fatica A. N 6-Methyladenosine (m 6A): A Promising New Molecular Target in Acute Myeloid Leukemia. Front Oncol 2019; 9:251. [PMID: 31024852 PMCID: PMC6465620 DOI: 10.3389/fonc.2019.00251] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/19/2019] [Indexed: 12/25/2022] Open
Abstract
Recent studies have uncovered an important role for RNA modifications in gene expression regulation, which led to the birth of the epitranscriptomics field. It is now acknowledged that RNA modifiers play a crucial role in the control of differentiation of stem and progenitor cells and that changes in their levels are a relevant feature of different types of cancer. To date, among more than 160 different RNA chemical modifications, the more relevant in cancer biology is the reversible and dynamic N6-methylation of adenosine, yielding N6-methyladenosine (m6A). m6A is the more abundant internal modification in mRNA, regulating the expression of the latter at different levels, from maturation to translation. Here, we will describe the emerging role of m6A modification in acute myeloid leukemia (AML), which, among first, has demonstrated how mis-regulation of the m6A modifying system can contribute to the development and progression of cancer. Moreover, we will discuss how AML is paving the way to the development of new therapeutic options based on the inhibition of m6A deposition.
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Affiliation(s)
- Zaira Ianniello
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences "A. Rossi Fanelli," Sapienza University of Rome, Rome, Italy
| | - Alessandro Fatica
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy
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374
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Chen J, Wang C, Fei W, Fang X, Hu X. Epitranscriptomic m6A modification in the stem cell field and its effects on cell death and survival. Am J Cancer Res 2019; 9:752-764. [PMID: 31106001 PMCID: PMC6511641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 03/14/2019] [Indexed: 06/09/2023] Open
Abstract
The reversible N6-methyl-adenosine (m6A) modification of messenger RNAs (mRNAs) has generated much interest in the field of stem cell modulation in recent years. Meanwhile, mounting evidence has shown that many physiopathological processes concerning cell death and survival harbor this chemical mark. Our review provides an overview of the m6A epitranscriptomic field and the updated mechanisms of m6A decoration in stem cell regulation. Furthermore, we focus on the role of m6A in DNA damage and the immune response, cell apoptosis, autophagy, and senescence, followed by recent advancements in m6A-induced viral replication. The function of abundant RNA-binding proteins (RBPs) identified in m6A regulatory systems will also be discussed in this review, highlighting their far-reaching implications in cellular m6A machinery and disease treatment.
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Affiliation(s)
- Jiaxin Chen
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University Hangzhou 310016, Zhejiang, China
| | - Chan Wang
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University Hangzhou 310016, Zhejiang, China
| | - Weiqiang Fei
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University Hangzhou 310016, Zhejiang, China
| | - Xiao Fang
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University Hangzhou 310016, Zhejiang, China
| | - Xiaotong Hu
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University Hangzhou 310016, Zhejiang, China
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375
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Functions of RNA N6-methyladenosine modification in cancer progression. Mol Biol Rep 2019; 46:2567-2575. [PMID: 30911972 DOI: 10.1007/s11033-019-04655-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/07/2018] [Indexed: 01/05/2023]
Abstract
N6-methyladenosine (m6A) serves as a major RNA methylation modification and impacts the initiation and progression of various human cancers through diverse mechanisms. It has been reported that m6A RNA methylation is involved in different physiological and pathological processes, including stem cell differentiation and motility, immune response, cellular stress, tissue renewal and viral infection. In this review, the m6A modification and its regulatory functions in a few major cancers is introduced. The detection approaches for the m6A sites identification are discussed. Additionally, the potential of the RNA m6A modification in clinical application is discussed.
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376
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Dorn LE, Tual-Chalot S, Stellos K, Accornero F. RNA epigenetics and cardiovascular diseases. J Mol Cell Cardiol 2019; 129:272-280. [PMID: 30880252 DOI: 10.1016/j.yjmcc.2019.03.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 03/11/2019] [Indexed: 12/24/2022]
Abstract
Cardiovascular disease (CVD) remains the leading cause of death in the Western world. Despite advances in the prevention and in the management of CVD, the role of RNA epigenetics in the cardiovascular system has been until recently unexplored. The rapidly expanding research field of RNA modifications has introduced a novel layer of gene regulation in mammalian cells. RNA modifications may control all aspects of RNA metabolism, and their study reveals previously unrecognized regulatory pathways that may determine gene expression at a post-transcriptional level. Understanding the role of RNA modifications in CVD may lead towards a better understanding of disease mechanisms and the development of novel biomarkers or therapeutic strategies. In this review, we highlight the most recent and major reports in the field of RNA methylation and adenosine to inosine RNA editing related to the cardiovascular field and we discuss how this breakthrough will advance the field of precision medicine.
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Affiliation(s)
- Lisa E Dorn
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Simon Tual-Chalot
- Cardiovascular Disease Prevention & Resilience Hub, Institute of Genetic Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Konstantinos Stellos
- Cardiovascular Disease Prevention & Resilience Hub, Institute of Genetic Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK; Department of Cardiology, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle, Upon Tyne, UK.
| | - Federica Accornero
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA.
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377
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Abstract
Posttranscriptional regulation of RNA has emerged as an important regulator of genetic information flow in eukaryotic systems. In particular, chemical modifications of RNA have recently been established as key regulatory marks that affect the lifetime, location, trafficking, and function of messenger RNA (mRNA). In mammalian systems, N6-methyladenosine (m6A) is the most prevalent mRNA modification, and the writer, eraser, and reader proteins that install, remove, or recognize m6A have been rapidly uncovered and studied at the whole cell level. Understanding the effects of specific m6A modifications and their regulation at the single transcript level is the key next step to understanding the mechanism and consequences of epitranscriptomic regulation. We recently developed programmable m6A reader proteins to study the effects of epitranscriptomic regulatory factors at individual RNA transcripts. In this chapter, we discuss the application of targeted m6A readers to study RNA regulation at single endogenous sites. We briefly introduce what is currently known about the N6-methyltranscriptome and the Cas13 RNA-targeting family of proteins before detailing our protocol to study RNA modifications with targeted reader proteins.
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Affiliation(s)
- Simone Rauch
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, United States; Department of Chemistry, The University of Chicago, Chicago, IL, United States
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL, United States.
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378
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Lobo J, Costa AL, Cantante M, Guimarães R, Lopes P, Antunes L, Braga I, Oliveira J, Pelizzola M, Henrique R, Jerónimo C. m 6A RNA modification and its writer/reader VIRMA/YTHDF3 in testicular germ cell tumors: a role in seminoma phenotype maintenance. J Transl Med 2019; 17:79. [PMID: 30866959 PMCID: PMC6416960 DOI: 10.1186/s12967-019-1837-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/08/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Covalent RNA modifications, such as N-6-methyladenosine (m6A), have been associated with various biological processes, but their role in cancer remains largely unexplored. m6A dynamics depends on specific enzymes whose deregulation may also impact in tumorigenesis. Herein, we assessed the differential abundance of m6A, its writer VIRMA and its reader YTHDF3, in testicular germ cell tumors (TGCTs), looking for clinicopathological correlates. METHODS In silico analysis of TCGA data disclosed altered expression of VIRMA (52%) and YTHDF3 (48%), prompting subsequent validation. Formalin-fixed paraffin-embedded tissues from 122 TGCTs (2005-2016) were selected. RNA extraction, cDNA synthesis and real-time qPCR (Taqman assays) for VIRMA and YTHDF3 were performed, as well as immunohistochemistry for VIRMA, YTHDF3 and m6A, for staining intensity assessment. Associations between categorical variables were assessed using Chi square and Fisher's exact test. Distribution of continuous variables between groups was compared using the nonparametric Mann-Whitney and Kruskal-Wallis tests. Biomarker performance was assessed through receiver operating characteristics (ROC) curve construction and a cut-off was established by Youden's index method. Statistical significance was set at p < 0.05. RESULTS In our cohort, VIRMA and YTHDF3 mRNA expression levels differed among TGCT subtypes, with Seminomas (SEs) depicting higher levels than Non-Seminomatous tumors (NSTs) (p < 0.01 for both). A positive correlation was found between VIRMA and YTHDF3 expression levels. VIRMA discriminated SEs from NSTs with AUC = 0.85 (Sensitivity 77.3%, Specificity 81.1%, PPV 71.6%, NPV 85.3%, Accuracy 79.7%). Immunohistochemistry paralleled transcript findings, as patients with strong m6A immunostaining intensity depicted significantly higher VIRMA mRNA expression levels and stronger VIRMA immunoexpression intensity (p < 0.001 and p < 0.01, respectively). CONCLUSION Abundance of m6A and expression of VIRMA/YTHDF3 were different among TGCT subtypes, with higher levels in SEs, suggesting a contribution to SE phenotype maintenance. VIRMA and YTHDF3 might cooperate in m6A establishment in TGCTs, and their transcript levels accurately discriminate between SEs and NSTs, constituting novel candidate biomarkers for patient management.
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Affiliation(s)
- João Lobo
- Cancer Biology and Epigenetics Group (CBEG), IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513, Porto, Portugal
| | - Ana Laura Costa
- Cancer Biology and Epigenetics Group (CBEG), IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Mariana Cantante
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Rita Guimarães
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Paula Lopes
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Luís Antunes
- Department of Epidemiology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Isaac Braga
- Department of Urology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Jorge Oliveira
- Department of Urology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Mattia Pelizzola
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Rui Henrique
- Cancer Biology and Epigenetics Group (CBEG), IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal. .,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal. .,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513, Porto, Portugal.
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group (CBEG), IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal. .,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513, Porto, Portugal.
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379
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Dang W, Xie Y, Cao P, Xin S, Wang J, Li S, Li Y, Lu J. N 6-Methyladenosine and Viral Infection. Front Microbiol 2019; 10:417. [PMID: 30891023 PMCID: PMC6413633 DOI: 10.3389/fmicb.2019.00417] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/18/2019] [Indexed: 12/12/2022] Open
Abstract
N6-methyladenosine (m6A), as a dynamic posttranscriptional RNA modification, recently gave rise to the field of viral epitranscriptomics. The interaction between virus and host is affected by m6A. Multiple m6A-modified viral RNAs have been observed. The epitranscriptome of m6A in host cells are altered after viral infection. The expression of viral genes, the replication of virus and the generation of progeny virions are influenced by m6A modifications in viral RNAs during virus infection. Meanwhile, the decorations of m6A in host mRNAs can make viral infections more likely to happen or can enhance the resistance of host to virus infection. However, the mechanism of m6A regulation in viral infection and host immune response has not been thoroughly elucidated to date. With the development of sequencing-based biotechnologies, transcriptome-wide mapping of m6A in viruses has been achieved, laying the foundation for expanding its functions and corresponding mechanisms. In this report, we summarize the positive and negative effects of m6A in distinct viral infection. Given the increasingly important roles of m6A in diverse viruses, m6A represents a novel potential target for antiviral therapy.
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Affiliation(s)
- Wei Dang
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Yan Xie
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Pengfei Cao
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
| | - Shuyu Xin
- Department of Microbiology, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Jia Wang
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Shen Li
- Department of Microbiology, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Yanling Li
- Department of Microbiology, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Jianhong Lu
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
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380
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Identification of novel mouse and rat CB1R isoforms and in silico modeling of human CB1R for peripheral cannabinoid therapeutics. Acta Pharmacol Sin 2019; 40:387-397. [PMID: 30202012 DOI: 10.1038/s41401-018-0152-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/18/2018] [Indexed: 01/28/2023] Open
Abstract
Targeting peripheral CB1R is desirable for the treatment of metabolic syndromes without adverse neuropsychiatric effects. We previously reported a human hCB1b isoform that is selectively enriched in pancreatic beta-cells and hepatocytes, providing a potential peripheral therapeutic hCB1R target. It is unknown whether there are peripherally enriched mouse and rat CB1R (mCB1 and rCB1, respectively) isoforms. In this study, we found no evidence of peripherally enriched rodent CB1 isoforms; however, some mCB1R isoforms are absent in peripheral tissues. We show that the mouse Cnr1 gene contains six exons that are transcribed from a single promoter. We found that mCB1A is a spliced variant of extended exon 1 and protein-coding exon 6; mCB1B is a novel spliced variant containing unspliced exon 1, intron 1, and exon 2, which is then spliced to exon 6; and mCB1C is a spliced variant including all 6 exons. Using RNAscope in situ hybridization, we show that the isoforms mCB1A and mCB1B are expressed at a cellular level and colocalized in GABAergic neurons in the hippocampus and cortex. RT-qPCR reveals that mCB1A and mCB1B are enriched in the brain, while mCB1B is not expressed in the pancreas or the liver. Rat rCB1R isoforms are differentially expressed in primary cultured neurons, astrocytes, and microglia. We also investigated modulation of Cnr1 expression by insulin in vivo and carried out in silico modeling of CB1R with JD5037, a peripherally restricted CB1R inverse agonist, using the published crystal structure of hCB1R. The results provide models for future CB1R peripheral targeting.
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381
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Lence T, Paolantoni C, Worpenberg L, Roignant JY. Mechanistic insights into m6A RNA enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:222-229. [DOI: 10.1016/j.bbagrm.2018.10.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/27/2018] [Indexed: 12/09/2022]
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382
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Functions of RNA N6-methyladenosine modification in cancer progression. Mol Biol Rep 2019; 46:1383-1391. [PMID: 30788764 DOI: 10.1007/s11033-018-4471-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/07/2018] [Indexed: 10/27/2022]
Abstract
N6-methyladenosine (m6A) serves as a major RNA methylation modification and impacts the initiation and progression of various human cancers through diverse mechanisms. It has been reported that m6A RNA methylation is involved in different physiological and pathological processes, including stem cell differentiation and motility, immune response, cellular stress, tissue renewal and viral infection. In this review, the m6A modification and its regulatory functions in a few major cancers is introduced. The detection approaches for the m6A sites identification are discussed. Additionally, the potential of the RNA m6A modification in clinical application is discussed.
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383
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Berlivet S, Scutenaire J, Deragon JM, Bousquet-Antonelli C. Readers of the m 6A epitranscriptomic code. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:329-342. [PMID: 30660758 DOI: 10.1016/j.bbagrm.2018.12.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 12/20/2018] [Accepted: 12/28/2018] [Indexed: 12/21/2022]
Abstract
N6-methyl adenosine (m6A) is the most prevalent and evolutionarily conserved, modification of polymerase II transcribed RNAs. By post-transcriptionally controlling patterns of gene expression, m6A deposition is crucial for organism reproduction, development and likely stress responses. m6A mostly mediates its effect by recruiting reader proteins that either directly accommodate the modified residue in a hydrophobic pocket formed by their YTH domain, or otherwise have their affinity positively influenced by the presence of m6A. We firstly describe here the evolutionary history, and review known molecular and physiological roles of eukaryote YTH readers. In the second part, we present non YTH-proteins whose roles as m6A readers largely remain to be explored. The diversity and multiplicity of m6A readers together with the possibility to regulate their expression and function in response to various cues, offers a multitude of possible combinations to rapidly and finely tune gene expression patterns and hence cellular plasticity. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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Affiliation(s)
- Soizik Berlivet
- LGDP-UMR5096 CNRS, 58 Av Paul Alduy, 66860 Perpignan, France; LGDP-UMR5096, Université de Perpignan, Via Domitia, 58 Av Paul Alduy, 66860 Perpignan, France
| | - Jérémy Scutenaire
- LGDP-UMR5096 CNRS, 58 Av Paul Alduy, 66860 Perpignan, France; LGDP-UMR5096, Université de Perpignan, Via Domitia, 58 Av Paul Alduy, 66860 Perpignan, France
| | - Jean-Marc Deragon
- LGDP-UMR5096 CNRS, 58 Av Paul Alduy, 66860 Perpignan, France; LGDP-UMR5096, Université de Perpignan, Via Domitia, 58 Av Paul Alduy, 66860 Perpignan, France; Institut Universitaire de France (IUF), 1 rue Descartes, 75231 Paris Cedex 05, France
| | - Cécile Bousquet-Antonelli
- LGDP-UMR5096 CNRS, 58 Av Paul Alduy, 66860 Perpignan, France; LGDP-UMR5096, Université de Perpignan, Via Domitia, 58 Av Paul Alduy, 66860 Perpignan, France.
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384
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Xie G, Vo TV, Thillainadesan G, Holla S, Zhang B, Jiang Y, Lv M, Xu Z, Wang C, Balachandran V, Shi Y, Li F, Grewal SIS. A conserved dimer interface connects ERH and YTH family proteins to promote gene silencing. Nat Commun 2019; 10:251. [PMID: 30651569 PMCID: PMC6335422 DOI: 10.1038/s41467-018-08273-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/21/2018] [Indexed: 12/18/2022] Open
Abstract
Gene regulatory mechanisms rely on a complex network of RNA processing factors to prevent untimely gene expression. In fission yeast, the highly conserved ortholog of human ERH, called Erh1, interacts with the YTH family RNA binding protein Mmi1 to form the Erh1-Mmi1 complex (EMC) implicated in gametogenic gene silencing. However, the structural basis of EMC assembly and its functions are poorly understood. Here, we present the co-crystal structure of the EMC that consists of Erh1 homodimers interacting with Mmi1 in a 2:2 stoichiometry via a conserved molecular interface. Structure-guided mutation of the Mmi1Trp112 residue, which is required for Erh1 binding, causes defects in facultative heterochromatin assembly and gene silencing while leaving Mmi1-mediated transcription termination intact. Indeed, EMC targets masked in mmi1∆ due to termination defects are revealed in mmi1W112A. Our study delineates EMC requirements in gene silencing and identifies an ERH interface required for interaction with an RNA binding protein.
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Affiliation(s)
- Guodong Xie
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Tommy V Vo
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Gobi Thillainadesan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sahana Holla
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Beibei Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Yiyang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Mengqi Lv
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Zheng Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Chongyuan Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yunyu Shi
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China.
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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385
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Borland K, Diesend J, Ito-Kureha T, Heissmeyer V, Hammann C, Buck AH, Michalakis S, Kellner S. Production and Application of Stable Isotope-Labeled Internal Standards for RNA Modification Analysis. Genes (Basel) 2019; 10:E26. [PMID: 30621251 PMCID: PMC6356711 DOI: 10.3390/genes10010026] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/17/2018] [Accepted: 12/26/2018] [Indexed: 12/04/2022] Open
Abstract
Post-transcriptional RNA modifications have been found to be present in a wide variety of organisms and in different types of RNA. Nucleoside modifications are interesting due to their already known roles in translation fidelity, enzyme recognition, disease progression, and RNA stability. In addition, the abundance of modified nucleosides fluctuates based on growth phase, external stress, or possibly other factors not yet explored. With modifications ever changing, a method to determine absolute quantities for multiple nucleoside modifications is required. Here, we report metabolic isotope labeling to produce isotopically labeled internal standards in bacteria and yeast. These can be used for the quantification of 26 different modified nucleosides. We explain in detail how these internal standards are produced and show their mass spectrometric characterization. We apply our internal standards and quantify the modification content of transfer RNA (tRNA) from bacteria and various eukaryotes. We can show that the origin of the internal standard has no impact on the quantification result. Furthermore, we use our internal standard for the quantification of modified nucleosides in mouse tissue messenger RNA (mRNA), where we find different modification profiles in liver and brain tissue.
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Affiliation(s)
- Kayla Borland
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Jan Diesend
- Department of Life Sciences and Chemistry, Jacobs University Bremen GmbH, Campus Ring 1, 28759 Bremen, Germany.
| | - Taku Ito-Kureha
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.
| | - Vigo Heissmeyer
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.
- Helmholtz Zentrum München, Research Unit Molecular Immune Regulation, Marchioninistr. 25, 81377 Munich, Germany.
| | - Christian Hammann
- Department of Life Sciences and Chemistry, Jacobs University Bremen GmbH, Campus Ring 1, 28759 Bremen, Germany.
| | - Amy H Buck
- Institute of Immunology & Infection and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
| | - Stylianos Michalakis
- Center for Integrated Protein Science Munich CiPSM at the Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstr. 5-13, 81377 Munich, Germany.
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386
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Chan C, Pham P, Dedon PC, Begley TJ. Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses. Genome Biol 2018; 19:228. [PMID: 30587213 PMCID: PMC6307160 DOI: 10.1186/s13059-018-1611-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cells adapt to stress by altering gene expression at multiple levels. Here, we propose a new mechanism regulating stress-dependent gene expression at the level of translation, with coordinated interplay between the tRNA epitranscriptome and biased codon usage in families of stress-response genes. In this model, auxiliary genetic information contained in synonymous codon usage enables regulation of codon-biased and functionally related transcripts by dynamic changes in the tRNA epitranscriptome. This model partly explains the association between synchronous stress-dependent epitranscriptomic marks and significant multi-codon usage skewing in families of translationally regulated transcripts. The model also predicts translational adaptation during viral infections.
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Affiliation(s)
- Cheryl Chan
- Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore
| | - Phuong Pham
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Thomas J Begley
- The RNA Institute, College of Arts and Science, University at Albany, SUNY, Albany, NY, 12222, USA.
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387
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Abstract
The central dogma of molecular biology introduced by Crick describes a linear flow of information from DNA to mRNA to protein. Since then it has become evident that RNA undergoes several maturation steps such as capping, splicing, 3'-end processing, and editing. Likewise, nucleotide modifications are common in mRNA and are present in all organisms impacting on the regulation of gene expression. The most abundant modification found in mRNA is N6-methyladenosine (m6A). Deposition of m6A is a nuclear process and is performed by a megadalton writer complex primarily on mRNAs, but also on microRNAs and lncRNAs. The m6A methylosome is composed of the enzymatic core components METTL3 and METTL14, and several auxiliary proteins necessary for its correct positioning and functioning, which are WTAP, VIRMA, FLACC, RBM15, and HAKAI. The m6A epimark is decoded by YTH domain-containing reader proteins YTHDC and YTHDF, but METTLs can act as "readers" as well. Eraser proteins, such as FTO and ALKBH5, can remove the methyl group. Here we review recent progress on the role of m6A in regulating gene expression in light of Crick's central dogma of molecular biology. In particular, we address the complexity of the writer complex from an evolutionary perspective to obtain insights into the mechanism of ancient m6A methylation and its regulation.
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Affiliation(s)
- Dario L Balacco
- School of Biosciences, College of Life and Environmental Sciences , University of Birmingham , Edgbaston, Birmingham B15 2TT , United Kingdom
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences , University of Birmingham , Edgbaston, Birmingham B15 2TT , United Kingdom
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388
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RNA-binding protein YTHDF3 suppresses interferon-dependent antiviral responses by promoting FOXO3 translation. Proc Natl Acad Sci U S A 2018; 116:976-981. [PMID: 30591559 DOI: 10.1073/pnas.1812536116] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
IFN-stimulated genes (ISGs) are essential effectors of the IFN-dependent antiviral immune response. Dysregulation of ISG expression can cause dysfunctional antiviral responses and autoimmune disorders. Epitranscriptomic regulation, such as N 6-methyladenosine (m6A) modification of mRNAs, plays key roles in diverse biological processes. Here, we found that the m6A "reader" YT521-B homology domain-containing family 3 (YTHDF3) suppresses ISG expression under basal conditions by promoting translation of the transcription corepressor forkhead box protein O3 (FOXO3). YTHDF3 cooperates with two cofactors, PABP1 and eIF4G2, to promote FOXO3 translation by binding to the translation initiation region of FOXO3 mRNA. Both the YTH and the P/Q/N-rich domains of YTHDF3 were required for FOXO3 RNA-binding capacity, however, METTL3-mediated m6A modification was not involved in the process observed. Moreover, YTHDF3-/- mice had increased ISG levels and were resistant to several viral infections. Our findings uncover the role of YTHDF3 as a negative regulator of antiviral immunity through the translational promotion of FOXO3 mRNA under homeostatic conditions, adding insight into the networks of RNA-binding protein-RNA interactions in homeostatically maintaining host antiviral immune function and preventing inflammatory response.
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389
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Coker H, Wei G, Brockdorff N. m6A modification of non-coding RNA and the control of mammalian gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:310-318. [PMID: 30550772 DOI: 10.1016/j.bbagrm.2018.12.002] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/27/2018] [Accepted: 12/07/2018] [Indexed: 12/27/2022]
Abstract
The biology of non-coding RNA (ncRNA) and the regulation of mammalian gene expression is a rapidly expanding field. In this review, we consider how recent advances in technology, enabling the precise mapping of modifications to RNA transcripts, has provided new opportunities to dissect post-transcriptional gene regulation. With this has come the realisation that in the absence of translation, the modification of ncRNAs may play a fundamental role in their regulation, protein interactome and subsequent downstream effector functions. We focus upon modification of RNA by N6-methyladenosine (m6A); its readers, writers and erasers, before considering the differing role of m6A modified lncRNAs MALAT1 and Xist. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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Affiliation(s)
- Heather Coker
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | - Guifeng Wei
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Neil Brockdorff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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390
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Zhu LY, Zhu YR, Dai DJ, Wang X, Jin HC. Epigenetic regulation of alternative splicing. Am J Cancer Res 2018; 8:2346-2358. [PMID: 30662796 PMCID: PMC6325479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 11/21/2018] [Indexed: 06/09/2023] Open
Abstract
Alternative splicing (AS) serves as an additional regulatory process for gene expression after transcription, and it generates distinct mRNA species, and even noncoding RNAs (ncRNAs), from one primary transcript. Generally, AS can be coupled with transcription and subjected to epigenetic regulation, such as DNA methylation and histone modifications. In addition, ncRNAs, especially long noncoding RNAs (lncRNAs), can be generated from AS and function as splicing factors ("interactors" or "hijackers") in AS. Recently, RNA modifications, such as the RNA N6-methyladenosine (m6A) modification, have been found to regulate AS. In this review, we summarize recent achievements related to the epigenetic regulation of AS.
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Affiliation(s)
- Li-Yuan Zhu
- Laboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Medical School of Zhejiang UniversityHangzhou, China
| | - Yi-Ran Zhu
- Laboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Medical School of Zhejiang UniversityHangzhou, China
| | - Dong-Jun Dai
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Medical School of Zhejiang UniversityHangzhou, China
| | - Xian Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Medical School of Zhejiang UniversityHangzhou, China
| | - Hong-Chuan Jin
- Laboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Medical School of Zhejiang UniversityHangzhou, China
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391
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Akichika S, Hirano S, Shichino Y, Suzuki T, Nishimasu H, Ishitani R, Sugita A, Hirose Y, Iwasaki S, Nureki O, Suzuki T. Cap-specific terminal N 6-methylation of RNA by an RNA polymerase II-associated methyltransferase. Science 2018; 363:science.aav0080. [PMID: 30467178 DOI: 10.1126/science.aav0080] [Citation(s) in RCA: 234] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 11/14/2018] [Indexed: 12/14/2022]
Abstract
N 6-methyladenosine (m6A), a major modification of messenger RNAs (mRNAs), plays critical roles in RNA metabolism and function. In addition to the internal m6A, N 6, 2'-O-dimethyladenosine (m6Am) is present at the transcription start nucleotide of capped mRNAs in vertebrates. However, its biogenesis and functional role remain elusive. Using a reverse genetics approach, we identified PCIF1, a factor that interacts with the serine-5-phosphorylated carboxyl-terminal domain of RNA polymerase II, as a cap-specific adenosine methyltransferase (CAPAM) responsible for N 6-methylation of m6Am. The crystal structure of CAPAM in complex with substrates revealed the molecular basis of cap-specific m6A formation. A transcriptome-wide analysis revealed that N 6-methylation of m6Am promotes the translation of capped mRNAs. Thus, a cap-specific m6A writer promotes translation of mRNAs starting from m6Am.
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Affiliation(s)
- Shinichiro Akichika
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Seiichi Hirano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuichi Shichino
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroshi Nishimasu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ai Sugita
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yutaka Hirose
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Shintaro Iwasaki
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo 277-8562, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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392
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Rubio RM, Depledge DP, Bianco C, Thompson L, Mohr I. RNA m 6 A modification enzymes shape innate responses to DNA by regulating interferon β. Genes Dev 2018; 32:1472-1484. [PMID: 30463905 PMCID: PMC6295168 DOI: 10.1101/gad.319475.118] [Citation(s) in RCA: 170] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/12/2018] [Indexed: 12/21/2022]
Abstract
In this study, Rubio et al. researched how the dynamic genome-wide landscape of m6A-modified mRNAs impacts virus infection and host immune responses. They show that type I interferon (IFN) production triggered by dsDNA or human cytomegalovirus (HCMV) is controlled by the cellular m6A methyltrasferase subunit METTL14 and ALKBH5 demethylase, and their results demonstrate that responses to nonmicrobial dsDNA in uninfected cells are regulated by enzymes controlling m6A epitranscriptomic changes. Modification of mRNA by N6-adenosine methylation (m6A) on internal bases influences gene expression in eukaryotes. How the dynamic genome-wide landscape of m6A-modified mRNAs impacts virus infection and host immune responses remains poorly understood. Here, we show that type I interferon (IFN) production triggered by dsDNA or human cytomegalovirus (HCMV) is controlled by the cellular m6A methyltrasferase subunit METTL14 and ALKBH5 demethylase. While METTL14 depletion reduced virus reproduction and stimulated dsDNA- or HCMV-induced IFNB1 mRNA accumulation, ALKBH5 depletion had the opposite effect. Depleting METTL14 increased both nascent IFNB1 mRNA production and stability in response to dsDNA. In contrast, ALKBH5 depletion reduced nascent IFNB1 mRNA production without detectably influencing IFN1B mRNA decay. Genome-wide transcriptome profiling following ALKBH5 depletion identified differentially expressed genes regulating antiviral immune responses, while METTL14 depletion altered pathways impacting metabolic reprogramming, stress responses, and aging. Finally, we determined that IFNB1 mRNA was m6A-modified within both the coding sequence and the 3′ untranslated region (UTR). This establishes that the host m6A modification machinery controls IFNβ production triggered by HCMV or dsDNA. Moreover, it demonstrates that responses to nonmicrobial dsDNA in uninfected cells, which shape host immunity and contribute to autoimmune disease, are regulated by enzymes controlling m6A epitranscriptomic changes.
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Affiliation(s)
- Rosa M Rubio
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Daniel P Depledge
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Christopher Bianco
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Letitia Thompson
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA.,Laura and Isaac Perlmutter Cancer Institute, New York University School of Medicine, New York, New York 10016, USA
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393
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Abstract
RNA modifications have generated much interest in the virology field, as recent works have shown that many viruses harbor these marks and modify cellular marks. The most abundant mRNA modification in eukaryotic cells, N6-methyladenosine (m6A), has been examined extensively at the genome-wide scale in both cellular and viral contexts. This Gem discusses the role of m6A in gene regulation and describes recent advancements in Kaposi's sarcoma-associated herpesvirus (KSHV) and simian virus 40 (SV40) research. We provide insights into future research related to m6A in DNA viruses.
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Affiliation(s)
- Brandon Tan
- Department of Systems Biology, City of Hope, Monrovia, California, USA
| | - Shou-Jiang Gao
- UPMC Hillman Cancer Center, Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, Guangdong, People's Republic of China
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394
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The Emerging Role of Epitranscriptomics in Cancer: Focus on Urological Tumors. Genes (Basel) 2018; 9:genes9110552. [PMID: 30428628 PMCID: PMC6265908 DOI: 10.3390/genes9110552] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/27/2018] [Accepted: 11/08/2018] [Indexed: 12/11/2022] Open
Abstract
Epitranscriptomics has gained ground in recent years, especially after the advent of techniques for accurately studying these mechanisms. Among all modifications occurring in RNA molecules, N6-methyladenosine (m6A) is the most frequent, especially among mRNAs. m6A has been demonstrated to play important roles in many physiological processes and several disease states, including various cancer models (from solid to liquid tumors). Tumor cells’ epitranscriptome is indeed disrupted in a way to promote cancer-prone features, by means of up/downregulating m6A-related players: the so-called writers, readers and erasers. These proteins modulate m6A establishment, removal and determine mRNAs fate, acting in a context-dependent manner, so that a single player may act as an oncogenic signal in one tumor model (methyltransferase like 3 (METTL3) in lung cancer) and as a tumor suppressor in another context (METTL3 in glioblastoma). Despite recent advances, however, little attention has been directed towards urological cancer. By means of a thorough analysis of the publicly available TCGA (The Cancer Genome Atlas) database, we disclosed the most relevant players in four major urogenital neoplasms—kidney, bladder, prostate and testicular cancer—for prognostic, subtype discrimination and survival purposes. In all tumor models assessed, the most promising player was shown to be Vir like m6A methyltransferase associated (VIRMA), which could constitute a potential target for personalized therapies.
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395
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Zhong L, Liao D, Zhang M, Zeng C, Li X, Zhang R, Ma H, Kang T. YTHDF2 suppresses cell proliferation and growth via destabilizing the EGFR mRNA in hepatocellular carcinoma. Cancer Lett 2018; 442:252-261. [PMID: 30423408 DOI: 10.1016/j.canlet.2018.11.006] [Citation(s) in RCA: 246] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/25/2018] [Accepted: 11/05/2018] [Indexed: 01/11/2023]
Abstract
N6-methyladenosin (m6A) is one of the most pervasive modification of mRNA in eukaryotes and the m6A methyltransferases and demethylases play critical roles in many types of cancer. However the role of m6A-binding proteins in cancer remains elusive. Here we report that the down-regulation of YTHDF2 was specifically induced by hypoxia in hepatocellular carcinoma (HCC) cells, and that overexpression of YTHDF2 suppressed cell proliferation, tumor growth and activation of MEK and ERK in HCC cells. Mechanistically, YTHDF2 directly bound the m6A modification site of EGFR 3'-UTR to promote the degradation of EGFR mRNA in HCC cells. This is the first report showing that YTHDF2 may act as a tumor suppressor to repress cell proliferation and growth via destabilizing the EGFR mRNA in HCC.
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Affiliation(s)
- Li Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dan Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Meifang Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Cuiling Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xinchun Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ruhua Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Haiqing Ma
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, Guangdong, China.
| | - Tiebang Kang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
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396
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Malla S, Melguizo-Sanchis D, Aguilo F. Steering pluripotency and differentiation with N 6-methyladenosine RNA modification. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:394-402. [PMID: 30412796 DOI: 10.1016/j.bbagrm.2018.10.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/21/2018] [Accepted: 10/27/2018] [Indexed: 11/15/2022]
Abstract
Chemical modifications of RNA provide a direct and rapid way to modulate the existing transcriptome, allowing the cells to adapt rapidly to the changing environment. Among these modifications, N6-methyladenosine (m6A) has recently emerged as a widely prevalent mark of messenger RNA in eukaryotes, linking external stimuli to an intricate network of transcriptional, post-transcriptional and translational processes. m6A modification modulates a broad spectrum of biochemical processes, including mRNA decay, translation and splicing. Both m6A modification and the enzymes that control m6A metabolism are essential for normal development. In this review, we summarized the most recent findings on the role of m6A modification in maintenance of the pluripotency of embryonic stem cells (ESCs), cell fate specification, the reprogramming of somatic cells into induced pluripotent stem cells (iPSCs), and differentiation of stem and progenitor cells. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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Affiliation(s)
- Sandhya Malla
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, SE-90185 Umeå, Sweden; Department of Medical Biosciences, Umeå University, SE-901 85 Umeå, Sweden
| | - Dario Melguizo-Sanchis
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, SE-90185 Umeå, Sweden; Department of Medical Biosciences, Umeå University, SE-901 85 Umeå, Sweden
| | - Francesca Aguilo
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, SE-90185 Umeå, Sweden; Department of Medical Biosciences, Umeå University, SE-901 85 Umeå, Sweden.
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397
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Olazagoitia-Garmendia A, Santin I, Castellanos-Rubio A. Functional implication of celiac disease associated lncRNAs in disease pathogenesis. Comput Biol Med 2018; 102:369-375. [DOI: 10.1016/j.compbiomed.2018.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/09/2018] [Accepted: 08/09/2018] [Indexed: 12/11/2022]
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398
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Sednev MV, Mykhailiuk V, Choudhury P, Halang J, Sloan KE, Bohnsack MT, Höbartner C. N 6 -Methyladenosine-Sensitive RNA-Cleaving Deoxyribozymes. Angew Chem Int Ed Engl 2018; 57:15117-15121. [PMID: 30276938 DOI: 10.1002/anie.201808745] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/22/2018] [Indexed: 12/31/2022]
Abstract
Deoxyribozymes are synthetic enzymes made of DNA that can catalyze the cleavage or formation of phosphodiester bonds and are useful tools for RNA biochemistry. Herein, we report new RNA-cleaving deoxyribozymes to interrogate the methylation status of target RNAs, thereby providing an alternative method for the biochemical validation of RNA methylation sites containing N6 -methyladenosine, which is the most wide-spread and extensively investigated natural RNA modification. The developed deoxyribozymes are sensitive to the presence of N6 -methyladenosine in RNA near the cleavage site. One class of these DNA enzymes shows faster cleavage of methylated RNA, while others are strongly inhibited by the modified nucleotide. The general applicability of the new deoxyribozymes is demonstrated for several examples of natural RNA sequences, including a lncRNA and a set of C/D box snoRNAs, which have been suggested to contain m6 A as a regulatory element that influences RNA folding and protein binding.
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Affiliation(s)
- Maksim V Sednev
- Universität Würzburg, Institut für Organische Chemie, Am Hubland, 97074, Würzburg, Germany
| | - Volodymyr Mykhailiuk
- International Max Planck Research School Molecular Biology, University of Göttingen, Göttingen, Germany.,Present address: Department of Physics, Technische Universität München, München, Germany
| | - Priyanka Choudhury
- International Max Planck Research School Molecular Biology, University of Göttingen, Göttingen, Germany.,Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Julia Halang
- Universität Würzburg, Institut für Organische Chemie, Am Hubland, 97074, Würzburg, Germany
| | - Katherine E Sloan
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Markus T Bohnsack
- International Max Planck Research School Molecular Biology, University of Göttingen, Göttingen, Germany.,Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Claudia Höbartner
- Universität Würzburg, Institut für Organische Chemie, Am Hubland, 97074, Würzburg, Germany.,International Max Planck Research School Molecular Biology, University of Göttingen, Göttingen, Germany
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399
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Sednev MV, Mykhailiuk V, Choudhury P, Halang J, Sloan KE, Bohnsack MT, Höbartner C. N
6
‐Methyladenosine‐Sensitive RNA‐Cleaving Deoxyribozymes. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808745] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Maksim V. Sednev
- Universität WürzburgInstitut für Organische Chemie Am Hubland 97074 Würzburg Germany
| | - Volodymyr Mykhailiuk
- International Max Planck Research School Molecular BiologyUniversity of Göttingen Göttingen Germany
- Present address: Department of PhysicsTechnische Universität München München Germany
| | - Priyanka Choudhury
- International Max Planck Research School Molecular BiologyUniversity of Göttingen Göttingen Germany
- Department of Molecular BiologyUniversity Medical Center Göttingen Humboldtallee 23 37073 Göttingen Germany
| | - Julia Halang
- Universität WürzburgInstitut für Organische Chemie Am Hubland 97074 Würzburg Germany
| | - Katherine E. Sloan
- Department of Molecular BiologyUniversity Medical Center Göttingen Humboldtallee 23 37073 Göttingen Germany
| | - Markus T. Bohnsack
- International Max Planck Research School Molecular BiologyUniversity of Göttingen Göttingen Germany
- Department of Molecular BiologyUniversity Medical Center Göttingen Humboldtallee 23 37073 Göttingen Germany
| | - Claudia Höbartner
- Universität WürzburgInstitut für Organische Chemie Am Hubland 97074 Würzburg Germany
- International Max Planck Research School Molecular BiologyUniversity of Göttingen Göttingen Germany
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400
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Perez-Perri JI, Rogell B, Schwarzl T, Stein F, Zhou Y, Rettel M, Brosig A, Hentze MW. Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture. Nat Commun 2018; 9:4408. [PMID: 30352994 PMCID: PMC6199288 DOI: 10.1038/s41467-018-06557-8] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/12/2018] [Indexed: 01/25/2023] Open
Abstract
Following the realization that eukaryotic RNA-binding proteomes are substantially larger than anticipated, we must now understand their detailed composition and dynamics. Methods such as RNA interactome capture (RIC) have begun to address this need. However, limitations of RIC have been reported. Here we describe enhanced RNA interactome capture (eRIC), a method based on the use of an LNA-modified capture probe, which yields numerous advantages including greater specificity and increased signal-to-noise ratios compared to existing methods. In Jurkat cells, eRIC reduces the rRNA and DNA contamination by >10-fold compared to RIC and increases the detection of RNA-binding proteins. Due to its low background, eRIC also empowers comparative analyses of changes of RNA-bound proteomes missed by RIC. For example, in cells treated with dimethyloxalylglycine, which inhibits RNA demethylases, eRIC identifies m6A-responsive RNA-binding proteins that escape RIC. eRIC will facilitate the unbiased characterization of RBP dynamics in response to biological and pharmacological cues. RNA interactome capture allows the detailed investigation of RNA-bound proteomes. Here the authors describe enhanced RNA-interactome capture using LNA-modified probes for increased sensitivity and specificity.
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Affiliation(s)
- Joel I Perez-Perri
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Birgit Rogell
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Frank Stein
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Yang Zhou
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Annika Brosig
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany. .,Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120, Heidelberg, Germany.
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