901
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Hsu PJ, Shi H, Zhu AC, Lu Z, Miller N, Edens BM, Ma YC, He C. The RNA-binding protein FMRP facilitates the nuclear export of N6-methyladenosine-containing mRNAs. J Biol Chem 2019; 294:19889-19895. [PMID: 31753916 PMCID: PMC6937581 DOI: 10.1074/jbc.ac119.010078] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 11/20/2019] [Indexed: 11/06/2022] Open
Abstract
N6-Methyladenosine (m6A) is the most abundant post-transcriptional mRNA modification in eukaryotes and exerts many of its effects on gene expression through reader proteins that bind specifically to m6A-containing transcripts. Fragile X mental retardation protein (FMRP), an RNA-binding protein, has previously been shown to affect the translation of target mRNAs and trafficking of mRNA granules. Loss of function of FMRP causes fragile X syndrome, the most common form of inherited intellectual disability in humans. Using HEK293T cells, siRNA-mediated gene knockdown, cytoplasmic and nuclear fractions, RNA-Seq, and LC-MS/MS analyses, we demonstrate here that FMRP binds directly to a collection of m6A sites on mRNAs. FMRP depletion increased mRNA m6A levels in the nucleus. Moreover, the abundance of FMRP targets in the cytoplasm relative to the nucleus was decreased in Fmr1-KO mice, an effect also observed in highly methylated genes. We conclude that FMRP may affect the nuclear export of m6A-modified RNA targets.
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Affiliation(s)
- Phillip J Hsu
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois 60637
- Medical Scientist Training Program/Committee on Immunology, University of Chicago, Chicago, Illinois 60637
| | - Hailing Shi
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois 60637
| | - Allen C Zhu
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois 60637
- Medical Scientist Training Program/Committee on Cancer Biology, University of Chicago, Chicago, Illinois 60637
| | - Zhike Lu
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois 60637
| | - Nimrod Miller
- Departments of Pediatrics, Neurology and Physiology, Northwestern University Feinberg School of Medicine, Anne and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611
| | - Brittany M Edens
- Departments of Pediatrics, Neurology and Physiology, Northwestern University Feinberg School of Medicine, Anne and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611
| | - Yongchao C Ma
- Departments of Pediatrics, Neurology and Physiology, Northwestern University Feinberg School of Medicine, Anne and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois 60637
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
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902
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van der Kwast RV, Quax PH, Nossent AY. An Emerging Role for isomiRs and the microRNA Epitranscriptome in Neovascularization. Cells 2019; 9:cells9010061. [PMID: 31881725 PMCID: PMC7017316 DOI: 10.3390/cells9010061] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/19/2019] [Accepted: 12/21/2019] [Indexed: 02/06/2023] Open
Abstract
Therapeutic neovascularization can facilitate blood flow recovery in patients with ischemic cardiovascular disease, the leading cause of death worldwide. Neovascularization encompasses both angiogenesis, the sprouting of new capillaries from existing vessels, and arteriogenesis, the maturation of preexisting collateral arterioles into fully functional arteries. Both angiogenesis and arteriogenesis are highly multifactorial processes that require a multifactorial regulator to be stimulated simultaneously. MicroRNAs can regulate both angiogenesis and arteriogenesis due to their ability to modulate expression of many genes simultaneously. Recent studies have revealed that many microRNAs have variants with altered terminal sequences, known as isomiRs. Additionally, endogenous microRNAs have been identified that carry biochemically modified nucleotides, revealing a dynamic microRNA epitranscriptome. Both types of microRNA alterations were shown to be dynamically regulated in response to ischemia and are able to influence neovascularization by affecting the microRNA’s biogenesis, or even its silencing activity. Therefore, these novel regulatory layers influence microRNA functioning and could provide new opportunities to stimulate neovascularization. In this review we will highlight the formation and function of isomiRs and various forms of microRNA modifications, and discuss recent findings that demonstrate that both isomiRs and microRNA modifications directly affect neovascularization and vascular remodeling.
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Affiliation(s)
- Reginald V.C.T. van der Kwast
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Paul H.A. Quax
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - A. Yaël Nossent
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Department of Laboratory Medicine and Department of Internal Medicine II, Medical University of Vienna, 1090 Vienna, Austria
- Correspondence:
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903
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Liu L, Wang J, Sun G, Wu Q, Ma J, Zhang X, Huang N, Bian Z, Gu S, Xu M, Yin M, Sun F, Pan Q. m 6A mRNA methylation regulates CTNNB1 to promote the proliferation of hepatoblastoma. Mol Cancer 2019; 18:188. [PMID: 31870368 PMCID: PMC6927193 DOI: 10.1186/s12943-019-1119-7] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/11/2019] [Indexed: 01/08/2023] Open
Abstract
Background N6-Methyladenosine (m6A) modification has been implicated in many biological processes. It is important for the regulation of messenger RNA (mRNA) stability, splicing, and translation. However, its role in cancer has not been studied in detail. Here we investigated the biological role and underlying mechanism of m6A modification in hepatoblastoma (HB). Methods We used Reverse transcription quantitative real-time PCR (RT-qPCR) and Western blotting to determine the expression of m6A related factors. And we clarified the effects of these factors on HB cells using cell proliferation assay, colony formation, apoptotic assay. Then we investigated of methyltransferase-like 13 (METTL3) and its correlation with clinicopathological features and used xenograft experiment to check METTL3 effect in vivo. m6A-Seq was used to profiled m6A transcriptome-wide in hepatoblastoma tumor tissue and normal tissue. Finally, methylated RNA immunoprecipitation (MeRIP) assay, RNA remaining assay to perform the regulator mechanism of MEETL3 on the target CTNNB1 in HB. Results In this research, we discovered that m6A modifications are increased in hepatoblastoma, and METTL3 is the main factor involved with aberrant m6A modification. We also profiled m6A across the whole transcriptome in hepatoblastoma tumor tissues and normal tissues. Our findings suggest that m6A is highly expressed in hepatoblastoma tumors. Also, m6A is enriched not only around the stop codon, but also around the coding sequence (CDS) region. Gene ontology analysis indicates that m6A mRNA methylation contributes significantly to regulate the Wnt/β-catenin pathway. Reduced m6A methylation can lead to a decrease in expression and stability of the CTNNB1. Conclusion Overall our findings suggest enhanced m6A mRNA methylation as an oncogenic mechanism in hepatoblastoma, METTL3 is significantly up-regulated in HB and promotes HB development. And identify CTNNB1 as a regulator of METTL3 guided m6A modification in HB.
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Affiliation(s)
- Li Liu
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of medicine, Shanghai Jiaotong University, Shanghai, 200127, China.,Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Jing Wang
- Department of Clinical Laboratory, Shanghai Fourth People's Hospital affiliated to Tongji University School of Medicine, Shanghai, 200081, China
| | - Guifeng Sun
- Department of Surgery, Shanghai Children's Medical Center, School of medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Qiong Wu
- School of Pharmacy, Guangdong Pharmaceutical University, Gaungzhou, 510006, China
| | - Ji Ma
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Xin Zhang
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Nan Huang
- Department of Surgery, Shanghai Children's Medical Center, School of medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Zhixuan Bian
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Song Gu
- Department of Clinical Laboratory, Shanghai Fourth People's Hospital affiliated to Tongji University School of Medicine, Shanghai, 200081, China
| | - Min Xu
- Department of Clinical Laboratory, Shanghai Fourth People's Hospital affiliated to Tongji University School of Medicine, Shanghai, 200081, China
| | - Minzhi Yin
- Department of Pathology, Shanghai Children's Medical Center, School of medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Fenyong Sun
- Department of Surgery, Shanghai Children's Medical Center, School of medicine, Shanghai Jiaotong University, Shanghai, 200127, China.
| | - Qiuhui Pan
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of medicine, Shanghai Jiaotong University, Shanghai, 200127, China.
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904
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microRNA: The Impact on Cancer Stemness and Therapeutic Resistance. Cells 2019; 9:cells9010008. [PMID: 31861404 PMCID: PMC7016867 DOI: 10.3390/cells9010008] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/12/2019] [Accepted: 12/16/2019] [Indexed: 12/24/2022] Open
Abstract
Cancer ranks as the second leading cause of death worldwide, causing a large social and economic burden. However, most anti-cancer treatments face the problems of tumor recurrence and metastasis. Therefore, finding an effective cure for cancer needs to be solved urgently. Recently, the discovery of cancer stem cells (CSCs) provides a new orientation for cancer research and therapy. CSCs share main characteristics with stem cells and are able to generate an entire tumor. Besides, CSCs usually escape from current anti-cancer therapies, which is partly responsible for tumor recurrence and poor prognosis. microRNAs (miRNAs) belong to small noncoding RNA and regulate gene post-transcriptional expression. The dysregulation of miRNAs leads to plenty of diseases, including cancer. The aberrant miRNA expression in CSCs enhances stemness maintenance. In this review, we summarize the role of miRNAs on CSCs in the eight most common cancers, hoping to bridge the research of miRNAs and CSCs with clinical applications. We found that miRNAs can act as tumor promoter or suppressor. The dysregulation of miRNAs enhances cell stemness and contributes to tumor metastasis and therapeutic resistance via the formation of feedback loops and constitutive activation of carcinogenic signaling pathways. More importantly, some miRNAs may be potential targets for diagnosis, prognosis, and cancer treatments.
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905
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Berulava T, Buchholz E, Elerdashvili V, Pena T, Islam MR, Lbik D, Mohamed BA, Renner A, von Lewinski D, Sacherer M, Bohnsack KE, Bohnsack MT, Jain G, Capece V, Cleve N, Burkhardt S, Hasenfuss G, Fischer A, Toischer K. Changes in m6A RNA methylation contribute to heart failure progression by modulating translation. Eur J Heart Fail 2019; 22:54-66. [PMID: 31849158 DOI: 10.1002/ejhf.1672] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/15/2019] [Accepted: 10/15/2019] [Indexed: 12/27/2022] Open
Abstract
AIMS Deregulation of epigenetic processes and aberrant gene expression are important mechanisms in heart failure. Here we studied the potential relevance of m6A RNA methylation in heart failure development. METHODS AND RESULTS We analysed m6A RNA methylation via next-generation sequencing. We found that approximately one quarter of the transcripts in the healthy mouse and human heart exhibit m6A RNA methylation. During progression to heart failure we observed that changes in m6A RNA methylation exceed changes in gene expression both in mouse and human. RNAs with altered m6A RNA methylation were mainly linked to metabolic and regulatory pathways, while changes in RNA expression level mainly represented changes in structural plasticity. Mechanistically, we could link m6A RNA methylation to altered RNA translation and protein production. Interestingly, differentially methylated but not differentially expressed RNAs showed differential polysomal occupancy, indicating transcription-independent modulation of translation. Furthermore, mice with a cardiomyocyte restricted knockout of the RNA demethylase Fto exhibited an impaired cardiac function compared to control mice. CONCLUSIONS We could show that m6A landscape is altered in heart hypertrophy and heart failure. m6A RNA methylation changes lead to changes in protein abundance, unconnected to mRNA levels. This uncovers a new transcription-independent mechanisms of translation regulation. Therefore, our data suggest that modulation of epitranscriptomic processes such as m6A methylation might be an interesting target for therapeutic interventions.
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Affiliation(s)
- Tea Berulava
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Eric Buchholz
- Clinic for Cardiology and Pneumology, University Medical Center, Göttingen, Germany.,German Centre for Cardiovascular Research (DZHK), partner site Göttingen, Göttingen, Germany
| | - Vakhtang Elerdashvili
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany.,Bioinformatics Unit, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Tonatiuh Pena
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany.,Bioinformatics Unit, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Md Rezaul Islam
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Dawid Lbik
- Clinic for Cardiology and Pneumology, University Medical Center, Göttingen, Germany.,German Centre for Cardiovascular Research (DZHK), partner site Göttingen, Göttingen, Germany
| | - Belal A Mohamed
- Clinic for Cardiology and Pneumology, University Medical Center, Göttingen, Germany.,German Centre for Cardiovascular Research (DZHK), partner site Göttingen, Göttingen, Germany
| | - Andre Renner
- Clinic for Thoracic and Cardiovascular Surgery, Heart and Diabetes Centre NRW, Ruhr-University Bochum, Bochum, Germany
| | | | - Michael Sacherer
- Department of Cardiology, Medical University Graz, Graz, Austria
| | | | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center, Göttingen, Germany
| | - Gaurav Jain
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany.,Bioinformatics Unit, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Vincenzo Capece
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Nicole Cleve
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Susanne Burkhardt
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Gerd Hasenfuss
- Clinic for Cardiology and Pneumology, University Medical Center, Göttingen, Germany.,German Centre for Cardiovascular Research (DZHK), partner site Göttingen, Göttingen, Germany
| | - Andre Fischer
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany.,Department of Psychiatry and Psychotherapy, University Medical Center, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
| | - Karl Toischer
- Clinic for Cardiology and Pneumology, University Medical Center, Göttingen, Germany.,German Centre for Cardiovascular Research (DZHK), partner site Göttingen, Göttingen, Germany
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906
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An epitranscriptomic mechanism underlies selective mRNA translation remodelling in melanoma persister cells. Nat Commun 2019; 10:5713. [PMID: 31844050 PMCID: PMC6915789 DOI: 10.1038/s41467-019-13360-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 11/04/2019] [Indexed: 01/20/2023] Open
Abstract
Cancer persister cells tolerate anticancer drugs and serve as the founders of acquired resistance and cancer relapse. Here we show that a subpopulation of BRAFV600 mutant melanoma cells that tolerates exposure to BRAF and MEK inhibitors undergoes a reversible remodelling of mRNA translation that evolves in parallel with drug sensitivity. Although this process is associated with a global reduction in protein synthesis, a subset of mRNAs undergoes an increased efficiency in translation. Inhibiting the eIF4A RNA helicase, a component of the eIF4F translation initiation complex, abrogates this selectively increased translation and is lethal to persister cells. Translation remodelling in persister cells coincides with an increased N6-methyladenosine modification in the 5′-untranslated region of some highly translated mRNAs. Combination of eIF4A inhibitor with BRAF and MEK inhibitors effectively inhibits the emergence of persister cells and may represent a new therapeutic strategy to prevent acquired drug resistance. Melanoma persister cells are tolerant to anti-BRAF and anti-MEK inhibition and can trigger cancer relapse. Here the authors show that a subset of N6-methyladenosine modified mRNAs is translationally activated in persister cells. This preferential translation can be abrogated via eIF4A inhibition.
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907
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Yang X, Liu QL, Xu W, Zhang YC, Yang Y, Ju LF, Chen J, Chen YS, Li K, Ren J, Sun Q, Yang YG. m 6A promotes R-loop formation to facilitate transcription termination. Cell Res 2019; 29:1035-1038. [PMID: 31606733 PMCID: PMC6951339 DOI: 10.1038/s41422-019-0235-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 09/05/2019] [Indexed: 12/21/2022] Open
Affiliation(s)
- Xin Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, School of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qian-Lan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, School of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Xu
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yi-Chang Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, School of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, School 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
| | - Lin-Fang Ju
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, School of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, School 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, School of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kuan Li
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jie Ren
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, School 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.
| | - Qianwen Sun
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, School 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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908
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Blatt P, Martin ET, Breznak SM, Rangan P. Post-transcriptional gene regulation regulates germline stem cell to oocyte transition during Drosophila oogenesis. Curr Top Dev Biol 2019; 140:3-34. [PMID: 32591078 DOI: 10.1016/bs.ctdb.2019.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
During oogenesis, several developmental processes must be traversed to ensure effective completion of gametogenesis including, stem cell maintenance and asymmetric division, differentiation, mitosis and meiosis, and production of maternally contributed mRNAs, making the germline a salient model for understanding how cell fate transitions are mediated. Due to silencing of the genome during meiotic divisions, there is little instructive transcription, barring a few examples, to mediate these critical transitions. In Drosophila, several layers of post-transcriptional regulation ensure that the mRNAs required for these processes are expressed in a timely manner and as needed during germline differentiation. These layers of regulation include alternative splicing, RNA modification, ribosome production, and translational repression. Many of the molecules and pathways involved in these regulatory activities are conserved from Drosophila to humans making the Drosophila germline an elegant model for studying the role of post-transcriptional regulation during stem cell differentiation and meiosis.
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Affiliation(s)
- Patrick Blatt
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY, United States; University at Albany SUNY, Albany, NY, United States
| | - Elliot T Martin
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY, United States; University at Albany SUNY, Albany, NY, United States
| | - Shane M Breznak
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY, United States; University at Albany SUNY, Albany, NY, United States
| | - Prashanth Rangan
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY, United States; University at Albany SUNY, Albany, NY, United States.
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909
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Taniguchi K, Kawai T, Kitawaki J, Tomikawa J, Nakabayashi K, Okamura K, Sago H, Hata K. Epitranscriptomic profiling in human placenta: N6-methyladenosine modification at the 5'-untranslated region is related to fetal growth and preeclampsia. FASEB J 2019; 34:494-512. [PMID: 31914637 PMCID: PMC7027905 DOI: 10.1096/fj.201900619rr] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 09/29/2019] [Accepted: 10/08/2019] [Indexed: 01/27/2023]
Abstract
Intracellular mRNA levels are not always proportional to their respective protein levels, especially in the placenta. This discrepancy may be attributed to various factors including post‐transcriptional regulation, such as mRNA methylation (N6‐methyladenosine: m6A). Here, we conducted a comprehensive m6A analysis of human placental tissue from neonates with various birth weights to clarify the involvement of m6A in placental biology. The augmented m6A levels at the 5′‐untranslated region (UTR) in mRNAs of small‐for‐date placenta samples were dominant compared to reduction of m6A levels, whereas a decrease in m6A in the vicinity of stop codons was common in heavy‐for‐date placenta samples. Notably, most of these genes showed similar expression levels between the different birth weight categories. In particular, preeclampsia placenta samples showed consistently upregulated SMPD1 protein levels and increased m6A at 5′‐UTR but did not show increased mRNA levels. Mutagenesis of adenosines at 5′‐UTR of SMPD1 mRNAs actually decreased protein levels in luciferase assay. Collectively, our findings suggest that m6A both at the 5′‐UTR and in the vicinity of stop codon in placental mRNA may play important roles in fetal growth and disease.
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Affiliation(s)
- Kosuke Taniguchi
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Jo Kitawaki
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Junko Tomikawa
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kohji Okamura
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Haruhiko Sago
- Center for Maternal-Fetal, Neonatal and Reproductive Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
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910
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Jia R, Chai P, Wang S, Sun B, Xu Y, Yang Y, Ge S, Jia R, Yang YG, Fan X. m 6A modification suppresses ocular melanoma through modulating HINT2 mRNA translation. Mol Cancer 2019; 18:161. [PMID: 31722709 PMCID: PMC6854757 DOI: 10.1186/s12943-019-1088-x] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/14/2019] [Indexed: 12/18/2022] Open
Abstract
Background Dynamic N6-methyladenosine (m6A) RNA modification generated and erased by N6-methyltransferases and demethylases regulates gene expression, alternative splicing and cell fate. Ocular melanoma, comprising uveal melanoma (UM) and conjunctival melanoma (CM), is the most common primary eye tumor in adults and the 2nd most common melanoma. However, the functional role of m6A modification in ocular melanoma remains unclear. Methods m6A assays and survival analysis were used to explore decreased global m6A levels, indicating a late stage of ocular melanoma and a poor prognosis. Multiomic analysis of miCLIP-seq, RNA-seq and Label-free MS data revealed that m6A RNA modification posttranscriptionally promoted HINT2 expression. RNA immunoprecipitation (RIP)-qPCR and dual luciferase assays revealed that HINT2 mRNA specifically interacted with YTHDF1. Furthermore, polysome profiling analysis indicated a greater amount of HINT2 mRNA in the translation pool in ocular melanoma cells with higher m6A methylation. Results Here, we show that RNA methylation significantly inhibits the progression of UM and CM. Ocular melanoma samples showed decreased m6A levels, indicating a poor prognosis. Changes in global m6A modification were highly associated with tumor progression in vitro and in vivo. Mechanistically, YTHDF1 promoted the translation of methylated HINT2 mRNA, a tumor suppressor in ocular melanoma. Conclusions Our work uncovers a critical function for m6A methylation in ocular melanoma and provides additional insight into the understanding of m6A modification.
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Affiliation(s)
- Ruobing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, People's Republic of China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, People's Republic of China
| | - Peiwei Chai
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, People's Republic of China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, People's Republic of China
| | - Shanzheng Wang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baofa Sun
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yangfan Xu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, People's Republic of China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, People's Republic of China
| | - Ying Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, People's Republic of China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, People's Republic of China
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, People's Republic of China. .,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, People's Republic of China.
| | - Yun-Gui Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. .,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049, China. .,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, People's Republic of China. .,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, People's Republic of China.
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911
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Rockwell AL, Hongay CF. The m 6A Dynamics of Profilin in Neurogenesis. Front Genet 2019; 10:987. [PMID: 31798620 PMCID: PMC6862867 DOI: 10.3389/fgene.2019.00987] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/17/2019] [Indexed: 01/22/2023] Open
Abstract
Our understanding of the biological role of N6-methyladenosine (m6A), a ubiquitous non-editing RNA modification, has increased greatly since 2011. More recently, work from several labs revealed that m6A methylation regulates several aspects of mRNA metabolism. The “writer” protein METTL3, known as MT-A70 in humans, DmIme4 in flies, and MTA in plants, has the catalytic site of the METTL3/14/16 subunit of the methyltransferase complex that includes many other proteins. METTL3 is evolutionarily conserved and essential for development in multicellular organisms. However, until recently, no study has been able to provide a mechanism that explains the essentiality of METTL3. The addition of m6A to gene transcripts has been compared with the epigenetic code of histone modifications because of its effects on gene expression and its reversibility, giving birth to the field of epitranscriptomics, the study of the biological role of this and similar RNA modifications. Here, we focus on METTL3 and its likely conserved role in profilin regulation in neurogenesis. However, this and many other subunits of the methyltransferase complex are starting to be identified in several developmental processes and diseases. A recent plethora of studies about the biological role of METTL3 and other components of the methyltransferase complex that erase (FTO) or recognize (YTH proteins) this modification on transcripts revealed that this RNA modification plays a variety of roles in many biological processes like neurogenesis. Our work in Drosophila shows that the ancient and evolutionarily conserved gene profilin (chic in Drosophila) is a target of the m6A writer. Here, we discuss the implications of our study in Drosophila and how it unveils a conserved mechanism in support of the essential function of METTL3 in metazoan development. Profilin (chic) is an essential gene of ancient evolutionary origins, present in sponges (Porifera), the oldest still extant metazoan phylum of the common metazoan ancestor Urmetazoa. We propose that the relationship between profilin and METTL3 is conserved in metazoans and it provides insights into possible regulatory roles of m6A modification of profilin transcripts in processes such as neurogenesis.
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Affiliation(s)
| | - Cintia F Hongay
- Department of Biology, Clarkson University, Potsdam, NY, United States
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912
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Casella G, Tsitsipatis D, Abdelmohsen K, Gorospe M. mRNA methylation in cell senescence. WILEY INTERDISCIPLINARY REVIEWS. RNA 2019; 10:e1547. [PMID: 31144457 PMCID: PMC8474013 DOI: 10.1002/wrna.1547] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/23/2019] [Accepted: 05/01/2019] [Indexed: 01/06/2023]
Abstract
Cellular senescence, a developmental program central to normal aging and aging pathologies, is robustly regulated at the post-transcriptional level. This regulation involves the interaction of RNA-binding proteins and noncoding RNAs with senescence-associated messenger RNAs (mRNAs). There is increasing evidence that these associations are modulated by chemical modifications of specific mRNA nucleotides which can enhance or reduce the binding of regulatory factors. Recent technological advances in mass spectrometry, next-generation sequencing, and genome mapping have improved markedly the detection of mRNA modifications. Given the rising interest in the epitranscriptomic control of gene expression in aging, we discuss our incipient understanding of the chemical mRNA modifications, specifically m6 A and m5 C, that influence cellular senescence. This article is categorized under: RNA Export and Localization > RNA Localization RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Gabriel Casella
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Dimitrios Tsitsipatis
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
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913
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Liu J, Li K, Cai J, Zhang M, Zhang X, Xiong X, Meng H, Xu X, Huang Z, Peng J, Fan J, Yi C. Landscape and Regulation of m 6A and m 6Am Methylome across Human and Mouse Tissues. Mol Cell 2019; 77:426-440.e6. [PMID: 31676230 DOI: 10.1016/j.molcel.2019.09.032] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 09/09/2019] [Accepted: 09/26/2019] [Indexed: 01/01/2023]
Abstract
N6-methyladenosine (m6A), the most abundant internal mRNA modification, and N6,2'-O-dimethyladenosine (m6Am), found at the first-transcribed nucleotide, are two reversible epitranscriptomic marks. However, the profiles and distribution patterns of m6A and m6Am across human and mouse tissues are poorly characterized. Here, we report the m6A and m6Am methylome through profiling of 43 human and 16 mouse tissues and demonstrate strongest tissue specificity for the brain tissues. A small subset of tissue-specific m6A peaks can also readily classify tissue types. The overall m6A and m6Am level is partially correlated with the expression level of their writers and erasers. Additionally, the m6A-containing regions are enriched for SNPs. Furthermore, cross-species analysis revealed that species rather than tissue type is the primary determinant of methylation. Collectively, our study provides an in-depth resource for dissecting the landscape and regulation of the m6A and m6Am epitranscriptomic marks across mammalian tissues.
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Affiliation(s)
- Jun'e Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Kai Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jiabin Cai
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai 200032, China; Human Phenome Institute, Fudan University, Shanghai 200032, China
| | - Mingchang Zhang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xiaoting Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xushen Xiong
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Haowei Meng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xizhan Xu
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhibin Huang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai 200032, China; Human Phenome Institute, Fudan University, Shanghai 200032, China.
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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914
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Shi Y, Fan S, Wu M, Zuo Z, Li X, Jiang L, Shen Q, Xu P, Zeng L, Zhou Y, Huang Y, Yang Z, Zhou J, Gao J, Zhou H, Xu S, Ji H, Shi P, Wu DD, Yang C, Chen Y. YTHDF1 links hypoxia adaptation and non-small cell lung cancer progression. Nat Commun 2019; 10:4892. [PMID: 31653849 PMCID: PMC6814821 DOI: 10.1038/s41467-019-12801-6] [Citation(s) in RCA: 241] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 09/29/2019] [Indexed: 12/12/2022] Open
Abstract
Hypoxia occurs naturally at high-altitudes and pathologically in hypoxic solid tumors. Here, we report that genes involved in various human cancers evolved rapidly in Tibetans and six Tibetan domestic mammals compared to reciprocal lowlanders. Furthermore, m6A modified mRNA binding protein YTHDF1, one of evolutionary positively selected genes for high-altitude adaptation is amplified in various cancers, including non-small cell lung cancer (NSCLC). We show that YTHDF1 deficiency inhibits NSCLC cell proliferation and xenograft tumor formation through regulating the translational efficiency of CDK2, CDK4, and cyclin D1, and that YTHDF1 depletion restrains de novo lung adenocarcinomas (ADC) progression. However, we observe that YTHDF1 high expression correlates with better clinical outcome, with its depletion rendering cancerous cells resistant to cisplatin (DDP) treatment. Mechanistic studies identified the Keap1-Nrf2-AKR1C1 axis as the downstream mediator of YTHDF1. Together, these findings highlight the critical role of YTHDF1 in both hypoxia adaptation and pathogenesis of NSCLC.
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Affiliation(s)
- Yulin Shi
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Songqing Fan
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, 410000, China
| | - Mengge Wu
- Kunming Medical University, Kunming, 650223, China
| | - Zhixiang Zuo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, China
| | - Xingyang Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, China
| | - Liping Jiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China
| | - Qiushuo Shen
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Peifang Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China
| | - Lin Zeng
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | | | | | | | - Jumin Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China
| | - Jing Gao
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Shuhua Xu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Hongbin Ji
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Peng Shi
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Dong-Dong Wu
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Cuiping Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China.
| | - Yongbin Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
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915
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Yang Q, Zhao J, Zhang W, Chen D, Wang Y. Aberrant alternative splicing in breast cancer. J Mol Cell Biol 2019; 11:920-929. [PMID: 31065692 PMCID: PMC6884705 DOI: 10.1093/jmcb/mjz033] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 02/19/2019] [Accepted: 03/03/2019] [Indexed: 12/11/2022] Open
Abstract
Alternative splicing is critical for human gene expression regulation, which plays a determined role in expanding the diversity of functional proteins. Importantly, alternative splicing is a hallmark of cancer and a potential target for cancer therapeutics. Based on the statistical data, breast cancer is one of the top leading causes of cancer-related deaths in women worldwide. Strikingly, alternative splicing is closely associated with breast cancer development. Here, we seek to provide a general review of the relationship between alternative splicing and breast cancer. We introduce the process of alternative splicing and its regulatory role in cancers. In addition, we highlight the functions of aberrant alternative splicing and mutations of splicing factors in breast cancer progression. Moreover, we discuss the role of alternative splicing in cancer drug resistance and the potential of being targets for cancer therapeutics.
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Affiliation(s)
- Quan Yang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Jinyao Zhao
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Wenjing Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Dan Chen
- Department of Pathology, First Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Yang Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
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916
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METTL3 Attenuates LPS-Induced Inflammatory Response in Macrophages via NF- κB Signaling Pathway. Mediators Inflamm 2019; 2019:3120391. [PMID: 31772500 PMCID: PMC6854952 DOI: 10.1155/2019/3120391] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/05/2019] [Indexed: 12/20/2022] Open
Abstract
Methyltransferase-like 3 (METTL3), an RNA N6-methyladenosine (m6A) methyltransferase, is essential for the m6A mRNA modification. As a key enzyme of m6A methylation modification, METTL3 has been implicated in immune and inflammation regulation. However, little is known of the role and underlying mechanism of METTL3 in rheumatoid arthritis (RA). The aim of the present study is to elucidate the function and potential mechanism of METTL3 in RA pathogenesis. We used quantitative real-time polymerase chain reaction to detect the expression of METTL3 in RA patients and controls as well as the macrophage cell line. CCK-8 was used for cell proliferation assay. Enzyme-linked immunosorbent assay (ELISA) was adopted to estimate the generation of IL-6 and TNF-α in macrophages. Western blot and immunofluorescence were applied to evaluate the activation of NF-κB in macrophages. The expression of METTL3 was significantly elevated in patients with RA. It was positively associated with CRP and ESR, two common markers for RA disease activity. Besides, LPS could enhance the expression and biological activity of METTL3 in macrophages, while overexpression of METTL3 significantly attenuated the inflammatory response induced by LPS in macrophages. Moreover, the effect of METTL3 on LPS-induced inflammation in macrophages was dependent on NF-κB. This study firstly demonstrates the critical role of METTL3 in RA, which provides novel insights into recognizing the pathogenesis of RA and a promising biomarker for RA.
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917
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Su Y, Huang J, Hu J. m 6A RNA Methylation Regulators Contribute to Malignant Progression and Have Clinical Prognostic Impact in Gastric Cancer. Front Oncol 2019; 9:1038. [PMID: 31681576 PMCID: PMC6813557 DOI: 10.3389/fonc.2019.01038] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/24/2019] [Indexed: 12/11/2022] Open
Abstract
N6-methyladenosine (m6A) is the most common form of mRNA modification, and is dynamically regulated by the m6A RNA methylation regulators. However, little is known about m6A in gastric cancer. The aim of this work is to investigate the effects of m6A RNA methylation regulators in gastric cancer. Here, we found that most of the 13 main m6A RNA methylation regulators are higher expressed in 375 patients with gastric cancer. We identified two subgroups of gastric cancer (cluster1 and 2) by applying consensus clustering to m6A RNA methylation regulators. Compared with the cluster1 subgroup, the cluster2 subgroup correlates with a poorer prognosis, and most of the 13 main m6A RNA methylation regulators are higher expressed in cluster2. Moreover, the cancer-specific pathways are also significantly enriched in the cluster2 subgroup. This finding indicates that m6A RNA methylation regulators are closely associated with gastric cancer. Based on this finding, we derived a risk signature, using 3 m6A RNA methylation regulators (FTO, RBM15, ALKBH5), that is not only an independent prognostic marker but can also predict the clinicopathological features of gastric cancer. Moreover, FTO is higher expressed in high risk scores subtype in gastric cancer. Thus, this first finding provide us clues to understand epigenetic modification of RNA in gastric cancer.
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Affiliation(s)
- Yunshu Su
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jinqi Huang
- Division of Cardiothoracic Surgery, Central Hospital of EnShi Tujia and Miao Autonomous Prefecture, EnShi Clinical College of Wuhan University, EnShi, China
| | - Jichang Hu
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
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918
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Kong W, Rivera-Serrano EE, Neidleman JA, Zhu J. HIV-1 Replication Benefits from the RNA Epitranscriptomic Code. J Mol Biol 2019; 431:5032-5038. [PMID: 31626810 DOI: 10.1016/j.jmb.2019.09.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/22/2019] [Accepted: 09/27/2019] [Indexed: 12/27/2022]
Abstract
The effects of RNA methylation on HIV-1 replication remain largely unknown. Recent studies have discovered new insights into the effect of 2'-O-methylation and 5-methylcytidine marks on the HIV-1 RNA genome. As so far, HIV-1 benefits from diverse RNA methylations through distinct mechanisms. In this review, we summarize the recent advances in this emerging field and discuss the role of RNA methylation writers and readers in HIV-1 infection, which may help to find alternative strategies to control HIV-1 infection.
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Affiliation(s)
- Weili Kong
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA; Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA, 94158, USA.
| | - Efraín E Rivera-Serrano
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, 95616, USA
| | - Jason A Neidleman
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA, 94158, USA
| | - Jian Zhu
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA.
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919
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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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920
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Matsuzawa S, Wakata Y, Ebi F, Isobe M, Kurosawa N. Development and validation of monoclonal antibodies against N6-methyladenosine for the detection of RNA modifications. PLoS One 2019; 14:e0223197. [PMID: 31577817 PMCID: PMC6774519 DOI: 10.1371/journal.pone.0223197] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/16/2019] [Indexed: 12/21/2022] Open
Abstract
RNA contains various chemical modifications, among which N6-methyladenosine (m6A) is the most prevalent modified nucleotide in eukaryotic mRNA. Emerging evidence suggests that m6A plays an important role in regulating a variety of cellular functions by controlling mRNA processing, translation and degradation. Because m6A is not detectable by standard chemical modification-based approaches, immunological methods, such as ELISA, immunoblotting, immunohistochemistry, m6A RNA immunoprecipitation sequencing and m6A individual-nucleotide resolution cross-linking and immunoprecipitation, have been employed to detect m6A in RNA. Although the most important factor determining the success of these methods is the integrity of highly specific antibodies against m6A, the development of m6A-specific monoclonal antibodies has been challenging. We developed anti-m6A monoclonal antibodies using our recently developed single cell-based monoclonal antibody production system. The binding of one selected antibody, #B1-3, to RNA oligoribonucleotide containing a single m6A had an equilibrium dissociation constant of 6.5 nM, and this antibody exhibited negligible binding to oligoribonucleotides containing a single N1-methyladenosine and unmodified adenosine. The binding was competed by the addition of increasing concentrations of N6-methyl-ATP but not N1-methyl-ATP or ATP. Furthermore, this mAb specifically crosslinked m6A-containing oligoribonucleotide by ultraviolet light, resulting in the induction of cDNA truncation at m6A position. These results show the feasibility of using the validated m6A monoclonal antibody for the specific detection of m6A in RNA.
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Affiliation(s)
- Shun Matsuzawa
- Graduate School of Innovative Life Science, University of Toyama, Toyama-shi, Toyama, Japan
- Medical & Biological Laboratories Co., Ltd., Akaho, Komagane, Nagano, Japan
| | - Yuka Wakata
- Graduate School of Innovative Life Science, University of Toyama, Toyama-shi, Toyama, Japan
| | - Fumiya Ebi
- Graduate School of Science and Engineering for Education, University of Toyama, Gofuku, Toyama-shi, Toyama, Japan
| | - Masaharu Isobe
- Laboratory of Molecular and Cellular Biology, Faculty of Science and Engineering, Graduate School, University of Toyama, Gofuku, Toyama-shi, Toyama, Japan
| | - Nobuyuki Kurosawa
- Laboratory of Molecular and Cellular Biology, Faculty of Science and Engineering, Graduate School, University of Toyama, Gofuku, Toyama-shi, Toyama, Japan
- * E-mail:
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921
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Zhao X, Cui L. Development and validation of a m 6A RNA methylation regulators-based signature for predicting the prognosis of head and neck squamous cell carcinoma. Am J Cancer Res 2019; 9:2156-2169. [PMID: 31720080 PMCID: PMC6834477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 09/25/2019] [Indexed: 06/10/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is among the most common types of cancers that threat the public health worldwide. A growing body of evidence has demonstrated that m6A RNA methylation plays a critical role in tumorigenesis. However, the association between m6A RNA methylation regulators and prognosis of HNSCC remains poorly known. This study aimed to construct a m6A RNA methylation regulators-based biomarker signature that efficiently predicted the prognosis of HNSCC. The gene expression profile of m6A RNA methylation regulators and the corresponding clinical information were downloaded from The Cancer Genome Atlas (TCGA) HNSCC dataset. The differentially expressed m6A RNA methylation regulators between tumor samples and normal control samples, as well as the interaction and correlation of m6A RNA methylation regulators were evaluated. Consensus clustering analysis was performed to identify the clusters of HNSCC with different clinical outcome. Then a prognostic signature was built on TCGA HNSCC cohort and further validated in an external independent cohort. The expression levels of METTL3, YTHDF1, KIAA1429, ALKBH5, YTHDF2, METTL14, FTO, WTAP, RBM15 and HNRNPC were significantly upregulated in tumor samples, while YTHDC2 was remarkably downregulated in the cancer specimens. WTAP and METTL14 might be the hub genes of the interaction network among m6A RNA methylation regulators. Two clusters of HNSCC cases were identified and significant differences were found with respect to overall survival (OS) and tumor grade between the two subgroups of patients. A two-gene prognostic signature including YTHDC2 and HNRNPC was constructed and could predict OS in HNSCC patients from TCGA dataset. In addition, the prognostic signature-based risk score was identified as an independent prognostic indicator for HNSCC. More importantly, these findings were successfully validated in an external independent HNSCC cohort. In conclusion, our study has built up a robust m6A RNA methylation regulators-based molecular signature that predicts the prognosis of patients with HNSCC with high accuracy, which might provide important guidance for therapeutic strategies.
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Affiliation(s)
- Xinyuan Zhao
- Stomatological Hospital, Southern Medical UniversityGuangzhou 510280, China
| | - Li Cui
- UCLA School of DentistryLos Angeles, CA 90095, USA
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922
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Li Y, Xiao J, Bai J, Tian Y, Qu Y, Chen X, Wang Q, Li X, Zhang Y, Xu J. Molecular characterization and clinical relevance of m 6A regulators across 33 cancer types. Mol Cancer 2019; 18:137. [PMID: 31521193 PMCID: PMC6744659 DOI: 10.1186/s12943-019-1066-3] [Citation(s) in RCA: 264] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/02/2019] [Indexed: 12/13/2022] Open
Abstract
The methylation of N6 adenosine (m6A) plays a critical role in diverse biological processes. However, knowledge regarding the reconstitution of m6A across cancer types is still lacking. Here, we systematically analyzed the molecular alterations and clinical relevance of m6A regulators across > 10,000 subjects representing 33 cancer types. We found that there are widespread genetic alterations to m6A regulators, and that their expression levels are significantly correlated with the activity of cancer hallmark-related pathways. Moreover, m6A regulators were found to be potentially useful for prognostic stratification, and we identified IGF2BP3 as a potential oncogene across multiple cancer types. Our results provide a valuable resource that will guide both mechanistic and therapeutic analyses of the role of m6A regulators in cancer.
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Affiliation(s)
- Yongsheng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China. .,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China.
| | - Jun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Jing Bai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yi Tian
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yinwei Qu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xiang Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Qi Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xinhui Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China. .,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China.
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China. .,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China.
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923
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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: 67] [Impact Index Per Article: 13.4] [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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924
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Wu B, Zhang D, Nie H, Shen S, Li Y, Li S. Structure of Arabidopsis thaliana N6-methyl-AMP deaminase ADAL with bound GMP and IMP and implications for N6-methyl-AMP recognition and processing. RNA Biol 2019; 16:1504-1512. [PMID: 31318636 DOI: 10.1080/15476286.2019.1642712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Arabidopsis thaliana aminohydrolase (AtADAL) has been shown to be involved in the metabolism of N6-methyl-AMP, a proposed intermediate during m6A-modified RNA metabolism, which can be subsequently incorporated into newly synthesized RNA by Pol II. It has been proposed that AtADAL will prevent N6-methyl-AMP reuse and catabolize it to inosine monophosphate (IMP). Here, we have solved the crystal structures of AtADAL in the apo form and in complex with GMP and IMP in the presence of Zn2+. We have identified the substrate-binding pocket of AtADAL and compared it with that for adenosine deaminase (ADA), adenine deaminase (ADE) and AMP deaminase (AMPD) from multiple species. The comparisons reveal that plant ADAL1 may have the potential ability to catalyze different alkyl-group substituted substrates.
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Affiliation(s)
- Baixing Wu
- Department of Biology, Southern University of Science and Technology , Shenzhen , Guangdong , China
| | - Dong Zhang
- Department of Biology, Southern University of Science and Technology , Shenzhen , Guangdong , China
| | - Hongbo Nie
- Department of Biology, Southern University of Science and Technology , Shenzhen , Guangdong , China
| | - Senlin Shen
- Department of Biology, Southern University of Science and Technology , Shenzhen , Guangdong , China
| | - Yan Li
- Department of Biology, Southern University of Science and Technology , Shenzhen , Guangdong , China
| | - Sisi Li
- Department of Biology, Southern University of Science and Technology , Shenzhen , Guangdong , China
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925
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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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926
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Sendinc E, Valle-Garcia D, Dhall A, Chen H, Henriques T, Navarrete-Perea J, Sheng W, Gygi SP, Adelman K, Shi Y. PCIF1 Catalyzes m6Am mRNA Methylation to Regulate Gene Expression. Mol Cell 2019; 75:620-630.e9. [PMID: 31279659 DOI: 10.1016/j.molcel.2019.05.030] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/25/2019] [Accepted: 05/21/2019] [Indexed: 10/26/2022]
Abstract
mRNA modifications play important roles in regulating gene expression. One of the most abundant mRNA modifications is N6,2-O-dimethyladenosine (m6Am). Here, we demonstrate that m6Am is an evolutionarily conserved mRNA modification mediated by the Phosphorylated CTD Interacting Factor 1 (PCIF1), which catalyzes m6A methylation on 2-O-methylated adenine located at the 5' ends of mRNAs. Furthermore, PCIF1 catalyzes only 5' m6Am methylation of capped mRNAs but not internal m6A methylation in vitro and in vivo. To study the biological role of m6Am, we developed a robust methodology (m6Am-Exo-Seq) to map its transcriptome-wide distribution, which revealed no global crosstalk between m6Am and m6A under assayed conditions, suggesting that m6Am is functionally distinct from m6A. Importantly, we find that m6Am does not alter mRNA transcription or stability but negatively impacts cap-dependent translation of methylated mRNAs. Together, we identify the only human mRNA m6Am methyltransferase and demonstrate a mechanism of gene expression regulation through PCIF1-mediated m6Am mRNA methylation.
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Affiliation(s)
- Erdem Sendinc
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - David Valle-Garcia
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Abhinav Dhall
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hao Chen
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Telmo Henriques
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Wanqiang Sheng
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Yang Shi
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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927
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Liu J, Harada BT, He C. Regulation of Gene Expression by N 6-methyladenosine in Cancer. Trends Cell Biol 2019; 29:487-499. [PMID: 30940398 PMCID: PMC6527461 DOI: 10.1016/j.tcb.2019.02.008] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/23/2022]
Abstract
As the most abundant mRNA modification in eukaryotic cells, N6-methyladenosine (m6A) has recently emerged as an important regulator of gene expression. m6A modification can be deposited by m6A methyltransferases, removed by m6A demethylases, and recognized by different reader proteins. Numerous lines of evidence have shown that m6A methylation plays critical roles regulating gene expression in development and disease. In this review, we summarize the molecular and cellular function of m6A and highlight some key results which demonstrate the role of m6A in various cancers. Finally, we discuss future directions for research into m6A and its effects in cancer and the potential for targeting RNA modification in cancer treatment.
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Affiliation(s)
- Jun Liu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, Chicago, IL 60637, USA
| | - Bryan T Harada
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, Chicago, IL 60637, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, Chicago, IL 60637, USA; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
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928
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Li XC, Jin F, Wang BY, Yin XJ, Hong W, Tian FJ. The m6A demethylase ALKBH5 controls trophoblast invasion at the maternal-fetal interface by regulating the stability of CYR61 mRNA. Am J Cancer Res 2019; 9:3853-3865. [PMID: 31281518 PMCID: PMC6587351 DOI: 10.7150/thno.31868] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/09/2019] [Indexed: 12/02/2022] Open
Abstract
N6-Methyladenosine (m6A) is the most prevalent internal modification in mammalian mRNAs. Although m6A is important in many biological processes, its roles in the placenta are unclear. Methods: Levels of global mRNA m6A methylation and ALKBH5 expression in recurrent miscarriage (RM) patients were determined using quantitative reverse transcription-PCR (qRT-PCR), m6A RNA methylation quantification, and immunohistochemical methods. Using ALKBH5 overexpression and knockdown methods, we determined the role of ALKBH5 in trophoblast invasion at the maternal interface through trophoblasts and an extravillous explant culture experiments. Furthermore, the regulation of CYR61 by ALKBH5 was explored by RNA-sequencing coupled with methylated RNA immunoprecipitation. Results: We found that the level of global mRNA m6A methylation was significantly decreased in placental villous tissue from RM patients, while ALKBH5 expression was specifically unregulated. Furthermore, we demonstrated that ALKBH5 knockdown in human trophoblast promoted trophoblast invasion. Conversely, overexpression of ALKBH5 inhibited cell invasion. ALKBH5 knockdown promoted trophoblast invasion in villous explant culture experiments, while overexpression of ALKBH5 repressed these effects. Furthermore, we clarified that ALKBH5 inhibited trophoblast invasion by regulating CYR61 mRNA stability, and this RNA regulation is m6A dependent. Mechanistic analyses showed that decreased ALKBH5 in trophoblast increased the half-life of CYR61 mRNA and promoted steady-state CYR61 mRNA expression levels. Conclusions: We elucidated the functional roles of ALKBH5 and mRNA m6A methylation in trophoblast and identified a novel RNA regulatory mechanism, providing a basis for further exploration of broad RNA epigenetic regulatory patterns in RM diseases.
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929
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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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930
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Deciphering the Epitranscriptomic Signatures in Cell Fate Determination and Development. Stem Cell Rev Rep 2019; 15:474-496. [DOI: 10.1007/s12015-019-09894-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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931
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Vandevenne M, Delmarcelle M, Galleni M. RNA Regulatory Networks as a Control of Stochasticity in Biological Systems. Front Genet 2019; 10:403. [PMID: 31134128 PMCID: PMC6514243 DOI: 10.3389/fgene.2019.00403] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/12/2019] [Indexed: 01/24/2023] Open
Abstract
The discovery that the non-protein coding part of human genome, dismissed as "junk DNA," is actively transcripted and carries out crucial functions is probably one of the most important discoveries of the past decades. These transcripts are becoming the rising stars of modern biology. In this review, we have casted a new light on RNAs. We have placed these molecules in the context of life origins, evolution with a big emphasize on the "RNA networks" concept. We discuss how this view can help us to understand the global role of RNA networks in modern cells, and can change our perception of the cell biology and therapy. Finally, although high-throughput methods as well as traditional case-to-case studies have laid the groundwork for our current knowledge of transcriptomes, we would like to discuss new strategies that are better suited to uncover and tackle these integrated and complex RNA networks.
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Affiliation(s)
- Marylène Vandevenne
- InBioS - Center for Protein Engineering, University of Liège, Liège, Belgium
| | - Michael Delmarcelle
- InBioS - Center for Protein Engineering, University of Liège, Liège, Belgium
| | - Moreno Galleni
- InBioS - Center for Protein Engineering, University of Liège, Liège, Belgium
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932
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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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933
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Park OH, Ha H, Lee Y, Boo SH, Kwon DH, Song HK, Kim YK. Endoribonucleolytic Cleavage of m6A-Containing RNAs by RNase P/MRP Complex. Mol Cell 2019; 74:494-507.e8. [DOI: 10.1016/j.molcel.2019.02.034] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 01/14/2019] [Accepted: 02/22/2019] [Indexed: 12/21/2022]
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934
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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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935
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Shen L, Liang Z, Wong CE, Yu H. Messenger RNA Modifications in Plants. TRENDS IN PLANT SCIENCE 2019; 24:328-341. [PMID: 30745055 DOI: 10.1016/j.tplants.2019.01.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/16/2019] [Accepted: 01/17/2019] [Indexed: 05/21/2023]
Abstract
Over 160 distinct RNA modifications are known and collectively termed the epitranscriptome. Some of these modifications have been discovered in mRNA, uncovering a new layer of gene regulation. Transcriptome-wide mapping of epitranscriptomic codes and the discovery of their writers, erasers, and readers that dynamically install, remove, and interpret RNA modifications, respectively, are fundamental to understanding the epitranscriptome. Recent technologies have enabled the transcriptome-wide profiling of several mRNA modifications in Arabidopsis thaliana, providing key insights into regulating these modifications and their effects on plant development. Here we review technological innovations and recent progress in epitranscriptomics, with specific focus on N6-methyladenosine (m6A), 5-methylcytosine (m5C), uridylation, and their roles in multiple aspects of plant development.
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Affiliation(s)
- Lisha Shen
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore; These authors contributed equally to this manuscript.
| | - Zhe Liang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore; These authors contributed equally to this manuscript
| | - Chui Eng Wong
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Hao Yu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore.
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936
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Xu S, Kamato D, Little PJ, Nakagawa S, Pelisek J, Jin ZG. Targeting epigenetics and non-coding RNAs in atherosclerosis: from mechanisms to therapeutics. Pharmacol Ther 2019; 196:15-43. [PMID: 30439455 PMCID: PMC6450782 DOI: 10.1016/j.pharmthera.2018.11.003] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Atherosclerosis, the principal cause of cardiovascular death worldwide, is a pathological disease characterized by fibro-proliferation, chronic inflammation, lipid accumulation, and immune disorder in the vessel wall. As the atheromatous plaques develop into advanced stage, the vulnerable plaques are prone to rupture, which causes acute cardiovascular events, including ischemic stroke and myocardial infarction. Emerging evidence has suggested that atherosclerosis is also an epigenetic disease with the interplay of multiple epigenetic mechanisms. The epigenetic basis of atherosclerosis has transformed our knowledge of epigenetics from an important biological phenomenon to a burgeoning field in cardiovascular research. Here, we provide a systematic and up-to-date overview of the current knowledge of three distinct but interrelated epigenetic processes (including DNA methylation, histone methylation/acetylation, and non-coding RNAs), in atherosclerotic plaque development and instability. Mechanistic and conceptual advances in understanding the biological roles of various epigenetic modifiers in regulating gene expression and functions of endothelial cells (vascular homeostasis, leukocyte adhesion, endothelial-mesenchymal transition, angiogenesis, and mechanotransduction), smooth muscle cells (proliferation, migration, inflammation, hypertrophy, and phenotypic switch), and macrophages (differentiation, inflammation, foam cell formation, and polarization) are discussed. The inherently dynamic nature and reversibility of epigenetic regulation, enables the possibility of epigenetic therapy by targeting epigenetic "writers", "readers", and "erasers". Several Food Drug Administration-approved small-molecule epigenetic drugs show promise in pre-clinical studies for the treatment of atherosclerosis. Finally, we discuss potential therapeutic implications and challenges for future research involving cardiovascular epigenetics, with an aim to provide a translational perspective for identifying novel biomarkers of atherosclerosis, and transforming precision cardiovascular research and disease therapy in modern era of epigenetics.
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Affiliation(s)
- Suowen Xu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
| | - Danielle Kamato
- School of Pharmacy, The University of Queensland, Wooloongabba, QLD 4102, Australia; Department of Pharmacy, Xinhua College of Sun Yat-sen University, Guangzhou 510520, China
| | - Peter J Little
- School of Pharmacy, The University of Queensland, Wooloongabba, QLD 4102, Australia; Department of Pharmacy, Xinhua College of Sun Yat-sen University, Guangzhou 510520, China
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Jaroslav Pelisek
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar der Technischen Universitaet Muenchen, Germany
| | - Zheng Gen Jin
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
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937
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Yu R, Li Q, Feng Z, Cai L, Xu Q. m6A Reader YTHDF2 Regulates LPS-Induced Inflammatory Response. Int J Mol Sci 2019; 20:ijms20061323. [PMID: 30875984 PMCID: PMC6470741 DOI: 10.3390/ijms20061323] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 03/06/2019] [Accepted: 03/12/2019] [Indexed: 12/27/2022] Open
Abstract
N6-methyladenosine (m6A) is an abundant mRNA modification that affects multiple biological processes, including those involved in the cell stress response and viral infection. YTH domain family 2 (YTHDF2) is an m6A-binding protein that affects the localization and stability of targeted mRNA. RNA-binding proteins (RBPs) can regulate the stability of inflammatory gene mRNA transcripts, thus participating in the regulation of inflammatory processes. As an RBP, the role of YTHDF2 in the LPS-induced inflammatory reaction has not been reported. To elucidate the function of YTHDF2 in the inflammatory response of macrophages, we first detected the expression level of YTHDF2 in RAW 264.7 cells, and found that it was upregulated after LPS stimulation. YTHDF2 knockdown significantly increased the LPS-induced IL-6, TNF-α, IL-1β, and IL-12 expression and the phosphorylation of p65, p38, and ERK1/2 in NF-κB and MAPK signaling. Moreover, the upregulated expression of TNF-α and IL-6 in cells with silenced YTHDF2 expression was downregulated by the NF-κB, p38, and ERK inhibitors. YTHDF2 depletion increased the expression and stability of MAP2K4 and MAP4K4 mRNAs. All of these results suggest that YTHDF2 knockdown increases mRNA expression levels of MAP2K4 and MAP4K4 via stabilizing the mRNA transcripts, which activate MAPK and NF-κB signaling pathways, which promote the expression of proinflammatory cytokines and aggravate the inflammatory response in LPS-stimulated RAW 264.7 cells.
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Affiliation(s)
- Ruiqing Yu
- Guanghua School of Stomatology & Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510055, China.
| | - Qimeng Li
- Guanghua School of Stomatology & Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510055, China.
| | - Zhihui Feng
- Guanghua School of Stomatology & Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510055, China.
| | - Luhui Cai
- Guanghua School of Stomatology & Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510055, China.
| | - Qiong Xu
- Guanghua School of Stomatology & Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510055, China.
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938
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Yao Y, Bi Z, Wu R, Zhao Y, Liu Y, Liu Q, Wang Y, Wang X. METTL3 inhibits BMSC adipogenic differentiation by targeting the JAK1/STAT5/C/EBPβ pathway via an m 6A-YTHDF2-dependent manner. FASEB J 2019; 33:7529-7544. [PMID: 30865855 DOI: 10.1096/fj.201802644r] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Bone marrow stem cells (BMSCs) are multipotent stem cells that can regenerate mesenchymal tissues, such as adipose tissue, bone, and muscle. Recent studies have shown that N6-methyladenosine (m6A) methylation, one of the most prevalent epigenetic modifications, is involved in the development process. However, whether it plays roles in BMSC differentiation is still elusive. Here, we found that the deletion of m6A "writer" protein methyltransferase-like (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expression via an m6A-dependent way. Knockdown of METTL3 decreased mRNA m6A levels of JAK1, leading to enhanced YTH m6A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) β, which could ultimately lead to a modulated adipogenic process. Collectively, our results reveal an orchestrated network linking the m6A methylation and JAK1/STAT5/C/EBPβ pathway in pBMSCs adipogenic differentiation. Our findings provide novel insights into the underlying molecular mechanisms of m6A modification in the regulation of BMSCs differentiating into adipocytes, which may pave a way to develop more effective therapeutic strategies in stem cell regenerative medicine and the treatment of obesity.-Yao, Y., Bi, Z., Wu, R., Zhao, Y., Liu, Y., Liu, Q., Wang, Y., Wang, X. METTL3 inhibits BMSC adipogenic differentiation by targeting the JAK1/STAT5/C/EBPβ pathway via an m6A-YTHDF2-dependent manner.
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Affiliation(s)
- Yongxi Yao
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Zhen Bi
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Ruifan Wu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yuanling Zhao
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Youhua Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Qing Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yizhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Animal Nutrition and Feed Sciences in Eastern China, Ministry of Agriculture, Hangzhou, China
| | - Xinxia Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Animal Nutrition and Feed Sciences in Eastern China, Ministry of Agriculture, Hangzhou, China
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939
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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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940
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Lu Z, Ma Y, Li Q, Liu E, Jin M, Zhang L, Wei C. The role of N 6-methyladenosine RNA methylation in the heat stress response of sheep (Ovis aries). Cell Stress Chaperones 2019; 24:333-342. [PMID: 30701478 PMCID: PMC6439051 DOI: 10.1007/s12192-018-00965-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 11/30/2022] Open
Abstract
With the intensive development of the sheep industry and increasing global temperatures, heat stress in sheep has become an increasingly severe and important issue in recent years. The level of N6-methyladenosine (m6A) RNA methylation changes in response to stress plays important roles in stress responses. However, the role of m6A in the heat stress response of sheep remains unclear. To explore this issue, we measured heat stress protein (HSP) expression, liver function indexes, m6A on RNA, m6A-related enzyme expression, and tissue damage in sheep that had been subjected to heat stress. At the transcriptome level, our results showed significant increases in m6A on RNA and increased mRNA levels of HSPs (HSP70, HSP90, and HSP110) and m6A-related enzymes [METTL3 (methyltransferase-like 3), METTL14 (methyltransferase-like 14), WTAP (wilms tumor 1-associated protein), FTO (fat mass and obesity-associated protein), ALKBH5 (alkB homologue 5), YTHDF1-3 (YTH domain family proteins), and YTHDC1-2 (YTH domain-containing proteins)] following heat stress. At the protein level, the expression of METTL3, YTHDF1-2, and YTHDC2 showed no significant differences following heat stress. However, in contrast to its mRNA level after heat stress, the protein expression of YTHDF3 was reduced, while the expression of HSPs (HSP70, HSP90, and HSP110), METTL14, WTAP, FTO, ALKBH5, YTHDF3, and YTHDC1 increased in line with their measured mRNA levels. Histological experiments revealed that heat stress caused varying degrees of damage to sheep liver tissue. Moreover, immunohistochemical staining indicated that the m6A-related enzymes were expressed in sheep hepatocytes, and differences in expression patterns were observed between the control and heat stress groups. In summary, differences in the level of m6A and the expression of m6A-related enzymes in the liver of sheep were observed after heat stress. This indicates that m6A is involved in the regulation of heat stress in sheep. Our findings provide a new avenue for studying the responses to heat stress in sheep.
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Affiliation(s)
- Zengkui Lu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Youji Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Qing Li
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Enmin Liu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Meilin Jin
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Liping Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Caihong Wei
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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941
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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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942
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Fleming AM, Nguyen NLB, Burrows CJ. Colocalization of m 6A and G-Quadruplex-Forming Sequences in Viral RNA (HIV, Zika, Hepatitis B, and SV40) Suggests Topological Control of Adenosine N 6-Methylation. ACS CENTRAL SCIENCE 2019; 5:218-228. [PMID: 30834310 PMCID: PMC6396389 DOI: 10.1021/acscentsci.8b00963] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Indexed: 05/09/2023]
Abstract
This Outlook calls attention to two seemingly disparate and emerging fields regarding viral genomics that may be correlated in a way previously overlooked. First, we describe identification of conserved potential G-quadruplex-forming sequences (PQSs) in viral genomes relevant to human health. Studies have demonstrated that PQSs are highly conserved and can fold to G-quadruplexes (G4s) to regulate viral processes. Key examples include G4s as a countermeasure to the host's immune system or G4-guided regulation of replication or transcription. Second, emerging data are discussed concerning the epitranscriptomic modification N 6-methyladenosine (m6A) in viral RNA installed by host proteins in a consensus sequence favoring 5'-GG(m6A)C-3'. The proposed pathways by which m6A is written, read, and erased in viral RNA genomes and the impact this has on viral replication are described. The structural reason why certain sites are selected for modification while others are not is still mysterious. Finally, we discuss our new observations regarding these previous sequencing data that identify m6A installation within the loops of two-tetrad PQSs in the RNA genomes of the Zika, HIV, hepatitis B, and SV40 viruses. We hypothesize that conserved viral PQSs can provide a framework (sequence and/or structural) for m6A installation. We also discuss literature sources suggesting that PQSs as sites of RNA modification could be a general phenomenon. We anticipate our observations will provide ample opportunities for exciting discoveries regarding the interplay between G4 structures and epitranscriptomic modifications of RNA.
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Affiliation(s)
- Aaron M. Fleming
- Department of Chemistry, University
of Utah, Salt Lake
City, Utah 84112-0850, United States
| | - Ngoc L. B. Nguyen
- Department of Chemistry, University
of Utah, Salt Lake
City, Utah 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University
of Utah, Salt Lake
City, Utah 84112-0850, United States
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943
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RNA N 6-Methyladenosine Modification in Normal and Malignant Hematopoiesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1143:75-93. [PMID: 31338816 DOI: 10.1007/978-981-13-7342-8_4] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
As the most abundant internal modification in eukaryotic messenger RNAs (mRNAs), N 6-methyladenosine (m6A) modification has been shown recently to posttranscriptionally regulate expression of thousands of messenger RNA (mRNA) transcripts in each mammalian cell type in a dynamic and reversible manner. This epigenetic mark is deposited by the m6A methyltransferase complex (i.e., the METTL3/METTL14/WTAP complex and other cofactor proteins) and erased by m6A demethylases such as FTO and ALKBH5. Specific recognition of these m6A-modified mRNAs by m6A-binding proteins (i.e., m6A readers) determines the fate of target mRNAs through affecting splicing, nuclear export, RNA stability, and/or translation. During the past few years, m6A modification has been demonstrated to play a critical role in many major normal bioprocesses including self-renewal and differentiation of embryonic stem cells and hematopoietic stem cells, tissue development, circadian rhythm, heat shock or DNA damage response, and sex determination. Thus, it is not surprising that dysregulation of the m6A machinery is also closely associated with pathogenesis and drug response of both solid tumors and hematologic malignancies. In this chapter, we summarize and discuss recent findings regarding the biological functions and underlying mechanisms of m6A modification and the associated machinery in normal hematopoiesis and the initiation, progression, and drug response of acute myeloid leukemia (AML), a major subtype of leukemia usually associated with unfavorable prognosis.
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944
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Transcriptome-wide reprogramming of N 6-methyladenosine modification by the mouse microbiome. Cell Res 2018; 29:167-170. [PMID: 30559439 PMCID: PMC6355850 DOI: 10.1038/s41422-018-0127-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/28/2018] [Indexed: 01/05/2023] Open
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945
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RNA Modification Level Estimation with pulseR. Genes (Basel) 2018; 9:genes9120619. [PMID: 30544755 PMCID: PMC6316556 DOI: 10.3390/genes9120619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/03/2018] [Accepted: 12/05/2018] [Indexed: 12/03/2022] Open
Abstract
RNA modifications regulate the complex life of transcripts. An experimental approach called LAIC-seq was developed to characterize modification levels on a transcriptome-wide scale. In this method, the modified and unmodified molecules are separated using antibodies specific for a given RNA modification (e.g., m6A). In essence, the procedure of biochemical separation yields three fractions: Input, eluate, and supernatent, which are subjected to RNA-seq. In this work, we present a bioinformatics workflow, which starts from RNA-seq data to infer gene-specific modification levels by a statistical model on a transcriptome-wide scale. Our workflow centers around the pulseR package, which was originally developed for the analysis of metabolic labeling experiments. We demonstrate how to analyze data without external normalization (i.e., in the absence of spike-ins), given high efficiency of separation, and how, alternatively, scaling factors can be derived from unmodified spike-ins. Importantly, our workflow provides an estimate of uncertainty of modification levels in terms of confidence intervals for model parameters, such as gene expression and RNA modification levels. We also compare alternative model parametrizations, log-odds, or the proportion of the modified molecules and discuss the pros and cons of each representation. In summary, our workflow is a versatile approach to RNA modification level estimation, which is open to any read-count-based experimental approach.
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946
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Hsu PJ, Fei Q, Dai Q, Shi H, Dominissini D, Ma L, He C. Single base resolution mapping of 2'-O-methylation sites in human mRNA and in 3' terminal ends of small RNAs. Methods 2018; 156:85-90. [PMID: 30471344 DOI: 10.1016/j.ymeth.2018.11.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 01/07/2023] Open
Abstract
The post-transcriptional modification 2'-O-Methyl (2'OMe) could be present on the ribose of all four ribonucleosides, and is highly prevalent in a wide variety of RNA species, including the 5' RNA cap of viruses and higher eukaryotes, as well as internally in transfer RNA and ribosomal RNA. Recent studies have suggested that 2'OMe is also located internally in low-abundance RNA species such as viral RNA and mRNA. To profile 2'OMe on different RNA species, we have developed Nm-seq, which could identify 2'OMe sites at single base resolution. Nm-seq is particularly useful for identifying 2'OMe sites located at the 3' terminal ends of small RNAs. Here, we present an optimized protocol for Nm-seq and a protocol for applying Nm-seq to identify 2'OMe sites on small RNA 3' terminal ends.
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Affiliation(s)
- Phillip J Hsu
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA; Medical Scientist Training Program, Committee on Immunology, The University of Chicago, Chicago, IL 60637, USA
| | - Qili Fei
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Qing Dai
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Hailing Shi
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Dan Dominissini
- Cancer Research Center, Wohl Centre for Translational Medicine, Chaim Sheba Medical Center, Tel-Hashomer 52621, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Lijia Ma
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
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947
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METTL3-mediated N 6-methyladenosine mRNA modification enhances long-term memory consolidation. Cell Res 2018; 28:1050-1061. [PMID: 30297870 PMCID: PMC6218447 DOI: 10.1038/s41422-018-0092-9] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 08/20/2018] [Accepted: 09/05/2018] [Indexed: 02/06/2023] Open
Abstract
The formation of long-term memory is critical for learning ability and social behaviors of humans and animals, yet its underlying mechanisms are largely unknown. We found that the efficacy of hippocampus-dependent memory consolidation is regulated by METTL3, an RNA N6-methyladenosine (m6A) methyltransferase, through promoting the translation of neuronal early-response genes. Such effect is exquisitely dependent on the m6A methyltransferase function of METTL3. Depleting METTL3 in mouse hippocampus reduces memory consolidation ability, yet unimpaired learning outcomes can be achieved if adequate training was given or the m6A methyltransferase function of METTL3 was restored. The abundance of METTL3 in wild-type mouse hippocampus is positively correlated with learning efficacy, and overexpression of METTL3 significantly enhances long-term memory consolidation. These findings uncover a direct role of RNA m6A modification in regulating long-term memory formation, and also indicate that memory efficacy difference among individuals could be compensated by repeated learning.
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948
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Masiello I, Siciliani S, Biggiogera M. Perichromatin region: a moveable feast. Histochem Cell Biol 2018; 150:227-233. [DOI: 10.1007/s00418-018-1703-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 02/07/2023]
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