601
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Reconstitution of Targeted Deadenylation by the Ccr4-Not Complex and the YTH Domain Protein Mmi1. Cell Rep 2017; 17:1978-1989. [PMID: 27851962 PMCID: PMC5120349 DOI: 10.1016/j.celrep.2016.10.066] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/10/2016] [Accepted: 10/19/2016] [Indexed: 12/22/2022] Open
Abstract
Ccr4-Not is a conserved protein complex that shortens the 3' poly(A) tails of eukaryotic mRNAs to regulate transcript stability and translation into proteins. RNA-binding proteins are thought to facilitate recruitment of Ccr4-Not to certain mRNAs, but lack of an in-vitro-reconstituted system has slowed progress in understanding the mechanistic details of this specificity. Here, we generate a fully recombinant Ccr4-Not complex that removes poly(A) tails from RNA substrates. The intact complex is more active than the exonucleases alone and has an intrinsic preference for certain RNAs. The RNA-binding protein Mmi1 is highly abundant in preparations of native Ccr4-Not. We demonstrate a high-affinity interaction between recombinant Ccr4-Not and Mmi1. Using in vitro assays, we show that Mmi1 accelerates deadenylation of target RNAs. Together, our results support a model whereby both RNA-binding proteins and the sequence context of mRNAs influence deadenylation rate to regulate gene expression.
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602
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Chen X, Sun YZ, Liu H, Zhang L, Li JQ, Meng J. RNA methylation and diseases: experimental results, databases, Web servers and computational models. Brief Bioinform 2017; 20:896-917. [DOI: 10.1093/bib/bbx142] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/12/2017] [Indexed: 12/15/2022] Open
Affiliation(s)
- Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Ya-Zhou Sun
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Hui Liu
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Lin Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Jian-Qiang Li
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Jia Meng
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University
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603
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Baser A, Skabkin M, Martin-Villalba A. Neural Stem Cell Activation and the Role of Protein Synthesis. Brain Plast 2017; 3:27-41. [PMID: 29765858 PMCID: PMC5928545 DOI: 10.3233/bpl-160038] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Adult neural stem cells are generated at embryonic stages by entering a quiescent state that allows their retention into adulthood and thereby maintenance of life-long brain homeostasis. Thus, a tight balance between the quiescence and activation state is instrumental to meet the brain demands for a specific cell type at the correct numbers, at a given time and position. Protein synthesis is the most energy-consuming process within the cell and, not surprisingly, it occurs at low rates in quiescent stem cells. This way quiescent cells adjust to energy constraints and avoid their premature depletion. Stem cell activation is characterized by upregulation of protein synthesis followed by cell division and differentiation. The role of such upregulation as causative or rather a consequence of the activation remains elusive. Here we summarize recent findings connecting stem cell activation to the regulation of protein synthesis, particularly focusing on embryonic and adult neural stem cells of the ventricular zone.
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Affiliation(s)
- Avni Baser
- Molecular Neurobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maxim Skabkin
- Molecular Neurobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ana Martin-Villalba
- Molecular Neurobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
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604
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Wang S, Sun C, Li J, Zhang E, Ma Z, Xu W, Li H, Qiu M, Xu Y, Xia W, Xu L, Yin R. Roles of RNA methylation by means of N6-methyladenosine (m6A) in human cancers. Cancer Lett 2017; 408:112-120. [DOI: 10.1016/j.canlet.2017.08.030] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 08/17/2017] [Accepted: 08/23/2017] [Indexed: 10/18/2022]
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605
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Au KS, Findley TO, Northrup H. Finding the genetic mechanisms of folate deficiency and neural tube defects-Leaving no stone unturned. Am J Med Genet A 2017; 173:3042-3057. [PMID: 28944587 PMCID: PMC5650505 DOI: 10.1002/ajmg.a.38478] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 08/11/2017] [Accepted: 08/21/2017] [Indexed: 12/21/2022]
Abstract
Neural tube defects (NTDs) occur secondary to failed closure of the neural tube between the third and fourth weeks of gestation. The worldwide incidence ranges from 0.3 to 200 per 10,000 births with the United States of American NTD incidence at around 3-6.3 per 10,000 dependent on race and socioeconomic background. Human NTD incidence has fallen by 35-50% in North America due to mandatory folic acid fortification of enriched cereal grain products since 1998. The US Food and Drug Administration has approved the folic acid fortification of corn masa flour with the goal to further reduce the incidence of NTDs, especially among individuals who are Hispanic. However, the genetic mechanisms determining who will benefit most from folate enrichment of the diet remains unclear despite volumes of literature published on studies of association of genes with functions related to folate metabolism and risk of human NTDs. The advances in omics technologies provides hypothesis-free tools to interrogate every single gene within the genome of NTD affected individuals to discover pathogenic variants and methylation targets throughout the affected genome. By identifying genes with expression regulated by presence of folate through transcriptome profiling studies, the genetic mechanisms leading to human NTDs due to folate deficiency may begin to be more efficiently revealed.
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Affiliation(s)
- KS Au
- Division of Medical Genetics, Department of Pediatrics, University of Texas Health Science Houston – McGovern Medical School, Houston, TX
| | - TO Findley
- Division of Neonatology, Department of Pediatrics, University of Texas Health Science Houston – McGovern Medical School, Houston, TX
| | - H Northrup
- Division of Medical Genetics, Department of Pediatrics, University of Texas Health Science Houston – McGovern Medical School, Houston, TX
- Shriners Hospitals for Children - Houston, Houston, TX
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606
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Zhou KI, Pan T. Structures of the m(6)A Methyltransferase Complex: Two Subunits with Distinct but Coordinated Roles. Mol Cell 2017; 63:183-185. [PMID: 27447983 DOI: 10.1016/j.molcel.2016.07.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In this issue of Molecular Cell, Wang et al. (2016a) report crystal structures of the core of the METTL3/METTL14 m(6)A methyltransferase complex and propose how the two subunits interact and cooperate to bind and methylate RNA.
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Affiliation(s)
- Katherine I Zhou
- Medical Scientist Training Program, The University of Chicago, Chicago, IL 60637, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA; Institute of Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.
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607
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Yadav PK, Rajvanshi PK, Rajasekharan R. The role of yeast m 6A methyltransferase in peroxisomal fatty acid oxidation. Curr Genet 2017; 64:417-422. [PMID: 29043484 DOI: 10.1007/s00294-017-0769-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 10/13/2017] [Accepted: 10/15/2017] [Indexed: 01/08/2023]
Abstract
The precise and controlled regulation of gene expression at transcriptional and post-transcriptional levels is crucial for the eukaryotic cell survival and functions. In eukaryotes, more than 100 types of post-transcriptional RNA modifications have been identified. The N6-methyladenosine (m6A) modification in mRNA is among the most common post-transcriptional RNA modifications known in eukaryotic organisms, and the m6A RNA modification can regulate gene expression. The role of yeast m6A methyltransferase (Ime4) in meiosis, sporulation, triacylglycerol metabolism, vacuolar morphology, and mitochondrial functions has been reported. Stress triggers triacylglycerol accumulation as lipid droplets. Lipid droplets are physically connected to the different organelles such as endoplasmic reticulum, mitochondria, and peroxisomes. However, the physiological relevance of these physical interactions remains poorly understood. In yeast, peroxisome is the sole site of fatty acid β-oxidation. The metabolic status of the cell readily governs the number and physiological function of peroxisomes. Under low-glucose or stationary-phase conditions, peroxisome biogenesis and proliferation increase in the cells. Therefore, we hypothesized a possible role of Ime4 in the peroxisomal functions. There is no report on the role of Ime4 in peroxisomal biology. Here, we report that IME4 gene deletion causes peroxisomal dysfunction under stationary-phase conditions in Saccharomyces cerevisiae; besides, the ime4Δ cells showed a significant decrease in the expression of the key genes involved in peroxisomal β-oxidation compared to the wild-type cells. Therefore, identification and determination of the target genes of Ime4 that are directly involved in the peroxisomal biogenesis, morphology, and functions will pave the way to better understand the role of m6A methylation in peroxisomal biology.
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Affiliation(s)
- Pradeep Kumar Yadav
- Lipidomic Centre, Department of Lipid Science, CSIR-Central Food Technological Research Institute (CFTRI), Council of Scientific and Industrial Research, Mysore, Karnataka, 570020, India.,Academy of Scientific and Innovative Research, CSIR-CFTRI, Mysore, India
| | - Praveen Kumar Rajvanshi
- Lipidomic Centre, Department of Lipid Science, CSIR-Central Food Technological Research Institute (CFTRI), Council of Scientific and Industrial Research, Mysore, Karnataka, 570020, India.,Academy of Scientific and Innovative Research, CSIR-CFTRI, Mysore, India
| | - Ram Rajasekharan
- Lipidomic Centre, Department of Lipid Science, CSIR-Central Food Technological Research Institute (CFTRI), Council of Scientific and Industrial Research, Mysore, Karnataka, 570020, India. .,Academy of Scientific and Innovative Research, CSIR-CFTRI, Mysore, India.
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608
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Yadav PK, Rajasekharan R. The m 6A methyltransferase Ime4 and mitochondrial functions in yeast. Curr Genet 2017; 64:353-357. [PMID: 28975387 DOI: 10.1007/s00294-017-0758-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 09/25/2017] [Accepted: 09/25/2017] [Indexed: 12/21/2022]
Abstract
In eukaryotes, the precise transcriptional and post-transcriptional regulations of gene expression are crucial for the developmental processes. More than 100 types of post-transcriptional RNA modifications have been identified in eukaryotes. The deposition of N6-methyladenosine (m6A) into mRNA is among the most common post-transcriptional RNA modifications known in eukaryotes. It has been reported that m6A RNA modification can regulate gene expression. The role of yeast m6A methyltransferase (Ime4) in meiosis and sporulation in diploid cells is very well proven, but its physiological role in haploid cells has remained unknown until recently. Previously, we have shown that Ime4 epitranscriptionally regulates triacylglycerol (TAG) metabolism and vacuolar morphology in haploid cells. Mitochondrial dysfunction leads to TAG accumulation as lipid droplets (LDs) in the cells; besides, LDs are physically connected to the mitochondria. As of now there are no reports on the role of Ime4 in mitochondrial biology. Here we report the important role played by Ime4 in the mitochondrial morphology and functions in Saccharomyces cerevisiae. The confocal microscopic analysis showed that IME4 gene deletion causes mitochondrial fragmentation; besides, the ime4Δ cells showed a significant decrease in cytochrome c oxidase and citrate synthase activities compared to the wild-type cells. IME4 gene deletion causes mitochondrial dysfunction, and it will be interesting to find out the target genes of Ime4 related to the mitochondrial biology. The determination of the role of Ime4 and its targets in mitochondrial biology could probably help in formulating potential cures for the mitochondria-linked rare genetic disorders.
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Affiliation(s)
- Pradeep Kumar Yadav
- Lipidomic Centre, Department of Lipid Science, CSIR-Central Food Technological Research Institute (CFTRI), Mysore, Karnataka, 570020, India.,Academy of Scientific and Innovative Research, CSIR-CFTRI, Mysore, India
| | - Ram Rajasekharan
- Lipidomic Centre, Department of Lipid Science, CSIR-Central Food Technological Research Institute (CFTRI), Mysore, Karnataka, 570020, India. .,Academy of Scientific and Innovative Research, CSIR-CFTRI, Mysore, India.
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609
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Davis JK, Broadie K. Multifarious Functions of the Fragile X Mental Retardation Protein. Trends Genet 2017; 33:703-714. [PMID: 28826631 PMCID: PMC5610095 DOI: 10.1016/j.tig.2017.07.008] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 01/01/2023]
Abstract
Fragile X syndrome (FXS), a heritable intellectual and autism spectrum disorder (ASD), results from the loss of Fragile X mental retardation protein (FMRP). This neurodevelopmental disease state exhibits neural circuit hyperconnectivity and hyperexcitability. Canonically, FMRP functions as an mRNA-binding translation suppressor, but recent findings have enormously expanded its proposed roles. Although connections between burgeoning FMRP functions remain unknown, recent advances have extended understanding of its involvement in RNA, channel, and protein binding that modulate calcium signaling, activity-dependent critical period development, and the excitation-inhibition (E/I) neural circuitry balance. In this review, we contextualize 3 years of FXS model research. Future directions extrapolated from recent advances focus on discovering links between FMRP roles to determine whether FMRP has a multitude of unrelated functions or whether combinatorial mechanisms can explain its multifaceted existence.
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Affiliation(s)
- Jenna K Davis
- Department of Biological Sciences, Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, TN 37235, USA
| | - Kendal Broadie
- Department of Biological Sciences, Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, TN 37235, USA.
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610
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Lewinska A, Adamczyk-Grochala J, Deregowska A, Wnuk M. Sulforaphane-Induced Cell Cycle Arrest and Senescence are accompanied by DNA Hypomethylation and Changes in microRNA Profile in Breast Cancer Cells. Theranostics 2017; 7:3461-3477. [PMID: 28912888 PMCID: PMC5596436 DOI: 10.7150/thno.20657] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 05/29/2017] [Indexed: 12/21/2022] Open
Abstract
Cancer cells are characterized by genetic and epigenetic alterations and phytochemicals, epigenetic modulators, are considered as promising candidates for epigenetic therapy of cancer. In the present study, we have investigated cancer cell fates upon stimulation of breast cancer cells (MCF-7, MDA-MB-231, SK-BR-3) with low doses of sulforaphane (SFN), an isothiocyanate. SFN (5-10 µM) promoted cell cycle arrest, elevation in the levels of p21 and p27 and cellular senescence, whereas at the concentration of 20 µM, apoptosis was induced. The effects were accompanied by nitro-oxidative stress, genotoxicity and diminished AKT signaling. Moreover, SFN stimulated energy stress as judged by decreased pools of ATP and AMPK activation, and autophagy induction. Anticancer effects of SFN were mediated by global DNA hypomethylation, decreased levels of DNA methyltransferases (DNMT1, DNMT3B) and diminished pools of N6-methyladenosine (m6A) RNA methylation. SFN (10 µM) also affected microRNA profiles, namely SFN caused upregulation of sixty microRNAs and downregulation of thirty two microRNAs, and SFN promoted statistically significant decrease in the levels of miR-23b, miR-92b, miR-381 and miR-382 in three breast cancer cells. Taken together, we show for the first time that SFN is an epigenetic modulator in breast cancer cells that results in cell cycle arrest and senescence, and SFN may be considered to be used in epigenome-focused anticancer therapy.
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Affiliation(s)
- Anna Lewinska
- Laboratory of Cell Biology, University of Rzeszow, Werynia 502, 36-100 Kolbuszowa, Poland
| | | | - Anna Deregowska
- Department of Genetics, University of Rzeszow, Kolbuszowa, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Maciej Wnuk
- Department of Genetics, University of Rzeszow, Kolbuszowa, Poland
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611
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Li HB, Tong J, Zhu S, Batista PJ, Duffy EE, Zhao J, Bailis W, Cao G, Kroehling L, Chen Y, Wang G, Broughton JP, Chen YG, Kluger Y, Simon MD, Chang HY, Yin Z, Flavell RA. m 6A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways. Nature 2017; 548:338-342. [PMID: 28792938 PMCID: PMC5729908 DOI: 10.1038/nature23450] [Citation(s) in RCA: 628] [Impact Index Per Article: 89.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 06/30/2017] [Indexed: 12/28/2022]
Abstract
N6 -methyladenosine (m6A) is the most common and abundant messenger RNA modification, modulated by ‘writers’, ‘erasers’ and ‘readers’ of this mark 1,2. In vitro data have shown that m6A influences all fundamental aspects of mRNA metabolism, mainly mRNA stability, to determine stem cell fates 3,4. However, its in vivo physiological function in mammals and adult mammalian cells is still unknown. Here we show that deletion of m6A ‘writer’ protein METTL3 in mouse T cells disrupts T cell homeostasis and differentiation. In a lymphopenic mouse adoptive transfer model, naive Mettl3 deficient T cells failed to undergo homeostatic expansion and remarkably remained in the naïve state up through 12 weeks, thereby preventing colitis. Consistent with these observations, the mRNAs of SOCS family genes encoding STAT- signaling inhibitory proteins, Socs1, Socs3 and Cish, were marked by m6A, exhibited slower mRNA decay and increased mRNAs and protein expression levels in Mettl3 deficient naïve T cells. This increased SOCS family activity consequently inhibited IL-7 mediated STAT5 activation and T cell homeostatic proliferation and differentiation. We also found that m6A plays important roles for inducible degradation of Socs mRNAs in response to IL-7 signaling in order to reprogram Naïve T cells for proliferation and differentiation. Our study elucidates for the first time the in vivo biological role of m6A modification in T cell mediated pathogenesis and reveals a novel mechanism of T cell homeostasis and signal-dependent induction of mRNA degradation.
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Affiliation(s)
- Hua-Bing Li
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Jiyu Tong
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,The First Affiliated Hospital, Biomedical Translational Research Institute and Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Shu Zhu
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Pedro J Batista
- Center for Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Erin E Duffy
- Department of Molecular Biophysics &Biochemistry, Yale University, New Haven, Connecticut 06511, USA.,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Jun Zhao
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Will Bailis
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Guangchao Cao
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,The First Affiliated Hospital, Biomedical Translational Research Institute and Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Lina Kroehling
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Yuanyuan Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,Institute of Surgical Research, Daping Hospital, the Third Military Medical University, Chongqing 400038, China
| | - Geng Wang
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - James P Broughton
- Center for Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Y Grace Chen
- Center for Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Yuval Kluger
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Matthew D Simon
- Department of Molecular Biophysics &Biochemistry, Yale University, New Haven, Connecticut 06511, USA.,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Howard Y Chang
- Center for Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Zhinan Yin
- The First Affiliated Hospital, Biomedical Translational Research Institute and Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815-6789, USA
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612
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Abstract
Gastric cancer is a deadly malignancy afflicting close to a million people worldwide. Patient survival is poor and largely due to late diagnosis and suboptimal therapies. Disease heterogeneity is a substantial obstacle, underscoring the need for precision treatment strategies. Studies have identified different subgroups of gastric cancer displaying not just genetic, but also distinct epigenetic hallmarks. Accumulating evidence suggests that epigenetic abnormalities in gastric cancer are not mere bystander events, but rather promote carcinogenesis through active mechanisms. Epigenetic aberrations, induced by pathogens such as Helicobacter pylori, are an early component of gastric carcinogenesis, probably preceding genetic abnormalities. This Review summarizes our current understanding of the gastric cancer epigenome, highlighting key advances in recent years in both tumours and pre-malignant lesions, made possible through targeted and genome-wide technologies. We focus on studies related to DNA methylation and histone modifications, linking these findings to potential therapeutic opportunities. Lessons learned from the gastric cancer epigenome might also prove relevant for other gastrointestinal cancers.
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613
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614
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Pendleton KE, Chen B, Liu K, Hunter OV, Xie Y, Tu BP, Conrad NK. The U6 snRNA m 6A Methyltransferase METTL16 Regulates SAM Synthetase Intron Retention. Cell 2017; 169:824-835.e14. [PMID: 28525753 DOI: 10.1016/j.cell.2017.05.003] [Citation(s) in RCA: 700] [Impact Index Per Article: 100.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/16/2017] [Accepted: 04/28/2017] [Indexed: 12/15/2022]
Abstract
Maintenance of proper levels of the methyl donor S-adenosylmethionine (SAM) is critical for a wide variety of biological processes. We demonstrate that the N6-adenosine methyltransferase METTL16 regulates expression of human MAT2A, which encodes the SAM synthetase expressed in most cells. Upon SAM depletion by methionine starvation, cells induce MAT2A expression by enhanced splicing of a retained intron. Induction requires METTL16 and its methylation substrate, a vertebrate conserved hairpin (hp1) in the MAT2A 3' UTR. Increasing METTL16 occupancy on the MAT2A 3' UTR is sufficient to induce efficient splicing. We propose that, under SAM-limiting conditions, METTL16 occupancy on hp1 increases due to inefficient enzymatic turnover, which promotes MAT2A splicing. We further show that METTL16 is the long-unknown methyltransferase for the U6 spliceosomal small nuclear RNA (snRNA). These observations suggest that the conserved U6 snRNA methyltransferase evolved an additional function in vertebrates to regulate SAM homeostasis.
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Affiliation(s)
- Kathryn E Pendleton
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Beibei Chen
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kuanqing Liu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Olga V Hunter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang Xie
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Benjamin P Tu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nicholas K Conrad
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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615
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DNA N 6-methyladenine in metazoans: functional epigenetic mark or bystander? Nat Struct Mol Biol 2017; 24:503-506. [PMID: 28586322 DOI: 10.1038/nsmb.3412] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 04/18/2017] [Indexed: 02/06/2023]
Abstract
The DNA-adenine modification N6-methyladenine (6mA), initially thought to be mainly restricted to prokaryotes and certain unicellular eukaryotes, has recently been found in metazoans. Proposed functions vary from gene activation to transposon suppression. However, since most metazoan genomes possess 5-methylcytosine (5mC) as a dominant epigenetic mark, it raises the question of why 6mA is required. This Perspective summarizes the latest discoveries and suggests potential functional roles for 6mA in metazoan genomes.
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616
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Guo M, Liu X, Zheng X, Huang Y, Chen X. m 6A RNA Modification Determines Cell Fate by Regulating mRNA Degradation. Cell Reprogram 2017; 19:225-231. [PMID: 28682669 DOI: 10.1089/cell.2016.0041] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Emerging evidence suggests that epitranscriptional modifications influence multiple cellular processes. N6-methyladenosine (m6A), as the most abundant reversible methylation of mRNA, has also been reported to play critical roles in modulating embryonic stem cell differentiation and somatic cell reprogramming by regulating gene expression. This review examined the characteristics of m6A, including the distribution profile and currently discovered "writer," "eraser," and "reader" proteins. Moreover, the hypothesis is proposed that m6A could influence cell fate determination, and the underlying mechanisms are due to the related mRNA degradation, causing weakening of previous cell characteristics and eventually leading them to develop into the reverse direction (pluripotency or differentiation state). Accordingly, m6A modifications presented its potential role in cell fate determination, which provides new insights into understanding the mechanisms of various diseases.
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Affiliation(s)
- Minjun Guo
- College of Life Science and Bioengineering, Beijing University of Technology , Beijing, China
| | - Xinhui Liu
- College of Life Science and Bioengineering, Beijing University of Technology , Beijing, China
| | - Xiaotong Zheng
- College of Life Science and Bioengineering, Beijing University of Technology , Beijing, China
| | - Yinghui Huang
- College of Life Science and Bioengineering, Beijing University of Technology , Beijing, China
| | - Xuechai Chen
- College of Life Science and Bioengineering, Beijing University of Technology , Beijing, China
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617
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Li L, Zang L, Zhang F, Chen J, Shen H, Shu L, Liang F, Feng C, Chen D, Tao H, Xu T, Li Z, Kang Y, Wu H, Tang L, Zhang P, Jin P, Shu Q, Li X. Fat mass and obesity-associated (FTO) protein regulates adult neurogenesis. Hum Mol Genet 2017; 26:2398-2411. [PMID: 28398475 PMCID: PMC6192412 DOI: 10.1093/hmg/ddx128] [Citation(s) in RCA: 216] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/12/2017] [Accepted: 03/28/2017] [Indexed: 12/20/2022] Open
Abstract
Fat mass and obesity-associated gene (FTO) is a member of the Fe (II)- and oxoglutarate-dependent AlkB dioxygenase family and is linked to both obesity and intellectual disability. The role of FTO in neurodevelopment and neurogenesis, however, remains largely unknown. Here we show that FTO is expressed in adult neural stem cells and neurons and displays dynamic expression during postnatal neurodevelopment. The loss of FTO leads to decreased brain size and body weight. We find that FTO deficiency could reduce the proliferation and neuronal differentiation of adult neural stem cells in vivo, which leads to impaired learning and memory. Given the role of FTO as a demethylase of N6-methyladenosine (m6A), we went on to perform genome-wide m6A profiling and observed dynamic m6A modification during postnatal neurodevelopment. The loss of FTO led to the altered expression of several key components of the brain derived neurotrophic factor pathway that were marked by m6A. These results together suggest FTO plays important roles in neurogenesis, as well as in learning and memory.
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Affiliation(s)
- Liping Li
- Institute of Genetics, College of Life Sciences, Zhejiang University,
Hangzhou 310058, China
- The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou
310052, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang
University, Hangzhou 310029, China
| | - Liqun Zang
- Institute of Genetics, College of Life Sciences, Zhejiang University,
Hangzhou 310058, China
- The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou
310052, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang
University, Hangzhou 310029, China
| | - Feiran Zhang
- Department of Human Genetics, Emory University School of Medicine, Atlanta,
GA 30322, USA
| | - Junchen Chen
- The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou
310052, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang
University, Hangzhou 310029, China
| | - Hui Shen
- The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou
310052, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang
University, Hangzhou 310029, China
| | - Liqi Shu
- Department of Human Genetics, Emory University School of Medicine, Atlanta,
GA 30322, USA
- School of Medicine and Health Sciences, George Washington University,
Washington, DC 20037, USA
| | - Feng Liang
- The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou
310052, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang
University, Hangzhou 310029, China
| | - Chunyue Feng
- The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou
310052, China
| | - Deng Chen
- State Key Laboratory of Medical Molecular Biology, Department of
Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of
Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005,
China
| | - Huikang Tao
- The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou
310052, China
| | - Tianlei Xu
- Department of Biostatistics and Bioinformatics, Rollins School of Public
Health, Emory University, Atlanta, GA 30322, USA
| | - Ziyi Li
- Department of Biostatistics and Bioinformatics, Rollins School of Public
Health, Emory University, Atlanta, GA 30322, USA
| | - Yunhee Kang
- Department of Human Genetics, Emory University School of Medicine, Atlanta,
GA 30322, USA
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Rollins School of Public
Health, Emory University, Atlanta, GA 30322, USA
| | - Lichun Tang
- National Center for Protein Sciences Beijing, Life Sciences Park, Beijing
102206, China
| | - Pumin Zhang
- National Center for Protein Sciences Beijing, Life Sciences Park, Beijing
102206, China
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta,
GA 30322, USA
| | - Qiang Shu
- The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou
310052, China
| | - Xuekun Li
- The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou
310052, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang
University, Hangzhou 310029, China
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618
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Růžička K, Zhang M, Campilho A, Bodi Z, Kashif M, Saleh M, Eeckhout D, El‐Showk S, Li H, Zhong S, De Jaeger G, Mongan NP, Hejátko J, Helariutta Y, Fray RG. Identification of factors required for m 6 A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI. THE NEW PHYTOLOGIST 2017; 215:157-172. [PMID: 28503769 PMCID: PMC5488176 DOI: 10.1111/nph.14586] [Citation(s) in RCA: 282] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 03/19/2017] [Indexed: 05/04/2023]
Abstract
N6-adenosine methylation (m6 A) of mRNA is an essential process in most eukaryotes, but its role and the status of factors accompanying this modification are still poorly understood. Using combined methods of genetics, proteomics and RNA biochemistry, we identified a core set of mRNA m6 A writer proteins in Arabidopsis thaliana. The components required for m6 A in Arabidopsis included MTA, MTB, FIP37, VIRILIZER and the E3 ubiquitin ligase HAKAI. Downregulation of these proteins led to reduced relative m6 A levels and shared pleiotropic phenotypes, which included aberrant vascular formation in the root, indicating that correct m6 A methylation plays a role in developmental decisions during pattern formation. The conservation of these proteins amongst eukaryotes and the demonstration of a role in writing m6 A for the E3 ubiquitin ligase HAKAI is likely to be of considerable relevance beyond the plant sciences.
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Affiliation(s)
- Kamil Růžička
- Functional Genomics and Proteomics of PlantsCentral European Institute of Technology and National Centre for Biomolecular ResearchMasaryk University62500BrnoCzech Republic
- Institute of BiotechnologyUniversity of Helsinki00014HelsinkiFinland
| | - Mi Zhang
- Plant Sciences DivisionSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughboroughLE12 5RDUK
| | - Ana Campilho
- Institute of BiotechnologyUniversity of Helsinki00014HelsinkiFinland
- Research Center in Biodiversity and Genetic ResourcesUniversity of Porto4485‐661 VairãoPortugal
| | - Zsuzsanna Bodi
- Plant Sciences DivisionSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughboroughLE12 5RDUK
| | - Muhammad Kashif
- Institute of BiotechnologyUniversity of Helsinki00014HelsinkiFinland
| | - Mária Saleh
- Functional Genomics and Proteomics of PlantsCentral European Institute of Technology and National Centre for Biomolecular ResearchMasaryk University62500BrnoCzech Republic
| | - Dominique Eeckhout
- Department of Plant Systems BiologyVIB9052GentBelgium
- Department of Plant Biotechnology and BioinformaticsGhent University9052GentBelgium
| | - Sedeer El‐Showk
- Institute of BiotechnologyUniversity of Helsinki00014HelsinkiFinland
| | - Hongying Li
- Plant Sciences DivisionSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughboroughLE12 5RDUK
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess PlateauMinistry of AgricultureTaiyuanShanxi030031China
| | - Silin Zhong
- Plant Sciences DivisionSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughboroughLE12 5RDUK
- The State Key Laboratory of AgrobiotechnologyThe School of Life SciencesThe Chinese University of Hong KongHong KongChina
| | - Geert De Jaeger
- Department of Plant Systems BiologyVIB9052GentBelgium
- Department of Plant Biotechnology and BioinformaticsGhent University9052GentBelgium
| | - Nigel P. Mongan
- School of Veterinary Medicine and SciencesUniversity of NottinghamSutton BoningtonLoughboroughLE12 5RDUK
| | - Jan Hejátko
- Functional Genomics and Proteomics of PlantsCentral European Institute of Technology and National Centre for Biomolecular ResearchMasaryk University62500BrnoCzech Republic
| | - Ykä Helariutta
- Institute of BiotechnologyUniversity of Helsinki00014HelsinkiFinland
- Sainsbury LaboratoryUniversity of CambridgeCambridgeCB2 1LRUK
| | - Rupert G. Fray
- Plant Sciences DivisionSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughboroughLE12 5RDUK
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619
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Yadav PK, Rajasekharan R. The m 6A methyltransferase Ime4 epitranscriptionally regulates triacylglycerol metabolism and vacuolar morphology in haploid yeast cells. J Biol Chem 2017; 292:13727-13744. [PMID: 28655762 DOI: 10.1074/jbc.m117.783761] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/02/2017] [Indexed: 12/20/2022] Open
Abstract
N6-Methyladenosine (m6A) is among the most common modifications in eukaryotic mRNA. The role of yeast m6A methyltransferase, Ime4, in meiosis and sporulation in diploid strains is very well studied, but its role in haploid strains has remained unknown. Here, with the help of an immunoblotting strategy and Ime4-GFP protein localization studies, we establish the physiological role of Ime4 in haploid cells. Our data showed that Ime4 epitranscriptionally regulates triacylglycerol metabolism and vacuolar morphology through the long-chain fatty acyl-CoA synthetase Faa1, independently of the RNA methylation complex (MIS complex). The MIS complex consists of the Ime4, Mum2, and Slz1 proteins. Our affinity enrichment strategy (methylated RNA immunoprecipitation assays) using m6A polyclonal antibodies coupled with mRNA isolation, quantitative real-time PCR, and standard PCR analyses confirmed the presence of m6A-modified FAA1 transcripts in haploid yeast cells. The term "epitranscriptional regulation" encompasses the RNA modification-mediated regulation of genes. Moreover, we demonstrate that the Aft2 transcription factor up-regulates FAA1 expression. Because the m6A methylation machinery is fundamentally conserved throughout eukaryotes, our findings will help advance the rapidly emerging field of RNA epitranscriptomics. The metabolic link identified here between m6A methylation and triacylglycerol metabolism via the Ime4 protein provides new insights into lipid metabolism and the pathophysiology of lipid-related metabolic disorders, such as obesity. Because the yeast vacuole is an analogue of the mammalian lysosome, our findings pave the way to better understand the role of m6A methylation in lysosome-related functions and diseases.
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Affiliation(s)
- Pradeep Kumar Yadav
- From the Lipidomic Centre, Department of Lipid Science, and.,the Academy of Scientific and Innovative Research, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka 570020, India
| | - Ram Rajasekharan
- From the Lipidomic Centre, Department of Lipid Science, and .,the Academy of Scientific and Innovative Research, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka 570020, India
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620
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Tudek B, Zdżalik-Bielecka D, Tudek A, Kosicki K, Fabisiewicz A, Speina E. Lipid peroxidation in face of DNA damage, DNA repair and other cellular processes. Free Radic Biol Med 2017; 107:77-89. [PMID: 27908783 DOI: 10.1016/j.freeradbiomed.2016.11.043] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/20/2016] [Accepted: 11/27/2016] [Indexed: 01/09/2023]
Abstract
Exocyclic adducts to DNA bases are formed as a consequence of exposure to certain environmental carcinogens as well as inflammation and lipid peroxidation (LPO). Complex family of LPO products gives rise to a variety of DNA adducts, which can be grouped in two classes: (i) small etheno-type adducts of strong mutagenic potential, and (ii) bulky, propano-type adducts, which block replication and transcription, and are lethal lesions. Etheno-DNA adducts are removed from the DNA by base excision repair (BER), AlkB and nucleotide incision repair enzymes (NIR), while substituted propano-type lesions by nucleotide excision repair (NER) and homologous recombination (HR). Changes of the level and activity of several enzymes removing exocyclic adducts from the DNA was reported during carcinogenesis. Also several beyond repair functions of these enzymes, which participate in regulation of cell proliferation and growth, as well as RNA processing was recently described. In addition, adducts of LPO products to proteins was reported during aging and age-related diseases. The paper summarizes pathways for exocyclic adducts removal and describes how proteins involved in repair of these adducts can modify pathological states of the organism.
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Affiliation(s)
- Barbara Tudek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Daria Zdżalik-Bielecka
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Ksiecia Trojdena 4, 02-109 Warsaw, Poland
| | - Agnieszka Tudek
- Department of Molecular Biology and Genetics, Aarhus University, C. F. Mollers Alle 3, 8000 Aarhus, Denmark
| | - Konrad Kosicki
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Anna Fabisiewicz
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, Warsaw 02-781, Poland
| | - Elżbieta Speina
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
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621
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Xiong X, Yi C, Peng J. Epitranscriptomics: Toward A Better Understanding of RNA Modifications. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:147-153. [PMID: 28533024 PMCID: PMC5487522 DOI: 10.1016/j.gpb.2017.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 02/18/2017] [Accepted: 03/22/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Xushen Xiong
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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622
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Vaidyanathan PP, AlSadhan I, Merriman DK, Al-Hashimi HM, Herschlag D. Pseudouridine and N6-methyladenosine modifications weaken PUF protein/RNA interactions. RNA (NEW YORK, N.Y.) 2017; 23:611-618. [PMID: 28138061 PMCID: PMC5393172 DOI: 10.1261/rna.060053.116] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/05/2017] [Indexed: 05/20/2023]
Abstract
RNA modifications are ubiquitous in biology, with over 100 distinct modifications. While the vast majority were identified and characterized on abundant noncoding RNA such as tRNA and rRNA, the advent of sensitive sequencing-based approaches has led to the discovery of extensive and regulated modification of eukaryotic messenger RNAs as well. The two most abundant mRNA modifications-pseudouridine (Ψ) and N6-methyladenosine (m6A)-affect diverse cellular processes including mRNA splicing, localization, translation, and decay and modulate RNA structure. Here, we test the hypothesis that RNA modifications directly affect interactions between RNA-binding proteins and target RNA. We show that Ψ and m6A weaken the binding of the human single-stranded RNA binding protein Pumilio 2 (hPUM2) to its consensus motif, with individual modifications having effects up to approximately threefold and multiple modifications giving larger effects. While there are likely to be some cases where RNA modifications essentially fully ablate protein binding, here we see modest responses that may be more common. Such modest effects could nevertheless profoundly alter the complex landscape of RNA:protein interactions, and the quantitative rather than qualitative nature of these effects underscores the need for quantitative, systems-level accounting of RNA:protein interactions to understand post-transcriptional regulation.
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Affiliation(s)
| | - Ishraq AlSadhan
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | - Dawn K Merriman
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Hashim M Al-Hashimi
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
- Departments of Chemical Engineering and Chemistry, Stanford University, Stanford, California 94305, USA
- Stanford ChEM-H (Chemistry, Engineering, and Medicine for Human Health), Stanford University, Stanford, California 94305, USA
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623
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Tao X, Chen J, Jiang Y, Wei Y, Chen Y, Xu H, Zhu L, Tang G, Li M, Jiang A, Shuai S, Bai L, Liu H, Ma J, Jin L, Wen A, Wang Q, Zhu G, Xie M, Wu J, He T, Huang C, Gao X, Li X. Transcriptome-wide N 6 -methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern. BMC Genomics 2017; 18:336. [PMID: 28454518 PMCID: PMC5410061 DOI: 10.1186/s12864-017-3719-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 04/25/2017] [Indexed: 01/10/2023] Open
Abstract
Background N6-methyladenosine (m6A) is the most prevalent internal form of modification in messenger RNA in higher eukaryotes and potential regulatory functions of reversible m6A methylation on mRNA have been revealed by mapping of m6A methylomes in several species. m6A modification in active gene regulation manifests itself as altered methylation profiles in a tissue-specific manner or in response to changing cellular or species living environment. However, up to date, there has no data on m6A porcine transcriptome-wide map and its potential biological roles in adipose deposition and muscle growth. Methods In this work, we used methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq) technique to acquire the first ever m6A porcine transcriptome-wide map. Transcriptomes of muscle and adipose tissues from three different pig breeds, the wild boar, Landrace, and Rongchang pig, were used to generate these maps. Results Our findings show that there were 5,872 and 2,826 m6A peaks respectively, in the porcine muscle and adipose tissue transcriptomes. Stop codons, 3′-untranslated regions, and coding regions were found to be mainly enriched for m6A peaks. Gene ontology analysis revealed that common m6A peaks in nuclear genes are associated with transcriptional factors, suggestive of a relationship between m6A mRNA methylation and nuclear genome transcription. Some genes showed tissue- and breed-differential methylation, and have novel biological functions. We also found a relationship between the m6A methylation extent and the transcript level, suggesting a regulatory role for m6A in gene expression. Conclusion This comprehensive map provides a solid basis for the determination of potential functional roles for RNA m6A modification in adipose deposition and muscle growth. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3719-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xuelian Tao
- Department of Zoology, College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an City, 625014, Sichuan Province, China
| | - Jianning Chen
- Department of Zoology, College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an City, 625014, Sichuan Province, China
| | - Yanzhi Jiang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an City, 625014, Sichuan Province, China.
| | - Yingying Wei
- Department of Zoology, College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an City, 625014, Sichuan Province, China
| | - Yan Chen
- Department of Zoology, College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an City, 625014, Sichuan Province, China
| | - Huaming Xu
- Department of Zoology, College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an City, 625014, Sichuan Province, China
| | - Li Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Guoqing Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Anan Jiang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Surong Shuai
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Lin Bai
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Haifeng Liu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Anxiang Wen
- Department of Zoology, College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an City, 625014, Sichuan Province, China
| | - Qin Wang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an City, 625014, Sichuan Province, China
| | - Guangxiang Zhu
- Department of Zoology, College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an City, 625014, Sichuan Province, China
| | - Meng Xie
- Department of Zoology, College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an City, 625014, Sichuan Province, China
| | - Jiayun Wu
- Department of Zoology, College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an City, 625014, Sichuan Province, China
| | - Tao He
- Department of Zoology, College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an City, 625014, Sichuan Province, China
| | - Chunyu Huang
- Genergy Biological Technology (Shanghai) Company of Limited Liability, Shanghai, 200233, China
| | - Xiang Gao
- Genergy Biological Technology (Shanghai) Company of Limited Liability, Shanghai, 200233, China
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
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624
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Abstract
Although it has been known for over 40 years that eukaryotic mRNAs bear internal base modifications, it is only in the last 5 years that the importance of these modifications has begun to come into focus. The most common mRNA modification, the addition of a methyl group to the N6 position of adenosine (m6A), has been shown to affect splicing, translation, and stability, and m6A is also essential for embryonic development in organisms ranging from plants to mice. While all viral transcripts examined so far have been found to be extensively m6A modified, the role, if any, of m6A in regulating viral gene expression and replication was previously unknown. However, recent data generated using HIV-1 as a model system strongly suggest that sites of m6A addition not only are evolutionarily conserved but also enhance virus replication. It is therefore likely that the field of viral epitranscriptomics, which can be defined as the study of functionally relevant posttranscriptional modifications of viral RNA transcripts that do not change the nucleotide sequence of that RNA, is poised for a major expansion in scientific interest and may well fundamentally change our understanding of how viral replication is regulated.
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625
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Yan W. Mark it for destruction: a novel role of mRNA methylation in maternal-to-zygotic transition†. Biol Reprod 2017; 96:829-830. [PMID: 28371885 DOI: 10.1093/biolre/iox016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 03/17/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA.,Department of Biology, University of Nevada, Reno, Nevada, USA
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626
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Yang Y, Fan X, Mao M, Song X, Wu P, Zhang Y, Jin Y, Yang Y, Chen LL, Wang Y, Wong CC, Xiao X, Wang Z. Extensive translation of circular RNAs driven by N 6-methyladenosine. Cell Res 2017; 27:626-641. [PMID: 28281539 PMCID: PMC5520850 DOI: 10.1038/cr.2017.31] [Citation(s) in RCA: 1276] [Impact Index Per Article: 182.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 02/03/2017] [Accepted: 02/19/2017] [Indexed: 12/16/2022] Open
Abstract
Extensive pre-mRNA back-splicing generates numerous circular RNAs (circRNAs) in human transcriptome. However, the biological functions of these circRNAs remain largely unclear. Here we report that N6-methyladenosine (m6A), the most abundant base modification of RNA, promotes efficient initiation of protein translation from circRNAs in human cells. We discover that consensus m6A motifs are enriched in circRNAs and a single m6A site is sufficient to drive translation initiation. This m6A-driven translation requires initiation factor eIF4G2 and m6A reader YTHDF3, and is enhanced by methyltransferase METTL3/14, inhibited by demethylase FTO, and upregulated upon heat shock. Further analyses through polysome profiling, computational prediction and mass spectrometry reveal that m6A-driven translation of circRNAs is widespread, with hundreds of endogenous circRNAs having translation potential. Our study expands the coding landscape of human transcriptome, and suggests a role of circRNA-derived proteins in cellular responses to environmental stress.
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Affiliation(s)
- Yun Yang
- Institute of Biochemistry, College of Life Sciences, Zhejiang University at Zijingang, Zhejiang, Hangzhou, Zhejiang 310058, China.,CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Department of Integrative Biology and Physiology and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xiaojuan Fan
- CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Miaowei Mao
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xiaowei Song
- CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ping Wu
- National Center for Protein Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201204, China
| | - Yang Zhang
- Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yongfeng Jin
- Institute of Biochemistry, College of Life Sciences, Zhejiang University at Zijingang, Zhejiang, Hangzhou, Zhejiang 310058, China
| | - Yi Yang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Ling-Ling Chen
- Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yang Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning 116044, China
| | - Catherine Cl Wong
- National Center for Protein Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201204, China
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Zefeng Wang
- CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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627
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Wu R, Jiang D, Wang Y, Wang X. N (6)-Methyladenosine (m(6)A) Methylation in mRNA with A Dynamic and Reversible Epigenetic Modification. Mol Biotechnol 2017; 58:450-9. [PMID: 27179969 DOI: 10.1007/s12033-016-9947-9] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
N (6)-methyladenosine (m(6)A) is the most abundant and reversible internal modification ubiquitously occurring in eukaryotic mRNA, albeit the significant biological roles of m(6)A methylation have remained largely unclear. The well-known DNA and histone methylations play crucial roles in epigenetic modification of biologic processes in eukaryotes. Analogously, the dynamic and reversible m(6)A RNA modification, which is installed by methyltransferase (METTL3, METTL14, and WTAP), reversed by demethylases (FTO, ALKBH5) and mediated by m(6)A-binding proteins (YTHDF1-3, YTHDC1), may also have a profound impact on gene expression regulation. Recent discoveries of the distributions, functions, and mechanisms of m(6)A modification suggest that this methylation functionally modulates the eukaryotic transcriptome to influence mRNA transcription, splicing, nuclear export, localization, translation, and stability. This reversible mRNA methylation shed light on a new dimension of post-transcriptional regulation of gene expression at the RNA level. m(6)A methylation also plays significant and broad roles in various physiological processes, such as development, fertility, carcinogenesis, stemness, early mortality, meiosis and circadian cycle, and links to obesity, cancer, and other human diseases. This review mainly describes the current knowledge of m(6)A and perspectives on future investigations.
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Affiliation(s)
- Ruifan Wu
- College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Zhejiang Provincial Laboratory of Feed and Animal Nutrition, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Denghu Jiang
- College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Zhejiang Provincial Laboratory of Feed and Animal Nutrition, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Yizhen Wang
- College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Zhejiang Provincial Laboratory of Feed and Animal Nutrition, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Xinxia Wang
- College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China. .,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China. .,Zhejiang Provincial Laboratory of Feed and Animal Nutrition, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.
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628
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He S, Wang H, Liu R, He M, Che T, Jin L, Deng L, Tian S, Li Y, Lu H, Li X, Jiang Z, Li D, Li M. mRNA N6-methyladenosine methylation of postnatal liver development in pig. PLoS One 2017; 12:e0173421. [PMID: 28267806 PMCID: PMC5340393 DOI: 10.1371/journal.pone.0173421] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/10/2017] [Indexed: 11/18/2022] Open
Abstract
N6-methyladenosine (m6A) is a ubiquitous reversible epigenetic RNA modification that plays an important role in the regulation of post-transcriptional protein coding gene expression. Liver is a vital organ and plays a major role in metabolism with numerous functions. Information concerning the dynamic patterns of mRNA m6A methylation during postnatal development of liver has been long overdue and elucidation of this information will benefit for further deciphering a multitude of functional outcomes of mRNA m6A methylation. Here, we profile transcriptome-wide m6A in porcine liver at three developmental stages: newborn (0 day), suckling (21 days) and adult (2 years). About 33% of transcribed genes were modified by m6A, with 1.33 to 1.42 m6A peaks per modified gene. m6A was distributed predominantly around stop codons. The consensus motif sequence RRm6ACH was observed in 78.90% of m6A peaks. A negative correlation (average Pearson's r = -0.45, P < 10-16) was found between levels of m6A methylation and gene expression. Functional enrichment analysis of genes consistently modified by m6A methylation at all three stages showed genes relevant to important functions, including regulation of growth and development, regulation of metabolic processes and protein catabolic processes. Genes with higher m6A methylation and lower expression levels at any particular stage were associated with the biological processes required for or unique to that stage. We suggest that differential m6A methylation may be important for the regulation of nutrient metabolism in porcine liver.
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Affiliation(s)
- Shen He
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Hong Wang
- Novogene Bioinformatics Institute, Beijing, China
| | - Rui Liu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mengnan He
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Tiandong Che
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lamei Deng
- Novogene Bioinformatics Institute, Beijing, China
| | - Shilin Tian
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Novogene Bioinformatics Institute, Beijing, China
| | - Yan Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Hongfeng Lu
- Novogene Bioinformatics Institute, Beijing, China
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhi Jiang
- Novogene Bioinformatics Institute, Beijing, China
- * E-mail: (ML); (DL); (ZJ)
| | - Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- * E-mail: (ML); (DL); (ZJ)
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- * E-mail: (ML); (DL); (ZJ)
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629
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Abstract
Nucleotide modifications constitute marks in RNA and DNA that contribute to gene regulation, development and other cellular processes. The understanding of their intricate molecular roles has been hampered by the high number of different modifications, the lack of effective methods and tools for their detection and quantification as well as by their complex structure-function relationship. The recent development of RNA and DNA immunoprecipitation followed by high-throughput sequencing (RIP- and DIP-seq) initiated detailed transcriptome- and genome-wide studies. Both techniques depend on highly specific and sensitive antibodies to specifically enrich the targeted modified nucleotides without background or potential biases. Here, we review the challenges and developments when generating and validating antibodies targeting modified nucleotides. We discuss antibody-antigen interactions, different strategies of antigen generation and compare different binder formats suitable for state-of-the-art high resolution mapping and imaging technologies.
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Affiliation(s)
- Regina Feederle
- a Monoclonal Antibody Core Facility and Research Group, Institute for Diabetes and Obesity , Helmholtz Zentrum München, German Research Center for Environmental Health GmbH , München , Germany
| | - Aloys Schepers
- a Monoclonal Antibody Core Facility and Research Group, Institute for Diabetes and Obesity , Helmholtz Zentrum München, German Research Center for Environmental Health GmbH , München , Germany
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630
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Next-Generation Sequencing-Based RiboMethSeq Protocol for Analysis of tRNA 2'-O-Methylation. Biomolecules 2017; 7:biom7010013. [PMID: 28208788 PMCID: PMC5372725 DOI: 10.3390/biom7010013] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 02/02/2017] [Indexed: 12/16/2022] Open
Abstract
Analysis of RNA modifications by traditional physico-chemical approaches is labor intensive, requires substantial amounts of input material and only allows site-by-site measurements. The recent development of qualitative and quantitative approaches based on next-generation sequencing (NGS) opens new perspectives for the analysis of various cellular RNA species. The Illumina sequencing-based RiboMethSeq protocol was initially developed and successfully applied for mapping of ribosomal RNA (rRNA) 2′-O-methylations. This method also gives excellent results in the quantitative analysis of rRNA modifications in different species and under varying growth conditions. However, until now, RiboMethSeq was only employed for rRNA, and the whole sequencing and analysis pipeline was only adapted to this long and rather conserved RNA species. A deep understanding of RNA modification functions requires large and global analysis datasets for other important RNA species, namely for transfer RNAs (tRNAs), which are well known to contain a great variety of functionally-important modified residues. Here, we evaluated the application of the RiboMethSeq protocol for the analysis of tRNA 2′-O-methylation in Escherichia coli and in Saccharomyces cerevisiae. After a careful optimization of the bioinformatic pipeline, RiboMethSeq proved to be suitable for relative quantification of methylation rates for known modified positions in different tRNA species.
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631
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Li Z, Weng H, Su R, Weng X, Zuo Z, Li C, Huang H, Nachtergaele S, Dong L, Hu C, Qin X, Tang L, Wang Y, Hong GM, Huang H, Wang X, Chen P, Gurbuxani S, Arnovitz S, Li Y, Li S, Strong J, Neilly MB, Larson RA, Jiang X, Zhang P, Jin J, He C, Chen J. FTO Plays an Oncogenic Role in Acute Myeloid Leukemia as a N 6-Methyladenosine RNA Demethylase. Cancer Cell 2017; 31:127-141. [PMID: 28017614 PMCID: PMC5234852 DOI: 10.1016/j.ccell.2016.11.017] [Citation(s) in RCA: 1062] [Impact Index Per Article: 151.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 06/02/2016] [Accepted: 11/21/2016] [Indexed: 12/30/2022]
Abstract
N6-Methyladenosine (m6A) represents the most prevalent internal modification in mammalian mRNAs. Despite its functional importance in various fundamental bioprocesses, the studies of m6A in cancer have been limited. Here we show that FTO, as an m6A demethylase, plays a critical oncogenic role in acute myeloid leukemia (AML). FTO is highly expressed in AMLs with t(11q23)/MLL rearrangements, t(15;17)/PML-RARA, FLT3-ITD, and/or NPM1 mutations. FTO enhances leukemic oncogene-mediated cell transformation and leukemogenesis, and inhibits all-trans-retinoic acid (ATRA)-induced AML cell differentiation, through regulating expression of targets such as ASB2 and RARA by reducing m6A levels in these mRNA transcripts. Collectively, our study demonstrates the functional importance of the m6A methylation and the corresponding proteins in cancer, and provides profound insights into leukemogenesis and drug response.
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Affiliation(s)
- Zejuan Li
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Hengyou Weng
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45219, USA
| | - Rui Su
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45219, USA
| | - Xiaocheng Weng
- Departments of Chemistry, Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA; College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Hubei, Wuhan 430072, PR China
| | - Zhixiang Zuo
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45219, USA; Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Chenying Li
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45219, USA; Key Laboratory of Hematopoietic Malignancies, Department of Hematology, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Huilin Huang
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45219, USA
| | - Sigrid Nachtergaele
- Departments of Chemistry, Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA
| | - Lei Dong
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45219, USA
| | - Chao Hu
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45219, USA; Key Laboratory of Hematopoietic Malignancies, Department of Hematology, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Xi Qin
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45219, USA
| | - Lichun Tang
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yungui Wang
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45219, USA; Key Laboratory of Hematopoietic Malignancies, Department of Hematology, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Gia-Ming Hong
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Hao Huang
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Xiao Wang
- Departments of Chemistry, Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA
| | - Ping Chen
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Sandeep Gurbuxani
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Stephen Arnovitz
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Yuanyuan Li
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Shenglai Li
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Jennifer Strong
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45219, USA
| | - Mary Beth Neilly
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Richard A Larson
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Xi Jiang
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45219, USA
| | - Pumin Zhang
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jie Jin
- Key Laboratory of Hematopoietic Malignancies, Department of Hematology, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Chuan He
- Departments of Chemistry, Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA.
| | - Jianjun Chen
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45219, USA.
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632
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Rintala-Dempsey AC, Kothe U. Eukaryotic stand-alone pseudouridine synthases - RNA modifying enzymes and emerging regulators of gene expression? RNA Biol 2017; 14:1185-1196. [PMID: 28045575 PMCID: PMC5699540 DOI: 10.1080/15476286.2016.1276150] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
For a long time, eukaryotic stand-alone pseudouridine synthases (Pus enzymes) were neglected as non-essential enzymes adding seemingly simple modifications to tRNAs and small nuclear RNAs. Most studies were limited to the identification and initial characterization of the yeast Pus enzymes. However, recent transcriptome-wide mapping of pseudouridines in yeast and humans revealed pervasive modification of mRNAs and other non-coding RNAs by Pus enzymes which is dynamically regulated in response to cellular stress. Moreover, mutations in at least 2 genes encoding human Pus enzymes cause inherited diseases affecting muscle and brain function. Together, the recent findings suggest a broader-than-anticipated role of the Pus enzymes which are emerging as potential regulators of gene expression. In this review, we summarize the current knowledge on Pus enzymes, generate hypotheses regarding their cellular function and outline future areas of research of pseudouridine synthases.
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Affiliation(s)
- Anne C Rintala-Dempsey
- a Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry , University of Lethbridge , Lethbridge , AB , Canada
| | - Ute Kothe
- a Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry , University of Lethbridge , Lethbridge , AB , Canada
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633
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Techniques for Single-Molecule mRNA Imaging in Living Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 978:425-441. [DOI: 10.1007/978-3-319-53889-1_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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634
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Xie LJ, Wang RL, Wang D, Liu L, Cheng L. Visible-light-mediated oxidative demethylation of N6-methyl adenines. Chem Commun (Camb) 2017; 53:10734-10737. [DOI: 10.1039/c7cc05544g] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A novel solution for the chemical modulation of RNA epigenetics via biologically compatible photo-catalysis under visible light irradiation has been described.
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Affiliation(s)
- Li-Jun Xie
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- CAS Key Laboratory of Molecular Recognition and Function
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Rui-Li Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- CAS Key Laboratory of Molecular Recognition and Function
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Dong Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- CAS Key Laboratory of Molecular Recognition and Function
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Li Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- CAS Key Laboratory of Molecular Recognition and Function
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- CAS Key Laboratory of Molecular Recognition and Function
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
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635
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Weinberg DE, Gross JD. Molecular biology: Messenger RNAs marked for longer life. Nature 2016; 541:293-294. [PMID: 28002405 DOI: 10.1038/nature21109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- David E Weinberg
- Department of Cellular and Molecular Pharmacology, and in the Sandler Faculty Fellows Program, University of California, San Francisco, San Francisco, California 94143, USA
| | - John D Gross
- Department of Cellular and Molecular Pharmacology, and in the Sandler Faculty Fellows Program, University of California, San Francisco, San Francisco, California 94143, USA
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636
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Abstract
The re-emergence of Zika virus (ZIKV) and its suspected link with various disorders in newborns and adults led the World Health Organization to declare a global health emergency. In response, the stem cell field quickly established platforms for modeling ZIKV exposure using human pluripotent stem cell-derived neural progenitors and brain organoids, fetal tissues, and animal models. These efforts provided significant insight into cellular targets, pathogenesis, and underlying biological mechanisms of ZIKV infection as well as platforms for drug testing. Here we review the remarkable progress in stem cell-based ZIKV research and discuss current challenges and future opportunities.
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Affiliation(s)
- Guo-Li Ming
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Hengli Tang
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Hongjun Song
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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637
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Interactions between the HIV-1 Unspliced mRNA and Host mRNA Decay Machineries. Viruses 2016; 8:v8110320. [PMID: 27886048 PMCID: PMC5127034 DOI: 10.3390/v8110320] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 11/12/2016] [Accepted: 11/14/2016] [Indexed: 02/06/2023] Open
Abstract
The human immunodeficiency virus type-1 (HIV-1) unspliced transcript is used both as mRNA for the synthesis of structural proteins and as the packaged genome. Given the presence of retained introns and instability AU-rich sequences, this viral transcript is normally retained and degraded in the nucleus of host cells unless the viral protein REV is present. As such, the stability of the HIV-1 unspliced mRNA must be particularly controlled in the nucleus and the cytoplasm in order to ensure proper levels of this viral mRNA for translation and viral particle formation. During its journey, the HIV-1 unspliced mRNA assembles into highly specific messenger ribonucleoproteins (mRNPs) containing many different host proteins, amongst which are well-known regulators of cytoplasmic mRNA decay pathways such as up-frameshift suppressor 1 homolog (UPF1), Staufen double-stranded RNA binding protein 1/2 (STAU1/2), or components of miRNA-induced silencing complex (miRISC) and processing bodies (PBs). More recently, the HIV-1 unspliced mRNA was shown to contain N⁶-methyladenosine (m⁶A), allowing the recruitment of YTH N⁶-methyladenosine RNA binding protein 2 (YTHDF2), an m⁶A reader host protein involved in mRNA decay. Interestingly, these host proteins involved in mRNA decay were shown to play positive roles in viral gene expression and viral particle assembly, suggesting that HIV-1 interacts with mRNA decay components to successfully accomplish viral replication. This review summarizes the state of the art in terms of the interactions between HIV-1 unspliced mRNA and components of different host mRNA decay machineries.
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638
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Abstract
Cells adapt to their environment by linking external stimuli to an intricate network of transcriptional, post-transcriptional and translational processes. Among these, mechanisms that couple environmental cues to the regulation of protein translation are not well understood. Chemical modifications of RNA allow rapid cellular responses to external stimuli by modulating a wide range of fundamental biochemical properties and processes, including the stability, splicing and translation of messenger RNA. In this Review, we focus on the occurrence of N6-methyladenosine (m6A), 5-methylcytosine (m5C) and pseudouridine (Ψ) in RNA, and describe how these RNA modifications are implicated in regulating pluripotency, stem cell self-renewal and fate specification. Both post-transcriptional modifications and the enzymes that catalyse them modulate stem cell differentiation pathways and are essential for normal development.
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Affiliation(s)
- Michaela Frye
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Sandra Blanco
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- CIC bioGUNE, Bizkaia Technology Park, Building 801A, Derio, Bizkaia 48160, Spain
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639
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Fullard JF, Halene TB, Giambartolomei C, Haroutunian V, Akbarian S, Roussos P. Understanding the genetic liability to schizophrenia through the neuroepigenome. Schizophr Res 2016; 177:115-124. [PMID: 26827128 PMCID: PMC4963306 DOI: 10.1016/j.schres.2016.01.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/14/2016] [Accepted: 01/18/2016] [Indexed: 12/17/2022]
Abstract
The Psychiatric Genomics Consortium-Schizophrenia Workgroup (PGC-SCZ) recently identified 108 loci associated with increased risk for schizophrenia (SCZ). The vast majority of these variants reside within non-coding sequences of the genome and are predicted to exert their effects by affecting the mechanism of action of cis regulatory elements (CREs), such as promoters and enhancers. Although a number of large-scale collaborative efforts (e.g. ENCODE) have achieved a comprehensive mapping of CREs in human cell lines or tissue homogenates, it is becoming increasingly evident that many risk-associated variants are enriched for expression Quantitative Trait Loci (eQTLs) and CREs in specific tissues or cells. As such, data derived from previous research endeavors may not capture fully cell-type and/or region specific changes associated with brain diseases. Coupling recent technological advances in genomics with cell-type specific methodologies, we are presented with an unprecedented opportunity to better understand the genetics of normal brain development and function and, in turn, the molecular basis of neuropsychiatric disorders. In this review, we will outline ongoing efforts towards this goal and will discuss approaches with the potential to shed light on the mechanism(s) of action of cell-type specific cis regulatory elements and their putative roles in disease, with particular emphasis on understanding the manner in which the epigenome and CREs influence the etiology of SCZ.
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Affiliation(s)
- John F. Fullard
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tobias B. Halene
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Mental Illness Research, Education, and Clinical Center (VISN 3), James J. Peters VA Medical Center, Bronx, NY, USA
| | | | - Vahram Haroutunian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Mental Illness Research, Education, and Clinical Center (VISN 3), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mental Illness Research, Education, and Clinical Center (VISN 3), James J. Peters VA Medical Center, Bronx, NY, USA.
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640
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Wang Y, Zhao JC. Update: Mechanisms Underlying N 6-Methyladenosine Modification of Eukaryotic mRNA. Trends Genet 2016; 32:763-773. [PMID: 27793360 DOI: 10.1016/j.tig.2016.09.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/27/2016] [Accepted: 09/30/2016] [Indexed: 12/19/2022]
Abstract
Eukaryotic mRNA undergoes chemical modification both at the 5' cap and internally. Among internal modifications, N6-methyladensone (m6A), by far the most abundant, is present in all eukaryotes examined so far, including mammals, flies, plants, and yeast. m6A modification has an essential role in diverse biological processes. Over the past few years, our knowledge relevant to the establishment and function of this modification has grown rapidly. In this review, we focus on technologies that have facilitated m6A detection in mRNAs, the identification of m6A methylation enzymes and binding proteins, and potential functions of the modification at the molecular level.
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Affiliation(s)
- Yang Wang
- Tumor Initiation And Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jing Crystal Zhao
- Tumor Initiation And Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
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641
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N6-Methyladenosine in Flaviviridae Viral RNA Genomes Regulates Infection. Cell Host Microbe 2016; 20:654-665. [PMID: 27773535 PMCID: PMC5123813 DOI: 10.1016/j.chom.2016.09.015] [Citation(s) in RCA: 337] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/31/2016] [Accepted: 09/28/2016] [Indexed: 01/01/2023]
Abstract
The RNA modification N6-methyladenosine (m6A) post-transcriptionally regulates RNA function. The cellular machinery that controls m6A includes methyltransferases and demethylases that add or remove this modification, as well as m6A-binding YTHDF proteins that promote the translation or degradation of m6A-modified mRNA. We demonstrate that m6A modulates infection by hepatitis C virus (HCV). Depletion of m6A methyltransferases or an m6A demethylase, respectively, increases or decreases infectious HCV particle production. During HCV infection, YTHDF proteins relocalize to lipid droplets, sites of viral assembly, and their depletion increases infectious viral particles. We further mapped m6A sites across the HCV genome and determined that inactivating m6A in one viral genomic region increases viral titer without affecting RNA replication. Additional mapping of m6A on the RNA genomes of other Flaviviridae, including dengue, Zika, yellow fever, and West Nile virus, identifies conserved regions modified by m6A. Altogether, this work identifies m6A as a conserved regulatory mark across Flaviviridae genomes. The RNA genomes of HCV, ZIKV, DENV, YFV, and WNV contain m6A modification The cellular m6A machinery regulates HCV infectious particle production YTHDF proteins reduce HCV particle production and localize at viral assembly sites m6A-abrogating mutations in HCV E1 increase infectious particle production
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642
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Liu F, Clark W, Luo G, Wang X, Fu Y, Wei J, Wang X, Hao Z, Dai Q, Zheng G, Ma H, Han D, Evans M, Klungland A, Pan T, He C. ALKBH1-Mediated tRNA Demethylation Regulates Translation. Cell 2016; 167:816-828.e16. [PMID: 27745969 DOI: 10.1016/j.cell.2016.09.038] [Citation(s) in RCA: 301] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 08/14/2016] [Accepted: 09/22/2016] [Indexed: 12/27/2022]
Abstract
tRNA is a central component of protein synthesis and the cell signaling network. One salient feature of tRNA is its heavily modified status, which can critically impact its function. Here, we show that mammalian ALKBH1 is a tRNA demethylase. It mediates the demethylation of N1-methyladenosine (m1A) in tRNAs. The ALKBH1-catalyzed demethylation of the target tRNAs results in attenuated translation initiation and decreased usage of tRNAs in protein synthesis. This process is dynamic and responds to glucose availability to affect translation. Our results uncover reversible methylation of tRNA as a new mechanism of post-transcriptional gene expression regulation.
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Affiliation(s)
- Fange Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Wesley Clark
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Guanzheng Luo
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Xiaoyun Wang
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Ye Fu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Jiangbo Wei
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Xiao Wang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Ziyang Hao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Qing Dai
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Guanqun Zheng
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Honghui Ma
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Dali Han
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Molly Evans
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, 0027 Oslo, Norway; Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
| | - Tao Pan
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA.
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA.
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643
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Chen CYA, Shyu AB. Emerging Themes in Regulation of Global mRNA Turnover in cis. Trends Biochem Sci 2016; 42:16-27. [PMID: 27647213 DOI: 10.1016/j.tibs.2016.08.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 11/25/2022]
Abstract
mRNA is the molecule that conveys genetic information from DNA to the translation apparatus. mRNAs in all organisms display a wide range of stability, and mechanisms have evolved to selectively and differentially regulate individual mRNA stability in response to intracellular and extracellular cues. In recent years, three seemingly distinct aspects of RNA biology-mRNA N6-methyladenosine (m6A) modification, alternative 3' end processing and polyadenylation (APA), and mRNA codon usage-have been linked to mRNA turnover, and all three aspects function to regulate global mRNA stability in cis. Here, we discuss the discovery and molecular dissection of these mechanisms in relation to how they impact the intrinsic decay rate of mRNA in eukaryotes, leading to transcriptome reprogramming.
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Affiliation(s)
- Chyi-Ying A Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ann-Bin Shyu
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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644
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Bar-Yaacov D, Frumkin I, Yashiro Y, Chujo T, Ishigami Y, Chemla Y, Blumberg A, Schlesinger O, Bieri P, Greber B, Ban N, Zarivach R, Alfonta L, Pilpel Y, Suzuki T, Mishmar D. Mitochondrial 16S rRNA Is Methylated by tRNA Methyltransferase TRMT61B in All Vertebrates. PLoS Biol 2016; 14:e1002557. [PMID: 27631568 PMCID: PMC5025228 DOI: 10.1371/journal.pbio.1002557] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 08/19/2016] [Indexed: 11/19/2022] Open
Abstract
The mitochondrial ribosome, which translates all mitochondrial DNA (mtDNA)-encoded proteins, should be tightly regulated pre- and post-transcriptionally. Recently, we found RNA-DNA differences (RDDs) at human mitochondrial 16S (large) rRNA position 947 that were indicative of post-transcriptional modification. Here, we show that these 16S rRNA RDDs result from a 1-methyladenosine (m1A) modification introduced by TRMT61B, thus being the first vertebrate methyltransferase that modifies both tRNA and rRNAs. m1A947 is conserved in humans and all vertebrates having adenine at the corresponding mtDNA position (90% of vertebrates). However, this mtDNA base is a thymine in 10% of the vertebrates and a guanine in the 23S rRNA of 95% of bacteria, suggesting alternative evolutionary solutions. m1A, uridine, or guanine may stabilize the local structure of mitochondrial and bacterial ribosomes. Experimental assessment of genome-edited Escherichia coli showed that unmodified adenine caused impaired protein synthesis and growth. Our findings revealed a conserved mechanism of rRNA modification that has been selected instead of DNA mutations to enable proper mitochondrial ribosome function. Two solutions were selected during evolution to allow proper function of the vertebrate mitochondrial 16S ribosomal RNAeither RNA methylation by a tRNA methyltransferase or ancient evolutionary mutation. RNA modifications constitute an important layer of information, with functional implications that are not written in the underlying DNA sequence. Recently, we observed an apparent RNA-DNA difference (RDD) at position 947 of the human mitochondrial 16S ribosomal RNA (rRNA), but its nature and mechanism were unclear. Here we show that this disparity reflects an m1A modification (methylation at position 1 of the adenine moiety), and demonstrated by a combination of knock-down experiments in cells and in vitro methylation assays that the tRNA methyltransferase TRMT61B is the best candidate enzyme to introduce this modification. We also show that this modification is present in most of the 16S rRNA molecules in isolated mitochondrial ribosomes, and that it occurs in all vertebrates with an adenine (90% of the vertebrates), but not in those with a thymidine at this 16S rRNA position. Finally, as the first step towards understanding the functional importance of this rRNA modification, we used a genome-edited bacterial system to demonstrate that an unmodified adenine reduced the growth and translation rates of the bacteria as compared to both wild-type bacteria and mutant bacteria with a thymidine in the relevant position. Hence, three solutions were selected during evolution to allow proper function of the mitochondrial 16S rRNA—either RNA modification or two alternative ancient evolutionary DNA mutations.
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Affiliation(s)
- Dan Bar-Yaacov
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Idan Frumkin
- Department of Molecular Genetics, the Weizmann Institute of Science, Rehovot, Israel
| | - Yuka Yashiro
- Department of Chemistry and Biotechnology, University of Tokyo, Tokyo, Japan
| | - Takeshi Chujo
- Department of Chemistry and Biotechnology, University of Tokyo, Tokyo, Japan
| | - Yuma Ishigami
- Department of Chemistry and Biotechnology, University of Tokyo, Tokyo, Japan
| | - Yonatan Chemla
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The Ilse Katz Institute for Nanoscale Science and Technology, Beer Sheva, Israel
| | - Amit Blumberg
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Orr Schlesinger
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The Ilse Katz Institute for Nanoscale Science and Technology, Beer Sheva, Israel
| | - Philipp Bieri
- Department of Biology, Institute of Molecular Biology and Biophysics, Zurich, Switzerland
| | - Basil Greber
- Department of Biology, Institute of Molecular Biology and Biophysics, Zurich, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, Zurich, Switzerland
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Lital Alfonta
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The Ilse Katz Institute for Nanoscale Science and Technology, Beer Sheva, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, the Weizmann Institute of Science, Rehovot, Israel
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, University of Tokyo, Tokyo, Japan
- * E-mail: (DM); (TS)
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- * E-mail: (DM); (TS)
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645
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Śledź P, Jinek M. Structural insights into the molecular mechanism of the m(6)A writer complex. eLife 2016; 5. [PMID: 27627798 PMCID: PMC5023411 DOI: 10.7554/elife.18434] [Citation(s) in RCA: 367] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/01/2016] [Indexed: 12/27/2022] Open
Abstract
Methylation of adenosines at the N(6) position (m(6)A) is a dynamic and abundant epitranscriptomic mark that regulates critical aspects of eukaryotic RNA metabolism in numerous biological processes. The RNA methyltransferases METTL3 and METTL14 are components of a multisubunit m(6)A writer complex whose enzymatic activity is substantially higher than the activities of METTL3 or METTL14 alone. The molecular mechanism underpinning this synergistic effect is poorly understood. Here we report the crystal structure of the catalytic core of the human m(6)A writer complex comprising METTL3 and METTL14. The structure reveals the heterodimeric architecture of the complex and donor substrate binding by METTL3. Structure-guided mutagenesis indicates that METTL3 is the catalytic subunit of the complex, whereas METTL14 has a degenerate active site and plays non-catalytic roles in maintaining complex integrity and substrate RNA binding. These studies illuminate the molecular mechanism and evolutionary history of eukaryotic m(6)A modification in post-transcriptional genome regulation.
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Affiliation(s)
- Paweł Śledź
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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646
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Xie P, Zang LQ, Li XK, Shu Q. An epigenetic view of developmental diseases: new targets, new therapies. World J Pediatr 2016; 12:291-297. [PMID: 27351564 DOI: 10.1007/s12519-016-0020-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 05/21/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Function of epigenetic modifications is one of the most competitive fields in life science. Over the past several decades, it has been revealed that epigenetic modifications play essential roles in development and diseases including developmental diseases. In the present review, we summarize the recent progress about the function of epigenetic regulation, especially DNA and RNA modifications in developmental diseases. DATA SOURCES Original research articles and literature reviews published in PubMed-indexed journals. RESULTS DNA modifications including methylation and demethylation can regulate gene expression, and are involved in development and multiple diseases including Rett syndrome, Autism spectrum disorders, congenital heart disease and cancer, etc. RNA methylation and demethylation play important roles in RNA processing, reprogramming, circadian, and neuronal activity, and then modulate development. CONCLUSIONS DNA and RNA modifications play important roles in development and diseases through regulating gene expression. Epigenetic components could serve as novel targets for the treatment of developmental diseases.
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Affiliation(s)
- Pei Xie
- Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Li-Qun Zang
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xue-Kun Li
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Qiang Shu
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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647
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Honigberg SM. Similar environments but diverse fates: Responses of budding yeast to nutrient deprivation. MICROBIAL CELL 2016; 3:302-328. [PMID: 27917388 PMCID: PMC5134742 DOI: 10.15698/mic2016.08.516] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Diploid budding yeast (Saccharomyces cerevisiae) can adopt one
of several alternative differentiation fates in response to nutrient limitation,
and each of these fates provides distinct biological functions. When different
strain backgrounds are taken into account, these various fates occur in response
to similar environmental cues, are regulated by the same signal transduction
pathways, and share many of the same master regulators. I propose that the
relationships between fate choice, environmental cues and signaling pathways are
not Boolean, but involve graded levels of signals, pathway activation and
master-regulator activity. In the absence of large differences between
environmental cues, small differences in the concentration of cues may be
reinforced by cell-to-cell signals. These signals are particularly essential for
fate determination within communities, such as colonies and biofilms, where fate
choice varies dramatically from one region of the community to another. The lack
of Boolean relationships between cues, signaling pathways, master regulators and
cell fates may allow yeast communities to respond appropriately to the wide
range of environments they encounter in nature.
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Affiliation(s)
- Saul M Honigberg
- Division of Cell Biology and Biophysics, University of Missouri-Kansas City, 5007 Rockhill Rd, Kansas City MO 64110, USA
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648
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Patil KM, Chen G. Recognition of RNA Sequence and Structure by Duplex and Triplex Formation: Targeting miRNA and Pre-miRNA. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-3-319-34175-0_13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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649
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Shojaei Saadi HA, Gagné D, Fournier É, Baldoceda Baldeon LM, Sirard MA, Robert C. Responses of bovine early embryos to S-adenosyl methionine supplementation in culture. Epigenomics 2016; 8:1039-60. [PMID: 27419740 DOI: 10.2217/epi-2016-0022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM There is a growing concern about the potential adverse effects of high dose folic acid (FA) supplementation before and during pregnancy. FA metabolism generates S-adenosyl methionine (SAM) which is an important cofactor of epigenetic programming. We sought to assess the impact of a large dose of SAM on early embryo development. MATERIALS & METHODS In vitro cultured bovine embryos were treated with SAM from the eight-cell stage to the blastocyst stage. In addition to the phenotype, the genome-wide epigenetic and transcription profiles were analyzed. RESULTS Treatment significantly improved embryo hatching and caused a shift in sex ratio in favor of males. SAM caused genome-wide hypermethylation mainly in exonic regions and in CpG islands. Although differentially expressed genes were associated with response to nutrients and developmental processes, no correspondence was found with the differentially methylated regions, suggesting that cellular responses to SAM treatment during early embryo development may not require DNA methylation-driven changes. CONCLUSION Since bovine embryos were not indifferent to SAM, effects of large-dose FA supplements on early embryonic development in humans cannot be ruled out.
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Affiliation(s)
- Habib A Shojaei Saadi
- Centre de recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des sciences animales, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Dominic Gagné
- Centre de recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des sciences animales, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Éric Fournier
- Centre de recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des sciences animales, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Luis Manuel Baldoceda Baldeon
- Centre de recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des sciences animales, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Marc-André Sirard
- Centre de recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des sciences animales, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Claude Robert
- Centre de recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des sciences animales, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, G1V 0A6, Canada
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650
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Shen L, Liang Z, Gu X, Chen Y, Teo ZWN, Hou X, Cai WM, Dedon PC, Liu L, Yu H. N(6)-Methyladenosine RNA Modification Regulates Shoot Stem Cell Fate in Arabidopsis. Dev Cell 2016; 38:186-200. [PMID: 27396363 DOI: 10.1016/j.devcel.2016.06.008] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/28/2016] [Accepted: 06/07/2016] [Indexed: 01/07/2023]
Abstract
N(6)-Methyladenosine (m(6)A) represents the most prevalent internal modification on mRNA and requires a multicomponent m(6)A methyltransferase complex in mammals. How their plant counterparts determine the global m(6)A modification landscape and its molecular link to plant development remain unknown. Here we show that FKBP12 INTERACTING PROTEIN 37 KD (FIP37) is a core component of the m(6)A methyltransferase complex, which underlies control of shoot stem cell fate in Arabidopsis. The mutants lacking FIP37 exhibit massive overproliferation of shoot meristems and a transcriptome-wide loss of m(6)A RNA modifications. We further demonstrate that FIP37 mediates m(6)A RNA modification on key shoot meristem genes inversely correlated with their mRNA stability, thus confining their transcript levels to prevent shoot meristem overproliferation. Our results suggest an indispensable role of FIP37 in mediating m(6)A mRNA modification, which is required for maintaining the shoot meristem as a renewable source for continuously producing all aerial organs in plants.
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Affiliation(s)
- Lisha Shen
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 10 Science Drive 4, Singapore 117543, Singapore
| | - Zhe Liang
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 10 Science Drive 4, Singapore 117543, Singapore
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ying Chen
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 10 Science Drive 4, Singapore 117543, Singapore
| | - Zhi Wei Norman Teo
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 10 Science Drive 4, Singapore 117543, Singapore
| | - Xingliang Hou
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Weiling Maggie Cai
- Singapore-MIT Alliance for Research and Technology, Campus for Research Excellence and Technical Enterprise (CREATE), Singapore 138602, Singapore
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Campus for Research Excellence and Technical Enterprise (CREATE), Singapore 138602, Singapore
| | - Lu Liu
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 10 Science Drive 4, Singapore 117543, Singapore
| | - Hao Yu
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 10 Science Drive 4, Singapore 117543, Singapore.
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