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Kim J, Muraoka M, Okada H, Toyoda A, Ajima R, Saga Y. The RNA helicase DDX6 controls early mouse embryogenesis by repressing aberrant inhibition of BMP signaling through miRNA-mediated gene silencing. PLoS Genet 2022; 18:e1009967. [PMID: 36197846 PMCID: PMC9534413 DOI: 10.1371/journal.pgen.1009967] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 08/11/2022] [Indexed: 11/29/2022] Open
Abstract
The evolutionarily conserved RNA helicase DDX6 is a central player in post-transcriptional regulation, but its role during embryogenesis remains elusive. We here show that DDX6 enables proper cell lineage specification from pluripotent cells by analyzing Ddx6 knockout (KO) mouse embryos and employing an in vitro epiblast-like cell (EpiLC) induction system. Our study unveils that DDX6 is an important BMP signaling regulator. Deletion of Ddx6 causes the aberrant upregulation of the negative regulators of BMP signaling, which is accompanied by enhanced expression of Nodal and related genes. Ddx6 KO pluripotent cells acquire higher pluripotency with a strong inclination toward neural lineage commitment. During gastrulation, abnormally expanded Nodal and Eomes expression in the primitive streak likely promotes endoderm cell fate specification while inhibiting mesoderm differentiation. We also genetically dissected major DDX6 pathways by generating Dgcr8, Dcp2, and Eif4enif1 KO models in addition to Ddx6 KO. We found that the miRNA pathway mutant Dgcr8 KO phenocopies Ddx6 KO, indicating that DDX6 mostly works along with the miRNA pathway during early development, whereas its P-body-related functions are dispensable. Therefore, we conclude that DDX6 prevents aberrant upregulation of BMP signaling inhibitors by participating in miRNA-mediated gene silencing processes. Overall, this study delineates how DDX6 affects the development of the three primary germ layers during early mouse embryogenesis and the underlying mechanism of DDX6 function.
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Affiliation(s)
- Jessica Kim
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Masafumi Muraoka
- Mammalian Development Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
| | - Hajime Okada
- Mammalian Development Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Rieko Ajima
- Mammalian Development Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Japan
- * E-mail: (RA); (YS)
| | - Yumiko Saga
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Mammalian Development Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Japan
- * E-mail: (RA); (YS)
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2
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A novel mRNA decay inhibitor abolishes pathophysiological cellular transition. Cell Death Dis 2022; 8:278. [PMID: 35672286 PMCID: PMC9174231 DOI: 10.1038/s41420-022-01076-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 11/30/2022]
Abstract
In cells, mRNA synthesis and decay are influenced by each other, and their balance is altered by either external or internal cues, resulting in changes in cell dynamics. We previously reported that it is important that an array of mRNAs that shape a phenotype are degraded before cellular transitions, such as cellular reprogramming and differentiation. In adipogenesis, the interaction between DDX6 and 4E-T had a definitive impact on the pathway in the processing body (PB). We screened a library of α-helix analogs with an alkaloid-like backbone to identify compounds that inhibit the binding between DDX6 and 4E-T proteins, which occurs between the α-helix of structured and internally disordered proteins. IAMC-00192 was identified as a lead compound. This compound directly inhibited the interaction between DDX6 and 4E-T. IAMC-00192 inhibited the temporal increase in PB formation that occurs during adipogenesis and epithelial-mesenchymal transition (EMT) and significantly suppressed these cellular transitions. In the EMT model, the half-life of preexisting mRNAs in PBs was extended twofold by the compound. The novel inhibitor of RNA decay not only represents a potentially useful tool to analyze in detail the pathological conditions affected by RNA decay and how it regulates the pathological state. The identification of this inhibitor may lead to the discovery of a first-in-class RNA decay inhibitor drug. ![]()
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Ma G, Babarinde IA, Zhou X, Hutchins AP. Transposable Elements in Pluripotent Stem Cells and Human Disease. Front Genet 2022; 13:902541. [PMID: 35719395 PMCID: PMC9201960 DOI: 10.3389/fgene.2022.902541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/20/2022] [Indexed: 11/18/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that can randomly integrate into other genomic sites. They have successfully replicated and now occupy around 40% of the total DNA sequence in humans. TEs in the genome have a complex relationship with the host cell, being both potentially deleterious and advantageous at the same time. Only a tiny minority of TEs are still capable of transposition, yet their fossilized sequence fragments are thought to be involved in various molecular processes, such as gene transcriptional activity, RNA stability and subcellular localization, and chromosomal architecture. TEs have also been implicated in biological processes, although it is often hard to reveal cause from correlation due to formidable technical issues in analyzing TEs. In this review, we compare and contrast two views of TE activity: one in the pluripotent state, where TEs are broadly beneficial, or at least mechanistically useful, and a second state in human disease, where TEs are uniformly considered harmful.
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Suthapot P, Xiao T, Felsenfeld G, Hongeng S, Wongtrakoongate P. The RNA helicases DDX5 and DDX17 facilitate neural differentiation of human pluripotent stem cells NTERA2. Life Sci 2022; 291:120298. [PMID: 35007564 DOI: 10.1016/j.lfs.2021.120298] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 12/21/2021] [Accepted: 12/31/2021] [Indexed: 12/31/2022]
Abstract
AIMS Understanding human neurogenesis is critical toward regenerative medicine for neurodegeneration. However, little is known how neural differentiation is regulated by DEAD box-containing RNA helicases, which comprise a diverse class of RNA remodeling enzymes. MATERIALS AND METHODS ChIP-seq was utilized to identify binding sites of DDX5 and DDX17 in both human pluripotent stem cell (hPSC) line NTERA2 and their retinoic acid-induced neural derivatives. RNA-seq was used to elucidate genes differentially expressed upon depletion of DDX5 and DDX17. Neurosphere assay, flow cytometry, and immunofluorescence staining were performed to test the effect of depletion of the two RNA helicases in neural differentiation. KEY FINDINGS We show here that expression of DDX5 and DDX17 is abundant throughout neural differentiation of NTERA2, and is mostly localized within the nucleus. The two RNA helicases occupy chromatin genome-wide at regions associated with neurogenesis-related genes in both hPSCs and their neural derivatives. Further, both DDX5 and DDX17 are mutually required for controlling transcriptional expression of these genes, but are not important for maintenance of stem cell state of hPSCs. In contrast, they facilitate early neural differentiation of hPSCs, generation of neurospheres from the stem cells, and transcriptional expression of key neurogenic transcription factors such as SOX1 and PAX6 during neural differentiation. Importantly, DDX5 and DDX17 are critical for differentiation of hPSCs toward NESTIN- and TUBB3-positive cells, which represent neural progenitors and mature neurons, respectively. SIGNIFICANCE Collectively, our findings suggest the role of DDX5 and DDX17 in transcriptional regulation of genes involved in neurogenesis, and hence in neural differentiation of hPSCs.
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Affiliation(s)
- Praewa Suthapot
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Tiaojiang Xiao
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda 20892-0540, MD, USA
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda 20892-0540, MD, USA
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Patompon Wongtrakoongate
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Center for Neuroscience, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
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Maeda R, Kami D, Shikuma A, Suzuki Y, Taya T, Matoba S, Gojo S. RNA decay in processing bodies is indispensable for adipogenesis. Cell Death Dis 2021; 12:285. [PMID: 33731683 PMCID: PMC7969960 DOI: 10.1038/s41419-021-03537-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 02/16/2021] [Accepted: 02/19/2021] [Indexed: 12/19/2022]
Abstract
The RNA decay pathway plays key regulatory roles in cell identities and differentiation processes. Although adipogenesis is transcriptionally and epigenetically regulated and has been thoroughly investigated, how RNA metabolism that contributes to the stability of phenotype-shaping transcriptomes participates in differentiation remains elusive. In this study, we investigated Ddx6, an essential component of processing bodies (PBs) that executes RNA decay and translational repression in the cytoplasm and participates in the cellular transition of reprogramming. Upon adipogenic induction, Ddx6 dynamically accumulated to form PBs with a binding partner, 4E-T, at the early phase prior to emergence of intracellular lipid droplets. In contrast, preadipocytes with Ddx6 knockout (KO) or 4E-T knockdown (KD) failed to generate PBs, resulting in significant suppression of adipogenesis. Transcription factors related to preadipocytes and negative regulators of adipogenesis that were not expressed under adipogenic stimulation were maintained in Ddx6-KO and 4E-T-KD preadipocytes under adipogenic induction. Elimination of Dlk1, a major negative regulator of adipogenesis, in 3T3L1 Ddx6-KO cells did not restore adipogenic differentiation capacity to any extent. Similar to murine cells, human primary mesenchymal stem cells, which can differentiate into adipocytes upon stimulation with adipogenic cocktails, required DDX6 to maturate into adipocytes. Therefore, RNA decay of the entire parental transcriptome, rather than removal of a strong negative regulator, could be indispensable for adipogenesis.
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Affiliation(s)
- Ryotaro Maeda
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Daisuke Kami
- Department of Regenerative Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Akira Shikuma
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yosuke Suzuki
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Toshihiko Taya
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoaki Matoba
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoshi Gojo
- Department of Regenerative Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan.
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Heck AM, Russo J, Wilusz J, Nishimura EO, Wilusz CJ. YTHDF2 destabilizes m 6A-modified neural-specific RNAs to restrain differentiation in induced pluripotent stem cells. RNA (NEW YORK, N.Y.) 2020; 26:739-755. [PMID: 32169943 PMCID: PMC7266156 DOI: 10.1261/rna.073502.119] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/12/2020] [Indexed: 06/10/2023]
Abstract
N6-methyladenosine (m6A) is an abundant post-transcriptional modification that can impact RNA fate via interactions with m6A-specific RNA binding proteins. Despite accumulating evidence that m6A plays an important role in modulating pluripotency, the influence of m6A reader proteins in pluripotency is less clear. Here, we report that YTHDF2, an m6A reader associated with mRNA degradation, is highly expressed in induced pluripotent stem cells (iPSCs) and down-regulated during neural differentiation. Through RNA sequencing, we identified a group of m6A-modified transcripts associated with neural development that are directly regulated by YTDHF2. Depletion of YTHDF2 in iPSCs leads to stabilization of these transcripts, loss of pluripotency, and induction of neural-specific gene expression. Collectively, our results suggest YTHDF2 functions to restrain expression of neural-specific mRNAs in iPSCs and facilitate their rapid and coordinated up-regulation during neural induction. These effects are both achieved by destabilization of the targeted transcripts.
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Affiliation(s)
- Adam M Heck
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
- Department of Microbiology, Immunology & Pathology
| | - Joseph Russo
- Department of Microbiology, Immunology & Pathology
| | - Jeffrey Wilusz
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
- Department of Microbiology, Immunology & Pathology
| | - Erin Osborne Nishimura
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Carol J Wilusz
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
- Department of Microbiology, Immunology & Pathology
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Chantarachot T, Sorenson RS, Hummel M, Ke H, Kettenburg AT, Chen D, Aiyetiwa K, Dehesh K, Eulgem T, Sieburth LE, Bailey-Serres J. DHH1/DDX6-like RNA helicases maintain ephemeral half-lives of stress-response mRNAs. NATURE PLANTS 2020; 6:675-685. [PMID: 32483330 DOI: 10.1038/s41477-020-0681-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 04/29/2020] [Indexed: 05/21/2023]
Abstract
Gene transcription is counterbalanced by messenger RNA decay processes that regulate transcript quality and quantity. We show here that the evolutionarily conserved DHH1/DDX6-like RNA hellicases of Arabidopsis thaliana control the ephemerality of a subset of cellular mRNAs. These RNA helicases co-localize with key markers of processing bodies and stress granules and contribute to their subcellular dynamics. They function to limit the precocious accumulation and ribosome association of stress-responsive mRNAs involved in auto-immunity and growth inhibition under non-stress conditions. Given the conservation of this RNA helicase subfamily, they may control basal levels of conditionally regulated mRNAs in diverse eukaryotes, accelerating responses without penalty.
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Affiliation(s)
- Thanin Chantarachot
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Reed S Sorenson
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Maureen Hummel
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Haiyan Ke
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Alek T Kettenburg
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Daniel Chen
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Karen Aiyetiwa
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Katayoon Dehesh
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Thomas Eulgem
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Leslie E Sieburth
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA.
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DDX6 Helicase Behavior and Protein Partners in Human Adipose Tissue-Derived Stem Cells during Early Adipogenesis and Osteogenesis. Int J Mol Sci 2020; 21:ijms21072607. [PMID: 32283676 PMCID: PMC7177724 DOI: 10.3390/ijms21072607] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/20/2022] Open
Abstract
DDX6 helicase is an RNA-binding protein involved in different aspects of gene expression regulation. The roles played by DDX6 depend on the complexes associated with it. Here, for the first time, we characterize the protein complexes associated with DDX6 in human adipose tissue-derived stem cells (hASCs) and analyze the dynamics of this helicase under different conditions of translational activity and differentiation. The results obtained demonstrated that the DDX6 helicase is associated with proteins involved in the control of mRNA localization, translation and metabolism in hASCs. DDX6 complexes may also assemble into more complex structures, such as RNA-dependent granules, the abundance and composition of which change upon inhibited translational activity. This finding supports the supposition that DDX6 is possibly involved in the regulation of the mRNA life cycle in hASCs. Although there was no significant variation in the protein composition of these complexes during early adipogenic or osteogenic induction, there was a change in the distribution pattern of DDX6: the number of DDX6 granules per cell was reduced during adipogenesis and was enhanced during osteogenesis.
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9
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Forrest ME, Pinkard O, Martin S, Sweet TJ, Hanson G, Coller J. Codon and amino acid content are associated with mRNA stability in mammalian cells. PLoS One 2020; 15:e0228730. [PMID: 32053646 PMCID: PMC7018022 DOI: 10.1371/journal.pone.0228730] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/21/2020] [Indexed: 12/31/2022] Open
Abstract
Messenger RNA (mRNA) degradation plays a critical role in regulating transcript levels in the cell and is a major control point for modulating gene expression. In yeast and other model organisms, codon identity is a powerful determinant of transcript stability, contributing broadly to impact half-lives. General principles governing mRNA stability are poorly understood in mammalian systems. Importantly, however, the degradation machinery is highly conserved, thus it seems logical that mammalian transcript half-lives would also be strongly influenced by coding determinants. Herein we characterize the contribution of coding sequence towards mRNA decay in human and Chinese Hamster Ovary cells. In agreement with previous studies, we observed that synonymous codon usage impacts mRNA stability in mammalian cells. Surprisingly, however, we also observe that the amino acid content of a gene is an additional determinant correlating with transcript stability. The impact of codon and amino acid identity on mRNA decay appears to be associated with underlying tRNA and intracellular amino acid concentrations. Accordingly, genes of similar physiological function appear to coordinate their mRNA stabilities in part through codon and amino acid content. Together, these results raise the possibility that intracellular tRNA and amino acid levels interplay to mediate coupling between translational elongation and mRNA degradation rate in mammals.
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Affiliation(s)
- Megan E. Forrest
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Otis Pinkard
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Sophie Martin
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Thomas J. Sweet
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Gavin Hanson
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Jeff Coller
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
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10
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Heck AM, Wilusz CJ. Small changes, big implications: The impact of m 6A RNA methylation on gene expression in pluripotency and development. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2019; 1862:194402. [PMID: 31325527 PMCID: PMC6742438 DOI: 10.1016/j.bbagrm.2019.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/21/2019] [Accepted: 07/12/2019] [Indexed: 12/20/2022]
Abstract
In order to maintain a state of self-renewal, yet retain the ability to rapidly differentiate in response to external signals, pluripotent cells exert tight control over gene expression at many levels. Recent studies have suggested that N6-methyladenosine (m6A) RNA methylation, one of the most abundant post-transcriptional modifications, is important for both pluripotency and differentiation. In this review, we summarize the current state of the m6A field, with emphasis on the impact of writers, erasers and readers of m6A on RNA metabolism and stem cell biology.
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Affiliation(s)
- Adam M Heck
- Program in Cell & Molecular Biology, and Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO 80525, United States of America
| | - Carol J Wilusz
- Program in Cell & Molecular Biology, and Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO 80525, United States of America.
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