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Liang M, Zhang L, Lai L, Li Z. Unraveling the role of Xist in X chromosome inactivation: insights from rabbit model and deletion analysis of exons and repeat A. Cell Mol Life Sci 2024; 81:156. [PMID: 38551746 PMCID: PMC10980640 DOI: 10.1007/s00018-024-05151-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 04/01/2024]
Abstract
X chromosome inactivation (XCI) is a process that equalizes the expression of X-linked genes between males and females. It relies on Xist, continuously expressed in somatic cells during XCI maintenance. However, how Xist impacts XCI maintenance and its functional motifs remain unclear. In this study, we conducted a comprehensive analysis of Xist, using rabbits as an ideal non-primate model. Homozygous knockout of exon 1, exon 6, and repeat A in female rabbits resulted in embryonic lethality. However, X∆ReAX females, with intact X chromosome expressing Xist, showed no abnormalities. Interestingly, there were no significant differences between females with homozygous knockout of exons 2-5 and wild-type rabbits, suggesting that exons 2, 3, 4, and 5 are less important for XCI. These findings provide evolutionary insights into Xist function.
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Affiliation(s)
- Mingming Liang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Lichao Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Liangxue Lai
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, 100039, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences, Guangzhou, 510530, China.
| | - Zhanjun Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
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2
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Yang J, Wang Y, Huang Z, Jiang Y, Pan X, Dong X, Yang G. Roles of rRNA N-methyladenosine modification in the function of ribosomes. Cell Biochem Funct 2023; 41:1106-1114. [PMID: 38041420 DOI: 10.1002/cbf.3891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/19/2023] [Accepted: 11/17/2023] [Indexed: 12/03/2023]
Abstract
The N-methyladenosine (m6A) modification of ribosomal RNA (rRNA) plays critical roles in regulating the function of ribosomes, the essential molecular machines that translate genetic information from mRNA into proteins. Specifically, m6A modification affects ribosome biogenesis, stability, and function by regulating the processing and maturation of rRNA, the assembly and composition of ribosomes, and the accuracy and efficiency of translation. Furthermore, m6A modification allows for dynamic regulation of translation in response to environmental and cellular signals. Therefore, a deeper understanding of the mechanisms and functions of m6A modification in rRNA will advance our knowledge of ribosome-mediated gene expression and facilitate the development of new therapeutic strategies for ribosome-related diseases.
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Affiliation(s)
- Jingyi Yang
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Yameng Wang
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Zekai Huang
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Yashuang Jiang
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Xiaolei Pan
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Xiaowei Dong
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Geng Yang
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
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3
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Krusnauskas R, Stakaitis R, Steponaitis G, Almstrup K, Vaitkiene P. Identification and comparison of m6A modifications in glioblastoma non-coding RNAs with MeRIP-seq and Nanopore dRNA-seq. Epigenetics 2023; 18:2163365. [PMID: 36597408 PMCID: PMC9980576 DOI: 10.1080/15592294.2022.2163365] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The most prominent RNA modification - N6-methyladenosine (m6A) - affects gene regulation and cancer progression. The extent and effect of m6A on long non-coding RNAs (lncRNAs) is, however, still not clear. The most established method for m6A detection is methylated RNA immunoprecipitation and sequencing (MeRIP-seq). However, Oxford Nanopore Technologies recently developed direct RNA-seq (dRNA-seq) method, allowing m6A identification at higher resolution and in its native form. We performed whole transcriptome sequencing of the glioblastoma cell line U87-MG with both MeRIP-seq and dRNA-seq. For MeRIP-seq, m6A peaks were identified using nf-core/chipseq, and for dRNA-seq - EpiNano pipeline. MeRIP-seq analysis revealed 5086 lncRNAs transcripts, while dRNA-seq identified 336 lncRNAs transcripts from which 556 and 198 were found to be m6A modified, respectively. While 24 lncRNAs with m6A overlapped between two methods. Gliovis database analysis revealed that the expression of the major part of identified overlapping lncRNAs was associated with glioma grade or patient survival prognosis. We found that the frequency of m6A occurrence in lncRNAs varied more than 9-fold throughout the provided list of 24 modified lncRNAs. The highest m6A frequency was detected in MIR1915HG, THAP9-AS1, MALAT1, NORAD1, and NEAT1 (49-88nt), while MIR99AHG, SNHG3, LOXL1-AS1, ILF3-DT showed the lowest m6A frequency (445-261nt). Taken together, (1) we provide a high accuracy list of 24 m6A modified lncRNAs of U87-MG cells; (2) we conclude that MeRIP-seq is more suitable for an initial m6A screening study, due to its higher lncRNA coverage, whereas dRNA-seq is most useful when more in-depth analysis of m6A quantity and precise location is of interest.Abbreviations: (dRNA-seq) direct RNA-seq, (GBM) glioblastoma, (LGG) low-grade glioma, (lncRNAs) long non-coding RNAs, (m6A) N6-methyladenosine, (MeRIP-seq) methylated RNA immunoprecipitation and sequencing, (ncRNA) non-coding RNA, (ONT) Oxford Nanopore Technologi; Lietuvos Mokslo Taryba.
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Affiliation(s)
- Raulas Krusnauskas
- Laboratory of Molecular Neurobiology, Neuroscience Institute, Lithuanian University of Health Sciences, Eiveniu str. 4, LT50161, Kaunas, Lithuania
| | - Rytis Stakaitis
- Laboratory of Molecular Neurooncology, Neuroscience Institute, Lithuanian University of Health Sciences, Eiveniu str. 4, LT50161, Kaunas, Lithuania
| | - Giedrius Steponaitis
- Laboratory of Molecular Neurooncology, Neuroscience Institute, Lithuanian University of Health Sciences, Eiveniu str. 4, LT50161, Kaunas, Lithuania
| | - Kristian Almstrup
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, GR-5064, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (Edmarc), Rigshospitalet, University of Copenhagen, GR-5064, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Paulina Vaitkiene
- Laboratory of Molecular Neurobiology, Neuroscience Institute, Lithuanian University of Health Sciences, Eiveniu str. 4, LT50161, Kaunas, Lithuania
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4
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Le Franc L, Petton B, Favrel P, Rivière G. m 6A Profile Dynamics Indicates Regulation of Oyster Development by m 6A-RNA Epitranscriptomes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:742-755. [PMID: 36496129 PMCID: PMC10787124 DOI: 10.1016/j.gpb.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/23/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
The N6-methylation of RNA adenosines (N6-methyladenosine, m6A) is an important regulator of gene expression with critical implications in vertebrate and insect development. However, the developmental significance of epitranscriptomes in lophotrochozoan organisms remains unknown. Using methylated RNA immunoprecipitation sequencing (MeRIP-seq), we generated transcriptome-wide m6A-RNA methylomes covering the entire development of the oyster from oocytes to juveniles. Oyster RNA classes display specific m6A signatures, with messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) exhibiting distinct profiles and being highly methylated compared to transposable element (TE) transcripts. Epitranscriptomes are dynamic and correspond to the chronological steps of development (cleavage, gastrulation, organogenesis, and metamorphosis), with minimal mRNA and lncRNA methylation at the morula stage followed by a global increase. mRNA m6A levels are correlated with transcript levels, and shifts in methylation profiles correspond to expression kinetics. Differentially methylated transcripts cluster according to embryo-larval stages and bear the corresponding developmental functions (cell division, signal transduction, morphogenesis, and cell differentiation). The m6A level of TE transcripts is also regulated and peaks during the gastrulation. We demonstrate that m6A-RNA methylomes are dynamic and associated with gene expression regulation during oyster development. The putative epitranscriptome implication in the cleavage, maternal-to-zygotic transition, and cell differentiation in a lophotrochozoan model brings new insights into the control and evolution of developmental processes.
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Affiliation(s)
- Lorane Le Franc
- Laboratoire de Biologie des Organismes et des Ecosystèmes Aquatiques (BOREA), Muséum d'Histoire Naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS UMR 8067, IRD, 14032 Caen, France
| | - Bruno Petton
- Ifremer, Laboratoire des Sciences de l'Environnement Marin, UMR 6539 CNRS/UBO/IRD/Ifremer, Centre Bretagne, 29280 Plouzané, France
| | - Pascal Favrel
- Laboratoire de Biologie des Organismes et des Ecosystèmes Aquatiques (BOREA), Muséum d'Histoire Naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS UMR 8067, IRD, 14032 Caen, France
| | - Guillaume Rivière
- Laboratoire de Biologie des Organismes et des Ecosystèmes Aquatiques (BOREA), Muséum d'Histoire Naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS UMR 8067, IRD, 14032 Caen, France.
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5
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Schwämmle T, Schulz EG. Regulatory principles and mechanisms governing the onset of random X-chromosome inactivation. Curr Opin Genet Dev 2023; 81:102063. [PMID: 37356341 PMCID: PMC10465972 DOI: 10.1016/j.gde.2023.102063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/27/2023]
Abstract
X-chromosome inactivation (XCI) has evolved in mammals to compensate for the difference in X-chromosomal dosage between the sexes. In placental mammals, XCI is initiated during early embryonic development through upregulation of the long noncoding RNA Xist from one randomly chosen X chromosome in each female cell. The Xist locus must thus integrate both X-linked and developmental trans-regulatory factors in a dosage-dependent manner. Furthermore, the two alleles must coordinate to ensure inactivation of exactly one X chromosome per cell. In this review, we summarize the regulatory principles that govern the onset of XCI. We go on to provide an overview over the factors that have been implicated in Xist regulation and discuss recent advances in our understanding of how Xist's cis-regulatory landscape integrates information in a precise fashion.
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Affiliation(s)
- Till Schwämmle
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany. https://twitter.com/@TSchwammle
| | - Edda G Schulz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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Zou X, Liu C, Wu X, Yuan Z, Yan F. Changes in N6-methyladenosine RNA methylomes of human periodontal ligament cells in response to inflammatory conditions. J Periodontal Res 2023; 58:444-455. [PMID: 36733232 DOI: 10.1111/jre.13105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/26/2022] [Accepted: 01/17/2023] [Indexed: 02/04/2023]
Abstract
OBJECTIVE To investigate the changes in the m6A methylation modification profile of human periodontal ligament cells (hPDLCs) in response to inflammatory conditions. BACKGROUND Periodontitis is an infectious disease of the periodontal support tissue that leads to the loss of alveolar bone. HPDLCs are primary cells that can repair periodontal tissue defects caused by periodontitis. However, the inflammatory conditions induce inflammatory damage and decrease ossification of hPDLCs. This inflammatory response depends on genetic and epigenetic mechanisms, including m6A methylation. METHODS HPDLCs were cultured with osteogenic induction medium (NC group), while TNF-α (10 ng/mL) and IL-1β (5 ng/mL) were added to simulate inflammatory conditions (Inflam group). Then RNA-seq and MeRIP-seq analyses were performed to identify m6A methylation modification in the transcriptome range of hPDLCs. RESULTS The results showed that the osteogenic differentiation of hPDLCs was inhibited under inflammatory conditions. RNA-seq analysis also revealed that the decreased genes in response to inflammatory conditions were primarily annotated in processes associated with ossification. Compared with the NC group, differentially m6A-methylated genes were primarily enriched in histone modification processes. Among 145 histone modification genes, 25 genes have been reported to be involved in the regulation of osteogenic differentiation, and they include KAT6B, EP300, BMI1, and KDMs (KDM1A, KDM2A, KDM3A, KDM4B, and KDM5A). CONCLUSION This study demonstrated that the m6A landscape of hPDLCs was changed in response to inflammation. M6A methylation differences among histone modification genes may act on the osteogenic differentiation of hPDLCs.
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Affiliation(s)
- Xihong Zou
- Department of Periodontology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Chaoyi Liu
- Hangzhou Stomatological Hospital, Hangzhou, China
| | - Xudong Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zhiyao Yuan
- Department of Periodontology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Fuhua Yan
- Department of Periodontology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
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7
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Gu Y, Wang Z, Wang R, Yang Y, Tong P, Lv S, Xiao L, Wang Z. N6-methyladenine regulator-mediated RNA methylation modification patterns in immune microenvironment regulation of osteoarthritis. Front Genet 2023; 14:1113515. [PMID: 36777725 PMCID: PMC9908960 DOI: 10.3389/fgene.2023.1113515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/13/2023] [Indexed: 01/27/2023] Open
Abstract
Background: Osteoarthritis is a common chronic degenerative disease, and recently, an increasing number of studies have shown that immunity plays an important role in the progression of osteoarthritis, which is exacerbated by local inflammation. The role of N6-methyladenine (m6A) modification in immunity is being explored. However, the role of m6A modification in regulating the immune microenvironment of osteoarthritis remains unknown. In this study, we sought to discuss the association between the N6-methyladenine (m6A) modification and the immune microenvironment of osteoarthritis. Methods: First, the data and gene expression profiles of 139 samples, including 33 healthy samples and 106 osteoarthritis samples, were obtained from the Genetics osteoARthritis and Progression (GARP) study. Then the differences in m6A regulators between healthy individuals and osteoarthritis patients were analyzed. The correlation between m6A regulators and immune characteristics was also investigated by single-sample gene set enrichment analysis (ssGSEA). Principal component analysis (PCA), Gene Set Variation Analysis (GSVA) enrichment analysis, weighted gene coexpression network analysis (WGCNA), and Associated R packages were used to identify the m6A phenotype and its biological functions. Results: A total of 23 m6A regulators were involved in this study. We found a close correlation between most m6A regulators in all samples as well as in osteoarthritis samples. VIRMA and LRPPRC were the most highly correlated m6A regulators and showed a positive correlation, whereas VIRMA and RBM15B were the most negatively correlated. M6A regulators are associated with osteoarthritis immune characteristics. For example, MDSC cell abundance was strongly correlated with RBM15B and HNRNPC. Meanwhile, RBM15B and HNRNPC were important effectors of natural killer cell immune responses. IGFBP3 is an important regulator of cytolytic activity immune function. We performed an unsupervised consensus cluster analysis of the osteoarthritis samples based on the expression of 23 m6A regulators. Three different m6A subtypes of osteoarthritis were identified, including 27 samples in subtype C1, 21 samples in subtype C2, and 58 samples in subtype C3. Different m6A subtypes have unique biological pathways and play different roles in the immune microenvironment of osteoarthritis. Conclusion: The m6A modification plays a crucial role in the diversity and complexity of the immune microenvironment in osteoarthritis.
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Affiliation(s)
- Yong Gu
- Translational Medical Innovation Center, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China,Department of Orthopedics, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China
| | - Zhengming Wang
- Shi’s Center of Orthopedics and Traumatology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China,Institute of Traumatology and Orthopedics, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Rui Wang
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang Provincial Hospital of Chinese Medicine, Hangzhou, China
| | - Yunshang Yang
- Translational Medical Innovation Center, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China,Department of Orthopedics, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China
| | - Peijian Tong
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang Provincial Hospital of Chinese Medicine, Hangzhou, China
| | - Shuaijie Lv
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang Provincial Hospital of Chinese Medicine, Hangzhou, China,*Correspondence: Zhirong Wang, ; Long Xiao, ; Shuaijie Lv,
| | - Long Xiao
- Translational Medical Innovation Center, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China,Department of Orthopedics, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China,*Correspondence: Zhirong Wang, ; Long Xiao, ; Shuaijie Lv,
| | - Zhirong Wang
- Translational Medical Innovation Center, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China,Department of Orthopedics, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China,*Correspondence: Zhirong Wang, ; Long Xiao, ; Shuaijie Lv,
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Zhang Z, Mei Y, Hou M. Knockdown RBM15 Inhibits Colorectal Cancer Cell Proliferation and Metastasis Via N6-Methyladenosine (m6A) Modification of MyD88 mRNA. Cancer Biother Radiopharm 2022; 37:976-986. [PMID: 34842457 DOI: 10.1089/cbr.2021.0226] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers worldwide. In this study, we explored the role of RNA binding motif protein 15 (RBM15)-mediated MyD88 mRNA N6-methyladenosine (m6A) in CRC development. Cell proliferation, apoptosis, and invasion were detected by EdU, Annexin V-FITC/PI staining, and Transwell assays, respectively. RBM15 and MyD88 expression was detected by RT-qPCR and Western blot. RNA-seq, RIP-seq, and MeRIP-seq were used for RBM15 downstream target gene prediction and expression detection. In this research, we confirmed that RBM15 was highly expressed in CRC tissues and was negatively correlated with overall and disease-free survival rate. Silencing RBM15 significantly inhibited the proliferative and invasive abilities and promoted cell apoptosis in the CRC cell lines (SW480 and HCT116). Moreover, tumor growth and CRC liver metastasis were inhibited by silencing RBM15 in vivo. m6A methylation level was decreased in RBM15-silenced SW480 and HCT116 cells. MyD88 was the target mRNA of RBM15-mediated m6A methylation in CRC. MyD88 was lowly expressed in CRC and negatively correlated with RBM15 expression. Taken together, RBM15 silencing inhibited the CRC growth and metastasis in vitro and in vivo. RBM15 mediated m6A methylation modification of MyD88 mRNA in CRC cells.
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Affiliation(s)
- Zhen Zhang
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China.,Department of Gastrointestinal Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Yan Mei
- Health Management (Physical Examination) Center, Inner Mongolia Autonomous Region People's Hospital, Hohhot, China
| | - Mingxing Hou
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
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Porman AM, Roberts JT, Duncan ED, Chrupcala ML, Levine AA, Kennedy MA, Williams MM, Richer JK, Johnson AM. A single N6-methyladenosine site regulates lncRNA HOTAIR function in breast cancer cells. PLoS Biol 2022; 20:e3001885. [PMID: 36441764 PMCID: PMC9731500 DOI: 10.1371/journal.pbio.3001885] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/08/2022] [Accepted: 10/24/2022] [Indexed: 11/29/2022] Open
Abstract
N6-methyladenosine (m6A) modification of RNA regulates normal and cancer biology, but knowledge of its function on long noncoding RNAs (lncRNAs) remains limited. Here, we reveal that m6A regulates the breast cancer-associated human lncRNA HOTAIR. Mapping m6A in breast cancer cell lines, we identify multiple m6A sites on HOTAIR, with 1 single consistently methylated site (A783) that is critical for HOTAIR-driven proliferation and invasion of triple-negative breast cancer (TNBC) cells. Methylated A783 interacts with the m6A "reader" YTHDC1, promoting chromatin association of HOTAIR, proliferation and invasion of TNBC cells, and gene repression. A783U mutant HOTAIR induces a unique antitumor gene expression profile and displays loss-of-function and antimorph behaviors by impairing and, in some cases, causing opposite gene expression changes induced by wild-type (WT) HOTAIR. Our work demonstrates how modification of 1 base in an lncRNA can elicit a distinct gene regulation mechanism and drive cancer-associated phenotypes.
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Affiliation(s)
- Allison M. Porman
- University of Colorado Anschutz Medical Campus, Biochemistry and Molecular Genetics Department, Aurora, Colorado, United States of America
| | - Justin T. Roberts
- University of Colorado Anschutz Medical Campus, Biochemistry and Molecular Genetics Department, Aurora, Colorado, United States of America
- University of Colorado Anschutz Medical Campus, Molecular Biology Graduate Program, Aurora, Colorado, United States of America
| | - Emily D. Duncan
- University of Colorado Anschutz Medical Campus, Molecular Biology Graduate Program, Aurora, Colorado, United States of America
- University of Colorado Anschutz Medical Campus, Cell and Developmental Biology Department, Aurora, Colorado, United States of America
| | - Madeline L. Chrupcala
- University of Colorado Anschutz Medical Campus, Biochemistry and Molecular Genetics Department, Aurora, Colorado, United States of America
- University of Colorado Anschutz Medical Campus, RNA Bioscience Initiative, Aurora, Colorado, United States of America
| | - Ariel A. Levine
- University of Colorado Anschutz Medical Campus, Biochemistry and Molecular Genetics Department, Aurora, Colorado, United States of America
- University of Colorado Anschutz Medical Campus, RNA Bioscience Initiative, Aurora, Colorado, United States of America
| | - Michelle A. Kennedy
- University of Colorado Anschutz Medical Campus, Biochemistry and Molecular Genetics Department, Aurora, Colorado, United States of America
| | - Michelle M. Williams
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Jennifer K. Richer
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Aaron M. Johnson
- University of Colorado Anschutz Medical Campus, Biochemistry and Molecular Genetics Department, Aurora, Colorado, United States of America
- University of Colorado Anschutz Medical Campus, Molecular Biology Graduate Program, Aurora, Colorado, United States of America
- University of Colorado Anschutz Medical Campus, RNA Bioscience Initiative, Aurora, Colorado, United States of America
- * E-mail:
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10
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Marakulina D, Vorontsov IE, Kulakovskiy IV, Lennartsson A, Drabløs F, Medvedeva Y. EpiFactors 2022: expansion and enhancement of a curated database of human epigenetic factors and complexes. Nucleic Acids Res 2022; 51:D564-D570. [PMID: 36350659 PMCID: PMC9825597 DOI: 10.1093/nar/gkac989] [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: 08/21/2022] [Revised: 09/30/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022] Open
Abstract
We present an update of EpiFactors, a manually curated database providing information about epigenetic regulators, their complexes, targets, and products which is openly accessible at http://epifactors.autosome.org. An updated version of the EpiFactors contains information on 902 proteins, including 101 histones and protamines, and, as a main update, a newly curated collection of 124 lncRNAs involved in epigenetic regulation. The amount of publications concerning the role of lncRNA in epigenetics is rapidly growing. Yet, the resource that compiles, integrates, organizes, and presents curated information on lncRNAs in epigenetics is missing. EpiFactors fills this gap and provides data on epigenetic regulators in an accessible and user-friendly form. For 820 of the genes in EpiFactors, we include expression estimates across multiple cell types assessed by CAGE-Seq in the FANTOM5 project. In addition, the updated EpiFactors contains information on 73 protein complexes involved in epigenetic regulation. Our resource is practical for a wide range of users, including biologists, bioinformaticians and molecular/systems biologists.
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Affiliation(s)
- Daria Marakulina
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Moscow Region, Russia
| | - Ilya E Vorontsov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ivan V Kulakovskiy
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia,Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, NEO, Karolinska Institutet, 14157, Huddinge, Sweden
| | - Finn Drabløs
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, PO Box 8905, NO-7491 Trondheim, Norway
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11
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Su S, Li S, Deng T, Gao M, Yin Y, Wu B, Peng C, Liu J, Ma J, Zhang K. Cryo-EM structures of human m 6A writer complexes. Cell Res 2022; 32:982-994. [PMID: 36167981 PMCID: PMC9652331 DOI: 10.1038/s41422-022-00725-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/05/2022] [Indexed: 02/06/2023] Open
Abstract
N6-methyladenosine (m6A) is the most abundant ribonucleotide modification among eukaryotic messenger RNAs. The m6A "writer" consists of the catalytic subunit m6A-METTL complex (MAC) and the regulatory subunit m6A-METTL-associated complex (MACOM), the latter being essential for enzymatic activity. Here, we report the cryo-electron microscopy (cryo-EM) structures of MACOM at a 3.0-Å resolution, uncovering that WTAP and VIRMA form the core structure of MACOM and that ZC3H13 stretches the conformation by binding VIRMA. Furthermore, the 4.4-Å resolution cryo-EM map of the MACOM-MAC complex, combined with crosslinking mass spectrometry and GST pull-down analysis, elucidates a plausible model of the m6A writer complex, in which MACOM binds to MAC mainly through WTAP and METTL3 interactions. In combination with in vitro RNA substrate binding and m6A methyltransferase activity assays, our results illustrate the molecular basis of how MACOM assembles and interacts with MAC to form an active m6A writer complex.
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Affiliation(s)
- Shichen Su
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Shanshan Li
- grid.59053.3a0000000121679639MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui China
| | - Ting Deng
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Minsong Gao
- grid.13402.340000 0004 1759 700XMOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, Zhejiang China
| | - Yue Yin
- grid.458506.a0000 0004 0497 0637National Facility for Protein Science in Shanghai, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, China
| | - Baixing Wu
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China ,grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Chao Peng
- grid.458506.a0000 0004 0497 0637National Facility for Protein Science in Shanghai, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, China
| | - Jianzhao Liu
- grid.13402.340000 0004 1759 700XMOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, Zhejiang China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China.
| | - Kaiming Zhang
- MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
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12
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Delli Ponti R, Broglia L, Vandelli A, Armaos A, Torrent Burgas M, Sanchez de Groot N, Tartaglia GG. A high-throughput approach to predict A-to-I effects on RNA structure indicates a change of double-stranded content in non-coding RNAs. IUBMB Life 2022; 75:411-426. [PMID: 36057100 DOI: 10.1002/iub.2673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/21/2022] [Indexed: 11/09/2022]
Abstract
RNA molecules undergo a number of chemical modifications whose effects can alter their structure and molecular interactions. Previous studies have shown that RNA editing can impact the formation of ribonucleoprotein complexes and influence the assembly of membrane-less organelles such as stress-granules. For instance, N6-methyladenosine (m6A) enhances SG formation and N1-methyladenosine (m1A) prevents their transition to solid-like aggregates. Yet, very little is known about adenosine to inosine (A-to-I) modification that is very abundant in human cells and not only impacts mRNAs but also non-coding RNAs. Here, we built the CROSSalive predictor of A-to-I effects on RNA structure based on high-throughput in-cell experiments. Our method shows an accuracy of 90% in predicting the single and double-stranded content of transcripts and identifies a general enrichment of double-stranded regions caused by A-to-I in long intergenic non-coding RNAs (lincRNAs). For the individual cases of NEAT1, NORAD and XIST, we investigated the relationship between A-to-I editing and interactions with RNA-binding proteins using available CLIP data and catRAPID predictions. We found that A-to-I editing is linked to alteration of interaction sites with proteins involved in phase-separation, which suggests that RNP assembly can be influenced by A-to-I. CROSSalive is available at http://service.tartaglialab.com/new_submission/crossalive. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Riccardo Delli Ponti
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore
| | - Laura Broglia
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Genoa, Italy
| | - Andrea Vandelli
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Alexandros Armaos
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Genoa, Italy
| | - Marc Torrent Burgas
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Natalia Sanchez de Groot
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Genoa, Italy.,Department of Biology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome, Italy
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13
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Xist-mediated silencing requires additive functions of SPEN and Polycomb together with differentiation-dependent recruitment of SmcHD1. Cell Rep 2022; 39:110830. [PMID: 35584662 DOI: 10.1016/j.celrep.2022.110830] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/17/2022] [Accepted: 04/26/2022] [Indexed: 11/20/2022] Open
Abstract
X chromosome inactivation (XCI) is mediated by the non-coding RNA Xist, which directs chromatin modification and gene silencing in cis. The RNA binding protein SPEN and associated corepressors have a central role in Xist-mediated gene silencing. Other silencing factors, notably the Polycomb system, have been reported to function downstream of SPEN. In recent work, we found that SPEN has an additional role in correct localization of Xist RNA in cis, indicating that its contribution to chromatin-mediated gene silencing needs to be reappraised. Making use of a SPEN separation-of-function mutation, we show that SPEN and Polycomb pathways, in fact, function in parallel to establish gene silencing. We also find that differentiation-dependent recruitment of the chromosomal protein SmcHD1 is required for silencing many X-linked genes. Our results provide important insights into the mechanism of X inactivation and the coordination of chromatin-based gene regulation with cellular differentiation and development.
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14
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Dossin F, Heard E. The Molecular and Nuclear Dynamics of X-Chromosome Inactivation. Cold Spring Harb Perspect Biol 2022; 14:a040196. [PMID: 34312245 PMCID: PMC9121902 DOI: 10.1101/cshperspect.a040196] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In female eutherian mammals, dosage compensation of X-linked gene expression is achieved during development through transcriptional silencing of one of the two X chromosomes. Following X chromosome inactivation (XCI), the inactive X chromosome remains faithfully silenced throughout somatic cell divisions. XCI is dependent on Xist, a long noncoding RNA that coats and silences the X chromosome from which it is transcribed. Xist coating triggers a cascade of chromosome-wide changes occurring at the levels of transcription, chromatin composition, chromosome structure, and spatial organization within the nucleus. XCI has emerged as a paradigm for the study of such crucial nuclear processes and the dissection of their functional interplay. In the past decade, the advent of tools to characterize and perturb these processes have provided an unprecedented understanding into their roles during XCI. The mechanisms orchestrating the initiation of XCI as well as its maintenance are thus being unraveled, although many questions still remain. Here, we introduce key aspects of the XCI process and review the recent discoveries about its molecular basis.
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Affiliation(s)
- François Dossin
- European Molecular Biology Laboratory, Director's Unit, 69117 Heidelberg, Germany
| | - Edith Heard
- European Molecular Biology Laboratory, Director's Unit, 69117 Heidelberg, Germany
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15
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Li J, Ming Z, Yang L, Wang T, Liu G, Ma Q. Long noncoding RNA XIST: Mechanisms for X chromosome inactivation, roles in sex-biased diseases, and therapeutic opportunities. Genes Dis 2022; 9:1478-1492. [PMID: 36157489 PMCID: PMC9485286 DOI: 10.1016/j.gendis.2022.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 11/30/2022] Open
Abstract
Sexual dimorphism has been reported in various human diseases including autoimmune diseases, neurological diseases, pulmonary arterial hypertension, and some types of cancers, although the underlying mechanisms remain poorly understood. The long noncoding RNA (lncRNA) X-inactive specific transcript (XIST) is involved in X chromosome inactivation (XCI) in female placental mammals, a process that ensures the balanced expression dosage of X-linked genes between sexes. XIST is abnormally expressed in many sex-biased diseases. In addition, escape from XIST-mediated XCI and skewed XCI also contribute to sex-biased diseases. Therefore, its expression or modification can be regarded as a biomarker for the diagnosis and prognosis of many sex-biased diseases. Genetic manipulation of XIST expression can inhibit the progression of some of these diseases in animal models, and therefore XIST has been proposed as a potential therapeutic target. In this manuscript, we summarize the current knowledge about the mechanisms for XIST-mediated XCI and the roles of XIST in sex-biased diseases, and discuss potential therapeutic strategies targeting XIST.
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16
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Huang H, Cui X, Qin X, Li K, Yan G, Lu D, Zheng M, Hu Z, Lei D, Lan N, Zheng L, Yuan Z, Zhu B, Zhao J. Analysis and identification of m 6A RNA methylation regulators in metastatic osteosarcoma. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:577-592. [PMID: 35036067 PMCID: PMC8738956 DOI: 10.1016/j.omtn.2021.12.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 12/08/2021] [Indexed: 11/18/2022]
Abstract
Osteosarcoma (OS) is characterized by rapid growth and early metastasis. However, its mechanism remains unclear. N6-methyladenosine (m6A) modification and its regulatory factors play essential roles in most cancers, including OS. In this study, we screened out 21 m6A modifiers using the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database, followed by the identification of the critical m6A methylation modifiers. The results revealed that the expression levels of three m6A methylation regulators, namely RBM15, METTL3, and LRPPRC, were associated with the low survival rate of patients with OS. We further studied the independent prognostic factors by performing univariate and multivariate Cox analyses and found that metastasis was an independent prognostic factor for patients with OS. Furthermore, we found for the first time that RBM15 was specific for metastatic OS rather than non-metastatic OS. Moreover, the significant overexpression of RBM15 was validated in metastatic OS cell lines and in actual human clinical specimens. We also revealed that RBM15 promoted the invasion, migration, and metastasis of OS cells through loss-functional and gain-functional experiments and an animal metastatic model. In conclusion, RBM15 has a high correlation with OS metastasis formation and the decreased survival rate of patients with OS, and this may serve as a useful biomarker for predicting metastasis and prognosis of patients with OS.
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Affiliation(s)
- Hanji Huang
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-ASEAN Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, Nanning 530021, China
| | - Xiaofei Cui
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-ASEAN Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, Nanning 530021, China
- Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Xiong Qin
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-ASEAN Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, Nanning 530021, China
- Department of Bone and Soft Tissue Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, China
| | - Kanglu Li
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-ASEAN Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, Nanning 530021, China
- Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Guohua Yan
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-ASEAN Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, Nanning 530021, China
- Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Dejie Lu
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-ASEAN Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, Nanning 530021, China
- Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Mingjun Zheng
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-ASEAN Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, Nanning 530021, China
- Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Ziwei Hu
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-ASEAN Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, Nanning 530021, China
| | - Danqing Lei
- The Medical and Scientific Research Center, Life Sciences Institute, Guangxi Medical University, Nanning 530021, China
| | - Nihan Lan
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Li Zheng
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Guangxi Key Laboratory of Regenerative Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Zhenchao Yuan
- Department of Bone and Soft Tissue Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, China
| | - Bo Zhu
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Jinmin Zhao
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-ASEAN Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, Nanning 530021, China
- Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Guangxi Key Laboratory of Regenerative Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Guangxi Key Laboratory of Regenerative Medicine, Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
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17
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Jones AN, Tikhaia E, Mourão A, Sattler M. Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1. Nucleic Acids Res 2022; 50:2350-2362. [PMID: 35166835 PMCID: PMC8887474 DOI: 10.1093/nar/gkac080] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/28/2021] [Accepted: 02/11/2022] [Indexed: 12/12/2022] Open
Abstract
The A-repeat region of the lncRNA Xist is critical for X inactivation and harbors several N6-methyladenosine (m6A) modifications. How the m6A modification affects the conformation of the conserved AUCG tetraloop hairpin of the A-repeats and how it can be recognized by the YTHDC1 reader protein is unknown. Here, we report the NMR solution structure of the (m6A)UCG hairpin, which reveals that the m6A base extends 5′ stacking of the A-form helical stem, resembling the unmethylated AUCG tetraloop. A crystal structure of YTHDC1 bound to the (m6A)UCG tetraloop shows that the (m6A)UC nucleotides are recognized by the YTH domain of YTHDC1 in a single-stranded conformation. The m6A base inserts into the aromatic cage and the U and C bases interact with a flanking charged surface region, resembling the recognition of single-stranded m6A RNA ligands. Notably, NMR and fluorescence quenching experiments show that the binding requires local unfolding of the upper stem region of the (m6A)UCG hairpin. Our data show that m6A can be readily accommodated in hairpin loop regions, but recognition by YTH readers requires local unfolding of flanking stem regions. This suggests how m6A modifications may regulate lncRNA function by modulating RNA structure.
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Affiliation(s)
- Alisha N Jones
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Ekaterina Tikhaia
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747, Garching, Germany
| | - André Mourão
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747, Garching, Germany
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18
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Wu J, Deng LJ, Xia YR, Leng RX, Fan YG, Pan HF, Ye DQ. Involvement of N6-methyladenosine modifications of long noncoding RNAs in systemic lupus erythematosus. Mol Immunol 2022; 143:77-84. [PMID: 35051888 DOI: 10.1016/j.molimm.2022.01.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/17/2021] [Accepted: 01/11/2022] [Indexed: 12/17/2022]
Abstract
BACKGROUND LncRNAs are potential biomarkers for SLE, but the epigenetic regulatory mechanisms of N6-methyladenosine (m6A) modification in SLE remain largely unclear. METHODS In this study, we established m6A modification profile and investigated the potential roles of m6A-related lncRNAs in SLE. The m6A modification profile of SLE was established using MeRIP-seq. Four potential m6A related-lncRNAs (linc02446, linc01410, Xist, and PSMB8-AS1) were selected for validation using qRT-PCR, and their expression and association with clinical characteristics with SLE were evaluated. RESULTS Overall, m6A level was lower in patients with SLE than in controls. Compared with controls, the expression of the two m6A related-lncRNAs (Xist and PSMB8-AS1) was downregulated in patients with SLE (all P < 0.05); the linc02446 was up-regulated in PBMCs of patients with SLE (Z=-2.738, P = 0.006), while it was not differentially expressed in T cells (Z=-0.387, P = 0.699). No significant alteration in linc01410 expression was observed in patients (Z=-0.940, P = 0.347). The lower expression levels of Xist and PSMB8-AS1 were associated with many clinical manifestations in patients with SLE (all P < 0.05). Additionally, mRNAs co-expressed with m6A related-lncRNAs (Xist, linc02446, and PSMB8-AS1) also participated in SLE. CONCLUSION These results suggest that m6A methylation and m6A related-lncRNAs might be involved in the pathogenesis of SLE. Thus, our findings provide some clues on the potential function of lncRNAs that m6A modification may target in novel therapeutic or diagnostic strategies for SLE.
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Affiliation(s)
- Jun Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Li-Jun Deng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Yuan-Rui Xia
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Rui-Xue Leng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Yin-Guang Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Dong-Qing Ye
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases, Anhui Medical University, Hefei, Anhui, 230032, China.
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19
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The tandem repeat modules of Xist lncRNA: a swiss army knife for the control of X-chromosome inactivation. Biochem Soc Trans 2021; 49:2549-2560. [PMID: 34882219 PMCID: PMC8786293 DOI: 10.1042/bst20210253] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 12/16/2022]
Abstract
X-inactive-specific transcript (Xist) is a long non-coding RNA (lncRNA) essential for X-chromosome inactivation (XCI) in female placental mammals. Thirty years after its discovery, it is still puzzling how this lncRNA triggers major structural and transcriptional changes leading to the stable silencing of an entire chromosome. Recently, a series of studies in mouse cells have uncovered domains of functional specialization within Xist mapping to conserved tandem repeat regions, known as Repeats A-to-F. These functional domains interact with various RNA binding proteins (RBPs) and fold into distinct RNA structures to execute specific tasks in a synergistic and coordinated manner during the inactivation process. This modular organization of Xist is mostly conserved in humans, but recent data point towards differences regarding functional specialization of the tandem repeats between the two species. In this review, we summarize the recent progress on understanding the role of Xist repetitive blocks and their involvement in the molecular mechanisms underlying XCI. We also discuss these findings in the light of the similarities and differences between mouse and human Xist.
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20
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Yao FY, Zhao C, Zhong FM, Qin TY, Wen F, Li MY, Liu J, Huang B, Wang XZ. m(6)A Modification of lncRNA NEAT1 Regulates Chronic Myelocytic Leukemia Progression via miR-766-5p/CDKN1A Axis. Front Oncol 2021; 11:679634. [PMID: 34354942 PMCID: PMC8329653 DOI: 10.3389/fonc.2021.679634] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/19/2021] [Indexed: 01/15/2023] Open
Abstract
Background Chronic myeloid leukemia (CML) is an acquired hematopoietic stem malignant disease originating from the myeloid system. Long non-coding RNAs (lncRNAs) have been widely explored in cancer tumorigenesis. However, their roles in CML remain largely unclear. Methods The peripheral blood mononuclear cells (PBMCs) and CML cell lines (K562, KCL22, MEG01, BV173) were collected for in vitro research. Real-time quantitative polymerase chain reaction was used to determine the mRNA expression levels. Cell viability and apoptosis were analyzed by cell counting kit 8 and flow cytometry assays. The targeting relationships were predicted using Starbase and TargetScan and ulteriorly verified by RNA pull-down and luciferase reporter assays. Western blotting assay was performed to assess the protein expressions. N6-methyladenosine (m6A) modification sites were predicted by SRAMP and confirmed by Methylated RNA immunoprecipitation (MeRIP) assay. Results LncRNA nuclear-enriched abundant transcript 1 (NEAT1) expression levels were decreased in the CML cell lines and PBMCs of CML patients. Moreover, METTL3-mediated m6A modification induced the aberrant expression of NEAT1 in CML. Overexpression of NEAT1 inhibited cell viability and promoted the apoptosis of CML cells. Additionally, miR-766-5p was upregulated in CML PBMCs and abrogated the effects of NEAT1 on cell viability and apoptosis of the CML cells. Further, CDKN1A was proved to be the target gene of miR-766-5p and was downregulated in the CML PBMCs. Knockdown of CDKN1A reversed the effects of NEAT1. Conclusion The current research elucidates a novel METTL3/NEAT1/miR-766-5p/CDKN1A axis which plays a critical role in the progression of CML.
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Affiliation(s)
- Fang-Yi Yao
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Cui Zhao
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Fang-Min Zhong
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ting-Yu Qin
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Fang Wen
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Mei-Yong Li
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jing Liu
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Bo Huang
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiao-Zhong Wang
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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21
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Wei G, Almeida M, Pintacuda G, Coker H, Bowness JS, Ule J, Brockdorff N. Acute depletion of METTL3 implicates N 6-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome. Genome Res 2021; 31:1395-1408. [PMID: 34131006 PMCID: PMC8327914 DOI: 10.1101/gr.271635.120] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 06/10/2021] [Indexed: 01/15/2023]
Abstract
RNA N 6-methyladenosine (m6A) modification plays important roles in multiple aspects of RNA regulation. m6A is installed cotranscriptionally by the METTL3/14 complex, but its direct roles in RNA processing remain unclear. Here, we investigate the presence of m6A in nascent RNA of mouse embryonic stem cells. We find that around 10% of m6A peaks are located in alternative introns/exons, often close to 5' splice sites. m6A peaks significantly overlap with RBM15 RNA binding sites and the histone modification H3K36me3. Acute depletion of METTL3 disrupts inclusion of alternative introns/exons in the nascent transcriptome, particularly at 5' splice sites that are proximal to m6A peaks. For terminal or variable-length exons, m6A peaks are generally located on or immediately downstream from a 5' splice site that is suppressed in the presence of m6A and upstream of a 5' splice site that is promoted in the presence of m6A. Genes with the most immediate effects on splicing include several components of the m6A pathway, suggesting an autoregulatory function. Collectively, our findings demonstrate crosstalk between the m6A machinery and the regulation of RNA splicing.
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Affiliation(s)
- Guifeng Wei
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Mafalda Almeida
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Greta Pintacuda
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Heather Coker
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Joseph S Bowness
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Jernej Ule
- The Francis Crick Institute, London NW1 1AT, United Kingdom.,Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
| | - Neil Brockdorff
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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22
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Khan RIN, Malla WA. m 6A modification of RNA and its role in cancer, with a special focus on lung cancer. Genomics 2021; 113:2860-2869. [PMID: 34118382 DOI: 10.1016/j.ygeno.2021.06.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 05/12/2021] [Accepted: 06/07/2021] [Indexed: 02/07/2023]
Abstract
Epitranscriptomics involves functionally relevant biochemical modifications of RNA taking place at the transcriptome level without a change in the sequence of ribonucleotides. Several types of modifications that affect the processing and function of differentRNA types have been reported. Methylation at N6 of Adenosine called m6A is one such modification, quite widespread in occurrence and reported in snRNAs, lncRNAs, circRNAs, rRNAs, miRNAs, and most abundantly, in mRNAs. The significant implications of m6A in various types of cancers are being widely recognized. Here, we give a brief about the enzymes that install the m6A modification (= m6A writers), that remove it (= m6A erasers) and certain RNA binding proteins (= m6A readers) which affect the fate of the m6A-containing RNA by recruiting various proteins. We also discuss the relevance of m6A in ncRNAs in various cancer types, followed by a discussion on the role of m6A of mRNA and ncRNA in lung cancer.
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23
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Physio-pathological effects of m6A modification and its potential contribution to melanoma. Clin Transl Oncol 2021; 23:2269-2279. [PMID: 34105069 PMCID: PMC8455380 DOI: 10.1007/s12094-021-02644-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/12/2021] [Indexed: 12/24/2022]
Abstract
Methylation of N6-adenosine (m6A) is the most prevalent internal RNA modification and is especially common among the messenger RNAs. These m6A modifications regulate splicing, translocation, stability and translation of RNA through dynamic and reversible interactions with m6A-binding proteins, namely the writers, erasers and readers. RNA methyltransferases catalyze the m6A modifications, while demethylases reverse this methylation. Deregulation of the m6A modification process has been implicated in human carcinogenesis, including melanoma—which carries one of the highest mutant rates. In this review, we provide an up-to-date summary of m6A regulation and its biological impacts on normal and cancer cells, with emphasis on the deregulation of m6A modification and m6A regulators in melanoma. In addition, we highlight the prospective potential of exploiting m6A modification in the treatment of melanoma and non-cancer diseases.
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24
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Giaimo BD, Robert-Finestra T, Oswald F, Gribnau J, Borggrefe T. Chromatin Regulator SPEN/SHARP in X Inactivation and Disease. Cancers (Basel) 2021; 13:cancers13071665. [PMID: 33916248 PMCID: PMC8036811 DOI: 10.3390/cancers13071665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Carcinogenesis is a multistep process involving not only the activation of oncogenes and disabling tumor suppressor genes, but also epigenetic modulation of gene expression. X chromosome inactivation (XCI) is a paradigm to study heterochromatin formation and maintenance. The double dosage of X chromosomal genes in female mammals is incompatible with early development. XCI is an excellent model system for understanding the establishment of facultative heterochromatin initiated by the expression of a 17,000 nt long non-coding RNA, known as Xinactivespecifictranscript (Xist), on the X chromosome. This review focuses on the molecular mechanisms of how epigenetic modulators act in a step-wise manner to establish facultative heterochromatin, and we put these in the context of cancer biology and disease. An in depth understanding of XCI will allow a better characterization of particular types of cancer and hopefully facilitate the development of novel epigenetic therapies. Abstract Enzymes, such as histone methyltransferases and demethylases, histone acetyltransferases and deacetylases, and DNA methyltransferases are known as epigenetic modifiers that are often implicated in tumorigenesis and disease. One of the best-studied chromatin-based mechanism is X chromosome inactivation (XCI), a process that establishes facultative heterochromatin on only one X chromosome in females and establishes the right dosage of gene expression. The specificity factor for this process is the long non-coding RNA Xinactivespecifictranscript (Xist), which is upregulated from one X chromosome in female cells. Subsequently, Xist is bound by the corepressor SHARP/SPEN, recruiting and/or activating histone deacetylases (HDACs), leading to the loss of active chromatin marks such as H3K27ac. In addition, polycomb complexes PRC1 and PRC2 establish wide-spread accumulation of H3K27me3 and H2AK119ub1 chromatin marks. The lack of active marks and establishment of repressive marks set the stage for DNA methyltransferases (DNMTs) to stably silence the X chromosome. Here, we will review the recent advances in understanding the molecular mechanisms of how heterochromatin formation is established and put this into the context of carcinogenesis and disease.
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Affiliation(s)
- Benedetto Daniele Giaimo
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
- Correspondence: (B.D.G.); (T.B.); Tel.: +49-641-9947-400 (T.B.)
| | - Teresa Robert-Finestra
- Department of Developmental Biology, Erasmus MC, Oncode Institute, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (T.R.-F.); (J.G.)
| | - Franz Oswald
- Center for Internal Medicine, Department of Internal Medicine I, University Medical Center Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany;
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, Oncode Institute, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (T.R.-F.); (J.G.)
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
- Correspondence: (B.D.G.); (T.B.); Tel.: +49-641-9947-400 (T.B.)
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25
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Yuan X, Shi L, Guo Y, Sun J, Miao J, Shi J, Chen Y. METTL3 Regulates Ossification of the Posterior Longitudinal Ligament via the lncRNA XIST/miR-302a-3p/USP8 Axis. Front Cell Dev Biol 2021; 9:629895. [PMID: 33748113 PMCID: PMC7973222 DOI: 10.3389/fcell.2021.629895] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/17/2021] [Indexed: 11/13/2022] Open
Abstract
The prevalence of ossification of the posterior longitudinal ligament (OPLL) is increasing, and currently there is no effective medical treatment for OPLL. Methyltransferase like 3 (METTL3), one of the components of the N6-methyladenosine (m6A) methyltransferase complex, regulates gene expression via modification of mRNA. Although METTL3 has been implicated in a variety of diseases, its role in OPLL remains to be elucidated. Primary ligament fibroblasts were used in this study. To investigate the role of METTL3 in OPLL, METTL3 was silenced or overexpressed. m6A RNA methylation was measured by commercially available kits. Luciferase reporter assay was performed to investigate the binding of miR-302a-3p and METTL3, and the binding of miR-302a-3p and USP8. Quantitative RT-PCR and western blots were used to evaluate mRNA and protein expression, respectively. OPLL increases METTL3 and its m6A modification. Overexpressing METTL3 significantly promoted osteogenic differentiation of primary ligament fibroblasts. Mechanism study showed that METTL3 increased m6A methylation of long non-coding RNA (lncRNA) X-inactive specific transcript (XIST). Further study showed that lncRNA XIST regulates osteogenic differentiation of primary ligament fibroblasts via miR-302a-3p, which targets ubiquitin-specific protease 8 (USP8). METTL3 enhanced osteogenic differentiation of primary ligament fibroblasts via the lncRNA XIST/miR-302a-3p/USP8 axis. The findings highlight the importance of METTL3-mediated m6A methylation of XIST in OPLL and provide new insights into therapeutic strategies for OPLL.
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Affiliation(s)
- Xiaoqiu Yuan
- Spine Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Lei Shi
- Spine Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yongfei Guo
- Spine Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Jingchuan Sun
- Spine Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Jinhao Miao
- Spine Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Jiangang Shi
- Spine Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yu Chen
- Spine Center, Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai, China
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26
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Chen J, Tian Y, Zhang Q, Ren D, Zhang Q, Yan X, Wang L, He Z, Zhang W, Zhang T, Yuan X. Novel Insights Into the Role of N6-Methyladenosine RNA Modification in Bone Pathophysiology. Stem Cells Dev 2020; 30:17-28. [PMID: 33231507 DOI: 10.1089/scd.2020.0157] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Thus far, there are more than known 150 modifications to RNA, in which common internal modifications of mRNA include N6-methyladenosine (m6A), N1-methyladenosine, and 5-methylcytosine. Among them, m6A RNA modification is one of the highest abundance modifications in eukaryotes, regulating mechanisms controlling gene expression at the post-transcription level. As an invertible and dynamic epigenetic marker, m6A base modification influences almost all vital biological processes, cellular components, and molecular functions. Once the m6A modification process is abnormal, a series of diseases-including cancer, neurological diseases, and growth disorders-will be caused. Besides, several base modification activities also have been created by noncoding RNAs (ncRNAs), for instance, microRNAs, and circular RNAs, long ncRNAs, which were dynamically regulated during bone and cartilage pathophysiology processes. Therefore, it has now been clear that dynamic modification on coding RNAs and ncRNAs represents a completely new way to modulate genetic information. In this review, we highlight up-to-date progress and applications of m6A RNA modification in bone and cartilage pathophysiology, and we discuss the pathological roles and underlying molecular mechanism of m6A modifications in osteoarthritis and osteoporosis and osteosarcoma pathogenesis.
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Affiliation(s)
- Junbo Chen
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China.,School of Stomatology, Qingdao University, Qingdao, China
| | - Yihong Tian
- School of Stomatology, Qingdao University, Qingdao, China
| | - Qi Zhang
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China.,School of Stomatology, Qingdao University, Qingdao, China
| | - Dapeng Ren
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Qiang Zhang
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiao Yan
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lingzhi Wang
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China.,School of Stomatology, Qingdao University, Qingdao, China
| | - Zijing He
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China.,School of Stomatology, Qingdao University, Qingdao, China
| | - Wei Zhang
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China.,School of Stomatology, Qingdao University, Qingdao, China
| | - Tianzhen Zhang
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China.,School of Stomatology, Qingdao University, Qingdao, China
| | - Xiao Yuan
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China.,School of Stomatology, Qingdao University, Qingdao, China
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27
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Lu Z, Guo JK, Wei Y, Dou DR, Zarnegar B, Ma Q, Li R, Zhao Y, Liu F, Choudhry H, Khavari PA, Chang HY. Structural modularity of the XIST ribonucleoprotein complex. Nat Commun 2020; 11:6163. [PMID: 33268787 PMCID: PMC7710737 DOI: 10.1038/s41467-020-20040-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 10/28/2020] [Indexed: 12/11/2022] Open
Abstract
Long noncoding RNAs are thought to regulate gene expression by organizing protein complexes through unclear mechanisms. XIST controls the inactivation of an entire X chromosome in female placental mammals. Here we develop and integrate several orthogonal structure-interaction methods to demonstrate that XIST RNA-protein complex folds into an evolutionarily conserved modular architecture. Chimeric RNAs and clustered protein binding in fRIP and eCLIP experiments align with long-range RNA secondary structure, revealing discrete XIST domains that interact with distinct sets of effector proteins. CRISPR-Cas9-mediated permutation of the Xist A-repeat location shows that A-repeat serves as a nucleation center for multiple Xist-associated proteins and m6A modification. Thus modular architecture plays an essential role, in addition to sequence motifs, in determining the specificity of RBP binding and m6A modification. Together, this work builds a comprehensive structure-function model for the XIST RNA-protein complex, and suggests a general strategy for mechanistic studies of large ribonucleoprotein assemblies.
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Affiliation(s)
- Zhipeng Lu
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA.
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, 90089, USA.
| | - Jimmy K Guo
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Diana R Dou
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Brian Zarnegar
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Qing Ma
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
- Synthetic Biology Department, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, PR China
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Yang Zhao
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Fan Liu
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Hani Choudhry
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
- Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, 22252, Saudi Arabia
| | - Paul A Khavari
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA.
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305, USA.
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28
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Abstract
The X inactive-specific transcript (Xist) gene is the master regulator of X chromosome inactivation in mammals. Xist produces a long noncoding (lnc)RNA that accumulates over the entire length of the chromosome from which it is transcribed, recruiting factors to modify underlying chromatin and silence X-linked genes in cis Recent years have seen significant progress in identifying important functional elements in Xist RNA, their associated RNA-binding proteins (RBPs), and the downstream pathways for chromatin modification and gene silencing. In this review, we summarize progress in understanding both how these pathways function in Xist-mediated silencing and the complex interplay between them.
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Affiliation(s)
- Neil Brockdorff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Joseph S Bowness
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Guifeng Wei
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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29
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Coker H, Wei G, Moindrot B, Mohammed S, Nesterova T, Brockdorff N. The role of the Xist 5' m6A region and RBM15 in X chromosome inactivation. Wellcome Open Res 2020; 5:31. [PMID: 32258426 PMCID: PMC7097882 DOI: 10.12688/wellcomeopenres.15711.1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2020] [Indexed: 12/14/2022] Open
Abstract
Background: X chromosome inactivation in mammals is regulated by the non-coding (nc) RNA, Xist, which represses the chromosome from which it is transcribed. High levels of the N6-methyladenosine (m6A) RNA modification occur within Xist exon I, close to the 5' end of the transcript, and also further 3', in Xist exon VII. The m6A modification is catalysed by the METTL3/14 complex that is directed to specific targets, including Xist, by the RNA binding protein RBM15/15B. m6A modification of Xist RNA has been reported to be important for Xist-mediated gene silencing. Methods: We use CRISPR/Cas9 mediated mutagenesis to delete sequences around the 5' m6A region in interspecific XX mouse embryonic stem cells (mESCs). Following induction of Xist RNA expression, we assay chromosome silencing using allelic RNA-seq and Xist m6A distribution using m6A-seq. Additionally, we use Xist RNA FISH to analyse the effect of deleting the 5' m6A region on the function of the endogenous Xist promoter. We purify epitope tagged RBM15 from mESCs, and then apply MS/MS analysis to define the RBM15 interactome. Results: We show that a deletion encompassing the entire Xist 5' m6A region results in a modest reduction in Xist-mediated silencing, and that the 5' m6A region overlaps essential DNA elements required for activation of the endogenous Xist promoter. Deletion of the Xist A-repeat, to which RBM15 binds, entirely abolishes deposition of m6A in the Xist 5' m6A region without affecting the modification in exon VII. We show that in mESCs, RBM15 interacts with the m6A complex, the SETD1B histone modifying complex, and several proteins linked to RNA metabolism. Conclusions: Our findings support that RBM15 binding to the Xist A-repeat recruits the m6A complex to the 5' Xist m6A region and that this region plays a role in Xist-mediated chromosome silencing.
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Affiliation(s)
- Heather Coker
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Guifeng Wei
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Benoit Moindrot
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Shabaz Mohammed
- Proteomics Technology Development and Application, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Tatyana Nesterova
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Neil Brockdorff
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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