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Chen F, Guo H, Lan W, Zhou M, Geng W, Shen G, Lin P, Xia Q, Zhao P, Li Z. Targeted DNA N 6-methyladenine editing by dCas9 fused to METTL4 in the lepidopteran model insect Bombyx mori. INSECT SCIENCE 2024; 31:646-650. [PMID: 37461250 DOI: 10.1111/1744-7917.13222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 04/12/2024]
Abstract
We have established a novel CRISPR-dCas9-METTL4 epigenome editing tool that can methylate target regions to achieve site-specific DNA 6mA methylation in both hypermethylated and hypomethylated genes. Targeted methylation on genes by dCas9-METTL4 results in misexpression, allowing for the functional investigation of target genes of interest in silkworm.
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Affiliation(s)
- Feng Chen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
| | - Hao Guo
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
| | - Weiqun Lan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
| | - Mingyi Zhou
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
| | - Wenjing Geng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
| | - Guanwang Shen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
| | - Ping Lin
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
| | - Ping Zhao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
| | - Zhiqing Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
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2
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Liu S, Tian H, Xu Y, Wang H. Juvenile hormone regulates silk gene expression by m 6A RNA methylation. Cell Mol Life Sci 2023; 80:331. [PMID: 37870631 PMCID: PMC11071706 DOI: 10.1007/s00018-023-04996-1] [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: 07/04/2023] [Revised: 09/21/2023] [Accepted: 10/01/2023] [Indexed: 10/24/2023]
Abstract
Juvenile hormone (JH) is an indispensable insect hormone that is critical in regulating insect development and physiology. N6-methyladenosine (m6A) is the most abundant modification of RNA that regulates RNA fate in eukaryotic organisms. However, the relationship between m6A and JH remains largely unknown. Here, we found that the application of a Juvenile hormone analog (JHA) extended the larval period of Bombyx mori and increased the weight and thickness of the cocoon. Interestingly, global transcriptional patterns revealed that m6A-related genes are specifically regulated by JHA in the posterior silk gland (PSG) that synthesizes the major component of cocoon silk. By transcriptome and m6A sequencing data conjointly, we discovered that JHA significantly regulated the m6A modification in the PSG of B. mori and many m6A-containing genes are related to nucleic acid binding, nucleus, and nucleobase-containing compound metabolism. Notably, 547 genes were significantly regulated by JHA at both the m6A modification and expression levels, especially 16 silk-associated genes, including sericin2, seroin1, Serine protease inhibitors 4 (BmSPI4), Serine protease inhibitors 5 (BmSPI5), and LIM domain-binding protein 2 (Ldb). Among them, 11 silk associated genes were significantly affected by METTL3 knockdown, validating that these genes are targets of m6A modification. Furthermore, we confirm that JHA directly regulates the expression of BmSPI4 and BmSPI5 through m6A modification of CDS regions. These results demonstrate the essential role of m6A methylation regulated by JH in PSG, and elucidate a novel mechanism by which JH affects silk gland development via m6A methylation. This study uncovers that m6A modification is a critical factor mediating the effect of JH in insects.
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Affiliation(s)
- Shuaiqi Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Huan Tian
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yusong Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Huabing Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
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3
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Chen Y, Lai Y, Liu R, Yao L, Yu XQ, Wang X. Transcriptome-wide analysis of mRNA N 6 -methyladenosine modification in the embryonic development of Spodoptera frugiperda. INSECT SCIENCE 2023; 30:1229-1244. [PMID: 36606528 DOI: 10.1111/1744-7917.13172] [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: 09/29/2022] [Revised: 12/17/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
N6 -methyladenosine (m6 A) RNA is the most abundant modification of mRNA, and has been demonstrated in regulating various post-transcriptional processes. Many studies have shown that m6 A methylation plays key roles in sex determination, neuronal functions, and embryonic development in Drosophila and mammals. Here, we analyzed transcriptome-wide profile of m6 A modification in the embryonic development of the destructive agricultural pest Spodoptera frugiperda. We found that the 2 key mRNA m6 A methyltransferases SfrMETTL3 and SfrMETTL14 have high homologies with other insects and mammals, suggesting that SfrMETTL3 and SfrMETTL14 may have conserved function among different species. From methylated RNA immunoprecipitation sequencing analysis, we obtained 46 869 m6 A peaks representing 8 587 transcripts in the 2-h embryos after oviposition, and 41 389 m6 A peaks representing 9 230 transcripts in the 24-h embryos. In addition, 5 995 m6 A peaks were differentially expressed including 3 752 upregulated and 2243 downregulated peaks. Functional analysis with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes suggested that differentially expressed m6 A peak-modified genes were enriched in cell and organ development between the 2- and 24-h embryos. By conjoint analysis of methylated RNA immunoprecipitation-seq and RNA-seq data, we found that RNA m6 A methylation may regulate the transcriptional levels of genes related to tissue and organ development from 2- to 24-h embryos. Our study reveals the role of RNA m6 A epigenetic regulation in the embryonic development of S. frugiperda, and provides new insights for the embryonic development of insects.
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Affiliation(s)
- Yaqing Chen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yushan Lai
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Runzhou Liu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Lin Yao
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xiao-Qiang Yu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xiaoyun Wang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
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4
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Muthu Lakshmi Bavithra C, Murugan M, Pavithran S, Naveena K. Enthralling genetic regulatory mechanisms meddling insecticide resistance development in insects: role of transcriptional and post-transcriptional events. Front Mol Biosci 2023; 10:1257859. [PMID: 37745689 PMCID: PMC10511911 DOI: 10.3389/fmolb.2023.1257859] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/18/2023] [Indexed: 09/26/2023] Open
Abstract
Insecticide resistance in insects severely threatens both human health and agriculture, making insecticides less compelling and valuable, leading to frequent pest management failures, rising input costs, lowering crop yields, and disastrous public health. Insecticide resistance results from multiple factors, mainly indiscriminate insecticide usage and mounted selection pressure on insect populations. Insects respond to insecticide stress at the cellular level by modest yet significant genetic propagations. Transcriptional, co-transcriptional, and post-transcriptional regulatory signals of cells in organisms regulate the intricate processes in gene expressions churning the genetic information in transcriptional units into proteins and non-coding transcripts. Upregulation of detoxification enzymes, notably cytochrome P450s (CYPs), glutathione S-transferases (GSTs), esterases [carboxyl choline esterase (CCE), carboxyl esterase (CarE)] and ATP Binding Cassettes (ABC) at the transcriptional level, modification of target sites, decreased penetration, or higher excretion of insecticides are the noted insect physiological responses. The transcriptional regulatory pathways such as AhR/ARNT, Nuclear receptors, CncC/Keap1, MAPK/CREB, and GPCR/cAMP/PKA were found to regulate the detoxification genes at the transcriptional level. Post-transcriptional changes of non-coding RNAs (ncRNAs) such as microRNAs (miRNA), long non-coding RNAs (lncRNA), and epitranscriptomics, including RNA methylation, are reported in resistant insects. Additionally, genetic modifications such as mutations in the target sites and copy number variations (CNV) are also influencing insecticide resistance. Therefore, these cellular intricacies may decrease insecticide sensitivity, altering the concentrations or activities of proteins involved in insecticide interactions or detoxification. The cellular episodes at the transcriptional and post-transcriptional levels pertinent to insecticide resistance responses in insects are extensively covered in this review. An overview of molecular mechanisms underlying these biological rhythms allows for developing alternative pest control methods to focus on insect vulnerabilities, employing reverse genetics approaches like RNA interference (RNAi) technology to silence particular resistance-related genes for sustained insect management.
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Affiliation(s)
| | - Marimuthu Murugan
- Department of Agricultural Entomology, Tamil Nadu Agricultural University, Coimbatore, India
| | | | - Kathirvel Naveena
- Centre for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, India
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5
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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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6
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Lei Y, Yuan Z, Zeng Q, Wan B, Liu J, Wang W. Dynamic N6-methyladenosine RNA methylation landscapes reveal epi-transcriptomic modulation induced by ammonia nitrogen exposure in the Pacific whiteleg shrimp Litopenaeus vannamei. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131996. [PMID: 37423135 DOI: 10.1016/j.jhazmat.2023.131996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
Despite the versatility of RNA m6A methylation in regulating various biological processes, its involvement in the physiological response to ammonia nitrogen toxicity in decapod crustaceans like shrimp remains enigmatic. Here, we provided the first characterization of dynamic RNA m6A methylation landscapes induced by toxic ammonia exposure in the Pacific whiteleg shrimp Litopenaeus vannamei. The global m6A methylation level showed significant decrease following ammonia exposure, and most of the m6A methyltransferases and m6A binding proteins were significantly repressed. Distinct from many well-studied model organisms, m6A methylated peaks in the transcriptome of L. vannamei were enriched not only near the termination codon and in the 3' untranslated region (UTR), but also around the start codon and in the 5' UTR. Upon ammonia exposure, 11,430 m6A peaks corresponding to 6113 genes were hypo-methylated, and 5660 m6A peaks from 3912 genes were hyper-methylated. The differentially methylated genes showing significant changes in expression were over-represented by genes associated with metabolism, cellular immune defense and apoptotic signaling pathways. Notably, the m6A-modified ammonia-responsive genes encompassed a subset of genes related to glutamine synthesis, purine conversion and urea production, implying that m6A methylation may modulate shrimp ammonia stress responses partly through these ammonia metabolic processes.
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Affiliation(s)
- Yiguo Lei
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China
| | - Zhixiang Yuan
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China
| | - Qingtian Zeng
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Boquan Wan
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Jianyong Liu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Provincial Modern Seed Industry Park of the Pacific Whiteleg Shrimp, Zhanjiang 524088, China
| | - Wei Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China; Guangdong Provincial Modern Seed Industry Park of the Pacific Whiteleg Shrimp, Zhanjiang 524088, China.
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7
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Li B, Hu P, Huang ZH, Yang JY, Wang J, Xie XZ, Wang YH, Li CC, Xu JP. RNA methyltransferase BmMettl3 and BmMettl14 in silkworm (Bombyx mori) and the regulation of silkworm embryonic development. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 113:e22005. [PMID: 36802092 DOI: 10.1002/arch.22005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 05/16/2023]
Abstract
N6-methyladenosine (m6A) is a ubiquitous reversible epigenetic RNA modification that plays an important role in regulating many biological processes, especially embryonic development. However, regulation of m6A methylation during silkworm embryonic development and diapause remains to be investigated. In this study, we analyzed the phylogeny of subunits of methyltransferases BmMettl3 and BmMettl14, and detected the expression patterns of BmMettl3 and BmMettl14 in different tissues and at different developmental stages in silkworm. To investigate the function of m6A on the development of silkworm embryo, we analyzed the m6A/A ratio in diapause and diapause termination eggs. The results showed that BmMettl3 and BmMettl14 were highly expressed in gonads and eggs. Moreover, the expression of BmMettl3 and BmMettl14 and the m6A/A ratio were significantly increased in diapause termination eggs compared with diapause eggs in the early stage of silkworm embryonic development. Furthermore, in BmN cell cycle experiments, the percentage of cells in the S phase increased when lacking BmMettl3 or BmMettl14. This work contributes to understanding the role of m6A methylation during insect embryogenesis and gametogenesis. It also provides a research orientation to further analyze the role of m6A methylation in diapause initiation and termination during insect embryonic development.
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Affiliation(s)
- Bing Li
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Institute of Sericulture, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Pei Hu
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Hangzhou Dongfang High School, Hangzhou, China
| | - Zhi-Hao Huang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Anhui International Joint Research and Developmental Centre of Sericulture Resources Utilization, Hefei, China
| | - Jia-Yue Yang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Anhui International Joint Research and Developmental Centre of Sericulture Resources Utilization, Hefei, China
| | - Jie Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Institute of Sericulture, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Xiu-Zhi Xie
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yu-Han Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Anhui International Joint Research and Developmental Centre of Sericulture Resources Utilization, Hefei, China
| | - Chen-Chen Li
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Anhui International Joint Research and Developmental Centre of Sericulture Resources Utilization, Hefei, China
| | - Jia-Ping Xu
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Anhui International Joint Research and Developmental Centre of Sericulture Resources Utilization, Hefei, China
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8
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Liu SQ, Jia SZ, Tian H, Li YH, Hu KW, Tao JG, Lu YC, Xu YS, Wang HB. Evolution of m6A-related genes in insects and the function of METTL3 in silkworm embryonic development. INSECT MOLECULAR BIOLOGY 2023; 32:316-327. [PMID: 36661853 DOI: 10.1111/imb.12832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/16/2023] [Indexed: 05/15/2023]
Abstract
N6-methyladenosine (m6A) plays a key role in many biological processes. However, the function and evolutionary relationship of m6A-related genes in insects remain largely unknown. Here we analysed the phylogeny of m6A-related genes among 207 insect species and found that m6A-related genes are evolutionarily conserved in insects. Subcellular localization experiments of m6A-related proteins in BmN cells confirmed that BmYTHDF3 was localized in the cytoplasm, BmMETTL3, BmMETTL14, and BmYTHDC were localized in the nucleus, and FL2D was localized to both the nucleus and cytoplasm. We examined the expression patterns of m6A-related genes during the embryonic development of Bombyx mori. To elucidate the function of BmMETTL3 during the embryonic stage, RNA sequencing was performed to measure changes in gene expression in silkworm eggs after BmMETTL3 knockdown, as well as in BmN cells overexpressing BmMETTL3. The global transcriptional pattern showed that knockdown of BmMETTL3 affected multiple cellular processes, including oxidoreductase activity, transcription regulator activity, and the cation binding. In addition, transcriptomic data revealed that many observed DEGs were associated with fundamental metabolic processes, including carbon metabolism, purine metabolism, amino acid biosynthesis, and the citrate cycle. Interestingly, we found that knockdown of BmMETTL3 significantly affected Wnt and Toll/Imd pathways in embryos. Taken together, these results suggest that BmMETTL3 plays an essential role in the embryonic development of B. mori, and deepen our understanding of the function of m6A-related genes in insects.
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Affiliation(s)
- Shuai-Qi Liu
- Department of Economic Zoology, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Shun-Ze Jia
- Department of Economic Zoology, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Huan Tian
- Department of Economic Zoology, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Ying-Hui Li
- Department of Economic Zoology, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Kai-Wen Hu
- Department of Economic Zoology, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Jian-Guo Tao
- Department of Economic Zoology, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yi-Cheng Lu
- Department of Economic Zoology, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yu-Song Xu
- Department of Economic Zoology, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Hua-Bing Wang
- Department of Economic Zoology, College of Animal Sciences, Zhejiang University, Hangzhou, China
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9
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Pan B, Ye F, Li T, Wei F, Warren A, Wang Y, Gao S. Potential role of N 6-adenine DNA methylation in alternative splicing and endosymbiosis in Paramecium bursaria. iScience 2023; 26:106676. [PMID: 37182097 PMCID: PMC10173741 DOI: 10.1016/j.isci.2023.106676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 12/02/2022] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
N6-adenine DNA methylation (6mA), a rediscovered epigenetic mark in eukaryotic organisms, diversifies in abundance, distribution, and function across species, necessitating its study in more taxa. Paramecium bursaria is a typical model organism with endosymbiotic algae of the species Chlorella variabilis. This consortium therefore serves as a valuable system to investigate the functional role of 6mA in endosymbiosis, as well as the evolutionary importance of 6mA among eukaryotes. In this study, we report the first genome-wide, base pair-resolution map of 6mA in P. bursaria and identify its methyltransferase PbAMT1. Functionally, 6mA exhibits a bimodal distribution at the 5' end of RNA polymerase II-transcribed genes and possibly participates in transcription by facilitating alternative splicing. Evolutionarily, 6mA co-evolves with gene age and likely serves as a reverse mark of endosymbiosis-related genes. Our results offer new insights for the functional diversification of 6mA in eukaryotes as an important epigenetic mark.
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Affiliation(s)
- Bo Pan
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Fei Ye
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
| | - Tao Li
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
| | - Fan Wei
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Yuanyuan Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- Corresponding author
| | - Shan Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao 266003, China
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Hu J, Cai J, Xu T, Kang H. Epitranscriptomic mRNA modifications governing plant stress responses: underlying mechanism and potential application. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2245-2257. [PMID: 36002976 PMCID: PMC9674322 DOI: 10.1111/pbi.13913] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 06/01/2023]
Abstract
Plants inevitably encounter environmental adversities, including abiotic and biotic stresses, which significantly impede plant growth and reduce crop yield. Thus, fine-tuning the fate and function of stress-responsive RNAs is indispensable for plant survival under such adverse conditions. Recently, post-transcriptional RNA modifications have been studied as a potent route to regulate plant gene expression under stress. Among over 160 mRNA modifications identified to date, N6 -methyladenosine (m6 A) in mRNAs is notable because of its multifaceted roles in plant development and stress response. Recent transcriptome-wide mapping has revealed the distribution and patterns of m6 A in diverse stress-responsive mRNAs in plants, building a foundation for elucidating the molecular link between m6 A and stress response. Moreover, the identification and characterization of m6 A writers, readers and erasers in Arabidopsis and other model crops have offered insights into the biological roles of m6 A in plant abiotic stress responses. Here, we review the recent progress of research on mRNA modifications, particularly m6 A, and their dynamics, distribution, regulation and biological functions in plant stress responses. Further, we posit potential strategies for breeding stress-tolerant crops by engineering mRNA modifications and propose the future direction of research on RNA modifications to gain a much deeper understanding of plant stress biology.
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Affiliation(s)
- Jianzhong Hu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouJiangsu ProvinceChina
- Department of Applied Biology, College of Agriculture and Life SciencesChonnam National UniversityGwangjuKorea
| | - Jing Cai
- Department of Applied Biology, College of Agriculture and Life SciencesChonnam National UniversityGwangjuKorea
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouJiangsu ProvinceChina
| | - Hunseung Kang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouJiangsu ProvinceChina
- Department of Applied Biology, College of Agriculture and Life SciencesChonnam National UniversityGwangjuKorea
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11
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Wang S, Zhang L, Xuan R, Li Q, Ji Z, Chao T, Wang J, Zhang C. Identification and functional analysis of m6A in the mammary gland tissues of dairy goats at the early and peak lactation stages. Front Cell Dev Biol 2022; 10:945202. [PMID: 36330333 PMCID: PMC9623301 DOI: 10.3389/fcell.2022.945202] [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: 05/16/2022] [Accepted: 10/04/2022] [Indexed: 12/01/2022] Open
Abstract
N6-methyladenosine (m6A) is the most common reversible epigenetic RNA modification in the mRNA of all higher eukaryotic organisms and plays an important role in the regulation of gene expression and cell function. In this study, m6A-modified methylated RNA immunoprecipitation sequencing (MeRIP-seq) and transcriptome sequencing (RNA-seq) were used to identify the key genes with m6A modification during mammary gland development and lactation in dairy goats. The results showed that m6A methylation occurred at 3,927 loci, which were significantly enriched in the 3′ untranslated region (3′UTR) and the termination codon region. In the early stage and peak stage of lactation, m6A methylation occurred extensively in mammary tissues, and a total of 725 differentially expressed m6A-modified genes were obtained, all negatively correlated with mRNA expression. In addition, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that different methylated genes were mainly involved in the growth and apoptosis of mammary epithelial cells through signaling pathways, such as the mitogen-activated protein kinase (MAPK) and phospholipase D pathways, and then affected the development and lactation of mammary gland. All in all, we identified and analyzed the methylation events related to the development and lactation regulation of mammary gland at the early and peak lactation stages, and provided a theoretical basis to reveal the physiological regulatory system of mammary gland development and lactation in dairy goats.
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Affiliation(s)
- Shujun Wang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Lu Zhang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Rong Xuan
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Qing Li
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Zhibin Ji
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
- *Correspondence: Zhibin Ji,
| | - Tianle Chao
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Jianmin Wang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Chunlan Zhang
- College of Biological and Agricultural Engineering, Weifang University, Weifang, China
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12
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Bataglia L, Simões ZLP, Nunes FMF. Transcriptional expression of m6A and m5C RNA methyltransferase genes in the brain and fat body of honey bee adult workers. Front Cell Dev Biol 2022; 10:921503. [PMID: 36105348 PMCID: PMC9467440 DOI: 10.3389/fcell.2022.921503] [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: 04/15/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Honey bee (Apis mellifera) adult workers change behaviors and nutrition according to age progression. Young workers, such as nurses, perform in-hive tasks and consume protein-rich pollen, while older workers (foragers) leave the colony to search for food, and consume carbohydrate-rich nectar. These environmentally stimulated events involve transcriptional and DNA epigenetic marks alterations in worker tissues. However, post-transcriptional RNA modifications (epitranscriptomics) are still poorly explored in bees. We investigated the transcriptional profiles of m6A and m5C RNA methyltransferases in the brain and fat body of adult workers of 1) different ages and performing different tasks [nurses of 8 days-old (N-8D) and foragers of 29 days-old (F-29D), sampled from wild-type colonies], and 2) same-aged young workers caged in an incubator and treated with a pollen-rich [PR] or a pollen-deprived [PD] diet for 8 days. In the brain, METTL3, DNMT2, NOP2, NSUN2, NSUN5, and NSUN7 genes increased expression during adulthood (from N-8D to F-29D), while the opposite pattern was observed in the fat body for METTL3, DNMT2, and NSUN2 genes. Regarding diet treatments, high expression levels were observed in the brains of the pollen-deprived group (DNMT2, NOP2, and NSUN2 genes) and the fat bodies of the pollen-rich group (NOP2, NSUN4, and NSUN5 genes) compared to the brains of the PR group and the fat bodies of the PD group, respectively. Our data indicate that RNA epigenetics may be an important regulatory layer in the development of adult workers, presenting tissue-specific signatures of RNA methyltransferases expression in response to age, behavior, and diet content.
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Affiliation(s)
- Luana Bataglia
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Zilá Luz Paulino Simões
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Biologia, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Francis Morais Franco Nunes
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
- *Correspondence: Francis Morais Franco Nunes,
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13
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Wu L, Quan W, Zhang Y, Wang M, Ou X, Mao S, Sun D, Yang Q, Wu Y, Wei Y, Jia R, Chen S, Zhu D, Liu M, Zhao X, Zhang S, Huang J, Gao Q, Tian B, Cheng A. Attenuated Duck Hepatitis A Virus Infection Is Associated With High mRNA Maintenance in Duckling Liver via m6A Modification. Front Immunol 2022; 13:839677. [PMID: 35757688 PMCID: PMC9218207 DOI: 10.3389/fimmu.2022.839677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/05/2022] [Indexed: 11/15/2022] Open
Abstract
Host translation is generally modulated by viral infection, including duck hepatitis A virus (DHAV) infection. Previously, we reported that cellular protein synthesis in a cell model of duck embryo fibroblasts is significantly inhibited by DHAV infection but not viral proteins, suggesting that an important viral-host interaction occurs at the translational level. In this study, we aim to further understand the impact of DHAV virulence on cellular N6-methyladenosine (m6A) modification, which is essential to a wide variety of RNA biological processes, such as mRNA stabilization and translation. Using m6A antibody-based immunoprecipitation, m6A-seq, and LC–MS/MS, we observed that m6A-modified mRNA exists in both virulent and attenuated DHAV-infected duckling livers. Importantly, m6A levels in mRNA were much higher in attenuated DHAV-infected livers compared with virulent DHAV-infected livers, suggesting virulence-dependent regulation of m6A modification. Analysis of modification motifs indicated that GAAGAAG is the most enriched motif. Combined m6A-seq and RNA-seq data analysis indicated a generally positive correlation between m6A and mRNA expression levels in DHAV-infected duckling livers. GO analysis of genes with decreased or increased m6A levels showed that these genes were enriched in various terms, including oxidation–reduction processes and antiviral immune responses. Collectively, our work reveals DHAV virulence-dependent coordination between m6A modification and mRNA expression in duckling livers.
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Affiliation(s)
- Liping Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Weili Quan
- ABLife BioBigData Institute, Wuhan, China
| | - Yi Zhang
- ABLife BioBigData Institute, Wuhan, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yaxun Wei
- Center for Genome Analysis, ABLife, Inc., Wuhan, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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14
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Dai Z, Etebari K, Asgari S. N 6-methyladenosine modification of the Aedes aegypti transcriptome and its alteration upon dengue virus infection in Aag2 cell line. Commun Biol 2022; 5:607. [PMID: 35725909 PMCID: PMC9209429 DOI: 10.1038/s42003-022-03566-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022] Open
Abstract
The N6-methyladenosine (m6A) modification of RNA has been reported to affect viral infections. Studies have confirmed the role of m6A in replication of several vector-borne flaviviruses, including dengue virus (DENV), in mammalian cells. Here, we explored the role of m6A in DENV replication in the mosquito Aedes aegypti Aag2 cell line. We first determined the presence of m6A on the RNAs from mosquito cells and using methylated RNA immunoprecipitation and sequencing (MeRIP-Seq) identified m6A modification of the mosquito transcriptome and those that changed upon DENV infection. Depletion of m6A methyltransferases and the m6A binding protein YTHDF3 RNAs decreased the replication of DENV. In particular, we found that the Ae. aegypti ubiquitin carrier protein 9 (Ubc9) is m6A modified and its expression increases after DENV infection. Silencing of the gene and ectopic expression of Ubc9 led to reduced and increased DENV replication, respectively. The abundance of Ubc9 mRNA and its stability were reduced with the inhibition of m6A modification, implying that m6A modification of Ubc9 might enhance expression of the gene. We also show that the genome of DENV is m6A modified at five sites in mosquito cells. Altogether, this work reveals the involvement of m6A modification in Ae. aegypti-DENV interaction. Analysis of m6A RNA modifications in the mosquito transcriptome and their changes upon dengue virus infection provides insight into the role of epigenetics in regulating viral replication in mosquitoes.
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Affiliation(s)
- Zhenkai Dai
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Kayvan Etebari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia.
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15
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Li J, Zhang X, Wang X, Sun C, Zheng J, Li J, Yi G, Yang N. The m6A methylation regulates gonadal sex differentiation in chicken embryo. J Anim Sci Biotechnol 2022; 13:52. [PMID: 35581635 PMCID: PMC9115958 DOI: 10.1186/s40104-022-00710-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/16/2022] [Indexed: 01/06/2023] Open
Abstract
Background As a ubiquitous reversible epigenetic RNA modification, N6-methyladenosine (m6A) plays crucial regulatory roles in multiple biological pathways. However, its functional mechanisms in sex determination and differentiation during gonadal development of chicken embryos are not clear. Therefore, we established a transcriptome-wide m6A map in the female and male chicken left gonads of embryonic day 7 (E7) by methylated RNA immunoprecipitation sequencing (MeRIP-seq) to offer insight into the landscape of m6A methylation and investigate the post-transcriptional modification underlying gonadal differentiation. Results The chicken embryonic gonadal transcriptome was extensively methylated. We found 15,191 and 16,111 m6A peaks in the female and male left gonads, respectively, which were mainly enriched in the coding sequence (CDS) and stop codon. Among these m6A peaks, we identified that 1013 and 751 were hypermethylated in females and males, respectively. These differential peaks covered 281 and 327 genes, such as BMP2, SMAD2, SOX9 and CYP19A1, which were primarily associated with development, morphogenesis and sex differentiation by functional enrichment. Further analysis revealed that the m6A methylation level was positively correlated with gene expression abundance. Furthermore, we found that YTHDC2 could regulate the expression of sex-related genes, especially HEMGN and SOX9, in male mesonephros/gonad mingle cells, which was verified by in vitro experiments, suggesting a regulatory role of m6A methylation in chicken gonad differentiation. Conclusions This work provided a comprehensive m6A methylation profile of chicken embryonic gonads and revealed YTHDC2 as a key regulator responsible for sex differentiation. Our results contribute to a better understanding of epigenetic factors involved in chicken sex determination and differentiation and to promoting the future development of sex manipulation in poultry industry. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-022-00710-6.
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Affiliation(s)
- Jianbo Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Xiuan Zhang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Xiqiong Wang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Congjiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Jiangxia Zheng
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Junying Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China.
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16
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Liu C, Cao J, Zhang H, Wu J, Yin J. Profiling of Transcriptome-Wide N6-Methyladenosine (m6A) Modifications and Identifying m6A Associated Regulation in Sperm Tail Formation in Anopheles sinensis. Int J Mol Sci 2022; 23:ijms23094630. [PMID: 35563020 PMCID: PMC9101273 DOI: 10.3390/ijms23094630] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/19/2022] [Accepted: 04/19/2022] [Indexed: 12/13/2022] Open
Abstract
Recent discoveries of reversible N6-methyladenosine (m6A) methylation on messenger RNA (mRNA) and mapping of m6A methylomes in many species have revealed potential regulatory functions of this RNA modification by m6A players—writers, readers, and erasers. Here, we first profile transcriptome-wide m6A in female and male Anopheles sinensis and reveal that m6A is also a highly conserved modification of mRNA in mosquitoes. Distinct from mammals and yeast but similar to Arabidopsis thaliana, m6A in An. sinensis is enriched not only around the stop codon and within 3′-untranslated regions but also around the start codon and 5′-UTR. Gene ontology analysis indicates the unique distribution pattern of m6A in An. sinensis is associated with mosquito sex-specific pathways such as tRNA wobble uridine modification and phospholipid-binding in females, and peptidoglycan catabolic process, exosome and signal recognition particle, endoplasmic reticulum targeting, and RNA helicase activity in males. The positive correlation between m6A deposition and mRNA abundance indicates that m6A can play a role in regulating gene expression in mosquitoes. Furthermore, many spermatogenesis-associated genes, especially those related to mature sperm flagellum formation, are positively modulated by m6A methylation. A transcriptional regulatory network of m6A in An. sinensis is first profiled in the present study, especially in spermatogenesis, which may provide a new clue for the control of this disease-transmitting vector.
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17
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Yin L, Ma C, Hou S, Ma X. Methyltransferase-like (METTL)14-mediated N6-methyladenosine modification modulates retinal pigment epithelial (RPE) activity by regulating the methylation of microtubule-associated protein (MAP)2. Bioengineered 2022; 13:4773-4785. [PMID: 35139773 PMCID: PMC8973965 DOI: 10.1080/21655979.2022.2032968] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The expression of METTL14 is significantly reduced in patients with retinitis pigmentosa (RP). To clarify the significance of the N6-methyladenosine (m6A) RNA modification in RP, we examined phagocytosis, apoptosis, and cell cycle distribution in a human RPE cell line, ARPE-19, following lentivirus-mediated knockdown of METTL14. Differentially expressed genes and changes in m6A level were evaluated by RNA sequencing (RNA-seq) and methylated RNA immunoprecipitation sequencing (MeRIP-seq), respectively. The results showed that phagocytosis and proliferation were decreased whereas apoptosis was increased in RPE cells by METTL14 silencing. We found that METTL14 directly regulated m6A level and the expression of MAP2, as determined by RNA-seq, MeRIP-seq, MeRIP quantitative PCR, and the RNA pull-down assay. Additionally, MAP2 could bind to neuronal differentiation (NEUROD)1, a pathogenic gene in RPE-associated diseases. A family member of the YTH domain, (YTHDF)2 was recognized as an m6A reader of MAP2 mRNA. MAP2 overexpression had the same effects as METTL14 knockdown in RPE cells. Thus, METTL14 regulates the expression of MAP2 via the modification of m6A, resulting in the dysregulation of NEUROD1 and pathologic changes in RPE cells. These findings suggest that therapeutic strategies targeting the m6A modification of MAP2 or the METTL14/YTHDF2/MAP2/NEUROD1 signaling axis may be effective in the treatment of RPE-associated ocular diseases.
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Affiliation(s)
- Lu Yin
- Department of Ophthalmology, The First Affiliated Hospital of Dalian Medical University, Dalian, China.,Liaoning Province Division of National Clinical Research Center for Ocular Diseases, Dalian, China.,Liaoning Key Laboratory of Vitreoretinal Diseases, Dalian, China.,Dalian Corneal Stem Cell Transplantation Engineering Research Center, Dalian, China
| | - Cong Ma
- The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Shengping Hou
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Lab of Ophthalmology, Chongqing, China.,Chongqing Eye Institute, Chongqing, China
| | - Xiang Ma
- Department of Ophthalmology, The First Affiliated Hospital of Dalian Medical University, Dalian, China.,Liaoning Province Division of National Clinical Research Center for Ocular Diseases, Dalian, China.,Liaoning Key Laboratory of Vitreoretinal Diseases, Dalian, China.,Dalian Corneal Stem Cell Transplantation Engineering Research Center, Dalian, China
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18
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Guo F, Deng T, Shi L, Wu P, Yan J, Ling G, Chen H, Huang Q, Mu J, Mo L. Identification of an m6A RNA Methylation Regulator Risk Score Model for Prediction of Clinical Prognosis in Astrocytoma. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:7168929. [PMID: 35047056 PMCID: PMC8763512 DOI: 10.1155/2022/7168929] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/05/2021] [Accepted: 12/09/2021] [Indexed: 12/25/2022]
Abstract
Astrocytoma (AS) is the most ubiquitous primary malignancy of the central nervous system (CNS). The vital involvement of the N6-methyladenosine (m6A) RNA modification in the growth of multiple human tumors is known. This study entailed probing m6A regulators with AS prognosis to construct a risk prediction model (RS) for potential clinical use. A total of 579 AS patients' (of the Chinese Glioma Genome Atlas,CGGA) data and the expression of 12 published m6A-related genes were included in this study. Cox and selection operator (LASSO) regression analyses for independent prognostic factors and multifactor Cox analysis established an R.S. model to predict the AS patient prognosis. This was subject to verification employing 331 samples from the TCGA data set followed by gene ontology and pathway enrichment study with gene set enrichment analysis (GSEA). The R.S. constructed with three m6A genes inclusive of WTAP, RBM15, and YTHDF2 emerged as independent prognostic factors in AS patients with vital involvement in the advancement and development of the malignancy. In a nutshell, this work reported an m6A-related gene risk model to predict the prognosis of AS patients to pave the way for discerning diagnostic and prognostic biomarkers. Further corroboration employing relevant wet-lab assays of this model is warranted.
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Affiliation(s)
- Fangzhou Guo
- Department of Neurosurgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Teng Deng
- Department of Neurosurgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Liu Shi
- Department of Neurosurgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Pinghua Wu
- Department of Neurosurgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Jun Yan
- Department of Neurosurgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Guoyuan Ling
- Department of Neurosurgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Hainan Chen
- Department of Neurosurgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Qianrong Huang
- Department of Neurosurgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Junbo Mu
- Department of Neurosurgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Ligen Mo
- Department of Neurosurgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
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19
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Bataglia L, Simões ZLP, Nunes FMF. Active genic machinery for epigenetic RNA modifications in bees. INSECT MOLECULAR BIOLOGY 2021; 30:566-579. [PMID: 34291855 DOI: 10.1111/imb.12726] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/25/2021] [Accepted: 07/19/2021] [Indexed: 05/06/2023]
Abstract
Epitranscriptomics is an emerging field of investigation dedicated to the study of post-transcriptional RNA modifications. RNA methylations regulate RNA metabolism and processing, including changes in response to environmental cues. Although RNA modifications are conserved from bacteria to eukaryotes, there is little evidence of an epitranscriptomic pathway in insects. Here we identified genes related to RNA m6 A (N6-methyladenine) and m5 C (5-methylcytosine) methylation machinery in seven bee genomes (Apis mellifera, Melipona quadrifasciata, Frieseomelitta varia, Eufriesea mexicana, Bombus terrestris, Megachile rotundata and Dufourea novaeangliae). In A. mellifera, we validated the expression of methyltransferase genes and found that the global levels of m6 A and m5 C measured in the fat body and brain of adult workers differ significantly. Also, m6 A levels were differed significantly mainly between the fourth larval instar of queens and workers. Moreover, we found a conserved m5 C site in the honeybee 28S rRNA. Taken together, we confirm the existence of epitranscriptomic machinery acting in bees and open avenues for future investigations on RNA epigenetics in a wide spectrum of hymenopteran species.
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Affiliation(s)
- L Bataglia
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Z L P Simões
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - F M F Nunes
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
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20
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Zhang K, Zhuang X, Dong Z, Xu K, Chen X, Liu F, He Z. The dynamics of N 6-methyladenine RNA modification in interactions between rice and plant viruses. Genome Biol 2021; 22:189. [PMID: 34167554 PMCID: PMC8229379 DOI: 10.1186/s13059-021-02410-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/14/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) is the most common RNA modification in eukaryotes and has been implicated as a novel epigenetic marker that is involved in various biological processes. The pattern and functional dissection of m6A in the regulation of several major human viral diseases have already been reported. However, the patterns and functions of m6A distribution in plant disease bursting remain largely unknown. RESULTS We analyse the high-quality m6A methylomes in rice plants infected with two devastating viruses. We find that the m6A methylation is mainly associated with genes that are not actively expressed in virus-infected rice plants. We also detect different m6A peak distributions on the same gene, which may contribute to different antiviral modes between rice stripe virus or rice black-stripe dwarf virus infection. Interestingly, we observe increased levels of m6A methylation in rice plant response to virus infection. Several antiviral pathway-related genes, such as RNA silencing-, resistance-, and fundamental antiviral phytohormone metabolic-related genes, are also m6A methylated. The level of m6A methylation is tightly associated with its relative expression levels. CONCLUSIONS We revealed the dynamics of m6A modification during the interaction between rice and viruses, which may act as a main regulatory strategy in gene expression. Our investigations highlight the significance of m6A modifications in interactions between plant and viruses, especially in regulating the expression of genes involved in key pathways.
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Affiliation(s)
- Kun Zhang
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu Province, People's Republic of China
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, People's Republic of China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Wenhui East Road No.48, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Xinjian Zhuang
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Zhuozhuo Dong
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Kai Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Xijun Chen
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Fang Liu
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu Province, People's Republic of China.
| | - Zhen He
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu Province, People's Republic of China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Wenhui East Road No.48, Yangzhou, 225009, Jiangsu Province, People's Republic of China.
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21
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Yang X, Wei X, Yang J, Du T, Yin C, Fu B, Huang M, Liang J, Gong P, Liu S, Xie W, Guo Z, Wang S, Wu Q, Nauen R, Zhou X, Bass C, Zhang Y. Epitranscriptomic regulation of insecticide resistance. SCIENCE ADVANCES 2021; 7:eabe5903. [PMID: 33952517 PMCID: PMC8099183 DOI: 10.1126/sciadv.abe5903] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/16/2021] [Indexed: 05/07/2023]
Abstract
N 6-methyladenosine (m6A) is the most prevalent messenger RNA modification in eukaryotes and an important posttranscriptional regulator of gene expression. However, the biological roles of m6A in most insects remain largely unknown. Here, we show that m6A regulates a cytochrome P450 gene (CYP4C64) in the global whitefly pest, Bemisia tabaci, leading to insecticide resistance. Investigation of the regulation of CYP4C64, which confers resistance to the insecticide thiamethoxam, revealed a mutation in the 5' untranslated region of this gene in resistant B. tabaci strains that introduces a predicted m6A site. We provide several lines of evidence that mRNA methylation of the adenine at this position, in combination with modified expression of m6A writers, acts to increase expression of CYP4C64 and resistance. Collectively, these results provide an example of the epitranscriptomic regulation of the xenobiotic response in insects and implicate the m6A regulatory axis in the development of insecticide resistance.
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Affiliation(s)
- Xin Yang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xuegao Wei
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jing Yang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tianhua Du
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cheng Yin
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Buli Fu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mingjiao Huang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinjin Liang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Peipan Gong
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shaonan Liu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wen Xie
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhaojiang Guo
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shaoli Wang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qingjun Wu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ralf Nauen
- Bayer AG, Crop Science Division, R&D, Alfred Nobel-Strasse 50, 40789 Monheim, Germany
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY 40546-0091, USA
| | - Chris Bass
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK.
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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22
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Cao Z, Zhang D, Wang Y, Tong X, Avalos LFC, Khan IM, Gao D, Xu T, Zhang L, G Knott J, Zhang Y. Identification and functional annotation of m6A methylation modification in granulosa cells during antral follicle development in pigs. Anim Reprod Sci 2020; 219:106510. [PMID: 32828396 DOI: 10.1016/j.anireprosci.2020.106510] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/13/2022]
Abstract
The N6-methyladenosine (m6A) derivative has the capacity for ubiquitous epigenetic modification of messenger RNA (mRNA) that regulates gene expression through post-transcriptional mRNA modifications. Findings with mapping of m6A methylomes have indicated there are potential functions of this derivative in different cell types of several species. A profile of m6A methylomes and potential functions in granulosa cells of pigs during antral follicle development, however, has not yet occurred. In the present study, there was profiling of an epitranscriptome-wide map of m6A methylation in granulosa cells of pigs derived from small and large follicles using methylated RNA immunoprecipitation techniques, next-generation sequencing and further annotation of the potential functions of m6A utilizing bioinformatic analyses procedures. The m6A modification is abundant in granulosa cells of pigs, and there are dynamic changes in m6A methylomes during the developmental transition from small (< 3 mm) to large (> 5 mm) sized follicles. In particular, there was a prevalence of 7289 and 6882 m6A in granulosa cells from follicles of two different sizes. There was an increased prevalence of m6A in close proximity to the 5' or 3'-untranslated coding regions and a shared conserved consensus motif. Results from further analysis indicated there was significant enrichment of differentially expressed m6A methylated genes in several signaling pathways associated with steroidogenesis, granulosa cell proliferation and follicular development. When considered as a whole, these results indicate there are differential m6A modifications in granulosa cells of pigs during follicle development that are potentially associated with steroidogenesis and folliculogenesis.
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Affiliation(s)
- Zubing Cao
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Dandan Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yiqing Wang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xu Tong
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Lourdes Felicidad Córdova Avalos
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Ibrar Muhammad Khan
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Di Gao
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Tengteng Xu
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Ling Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Jason G Knott
- Developmental Epigenetics Laboratory, Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Yunhai Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China.
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23
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Zhu Z, Guan Z, Liu G, Wang Y, Zhang Z. SGID: a comprehensive and interactive database of the silkworm. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5677404. [PMID: 31836898 PMCID: PMC6911161 DOI: 10.1093/database/baz134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/27/2019] [Accepted: 11/01/2019] [Indexed: 11/12/2022]
Abstract
Although the domestic silkworm (Bombyx mori) is an important model and economic animal, there is a lack of comprehensive database for this organism. Here, we developed the silkworm genome informatics database (SGID). It aims to bring together all silkworm-related biological data and provide an interactive platform for gene inquiry and analysis. The function annotation in SGID is thorough and covers 98% of the silkworm genes. The annotation details include function description, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway, subcellular location, transmembrane topology, protein secondary/tertiary structure, homologous group and transcription factor. SGID provides genome-scale visualization of population genetics test results based on high-depth resequencing data of 158 silkworm samples. It also provides interactive analysis tools of transcriptomic and epigenomic data from 79 NCBI BioProjects. SGID will be extremely useful to silkworm research in the future.
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Affiliation(s)
- Zhenglin Zhu
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China
| | - Zhufen Guan
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China
| | - Gexin Liu
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China
| | - Yawang Wang
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China.,Khoury College of Computer Sciences, Northeastern University, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Ze Zhang
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China
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24
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The emerging molecular mechanism of m 6A modulators in tumorigenesis and cancer progression. Biomed Pharmacother 2020; 127:110098. [PMID: 32299028 DOI: 10.1016/j.biopha.2020.110098] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/24/2020] [Accepted: 03/09/2020] [Indexed: 02/08/2023] Open
Abstract
N6-methyladenosine (m6A) is the most abundant RNA modification; m6A modifications are installed by methyltransferases, removed by demethylases and recognized by reader proteins. M6A plays crucial roles in a variety of biological processes by regulating target RNA translation, splicing, nuclear export, and decay. Since the establishment of methylated RNA immunoprecipitation-sequencing methodology, over three hundred articles about m6A modulators, including "writers", "erasers" and "readers", have been reported in the last four years. In addition, an increasing number of molecular mechanisms underlying m6A RNA methylation in human cancers have been comprehensively clarified. The recently emerged molecular mechanisms of m6A modulators in cancer cell proliferation, cell cycle progression, migration and invasion, apoptosis, and autophagy remain to be summarized. Hence, this review specifically summarizes these recent advances in the understanding of m6A molecular mechanisms in tumorigenesis and cancer progression. In addition, we discuss the prospect of using an m6A methylation modulator as a new diagnostic biomarker and therapeutic target for human cancers.
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25
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Zhang X, Zhang Y, Dai K, Liang Z, Zhu M, Pan J, Zhang M, Yan B, Zhu H, Zhang Z, Dai Y, Cao M, Gu Y, Xue R, Cao G, Hu X, Gong C. N 6-Methyladenosine Level in Silkworm Midgut/Ovary Cell Line Is Associated With Bombyx mori Nucleopolyhedrovirus Infection. Front Microbiol 2020; 10:2988. [PMID: 31998272 PMCID: PMC6965365 DOI: 10.3389/fmicb.2019.02988] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 12/10/2019] [Indexed: 12/31/2022] Open
Abstract
Bombyx mori nucleopolyhedrovirus (BmNPV) is one of the most serious pathogens in sericulture and causes huge economic loss annually. The roles of N6-methyladenosine (m6A) modification in silkworms following BmNPV infection are currently unclear. Here, methylated RNA immunoprecipitation with next-generation sequencing were applied to investigate the m6A profiles in silkworm midgut following BmNPV infection. A total of 9144 and 7384 m6A peaks were identified from the BmNPV-infected (TEST) and uninfected silkworm midguts (CON), respectively, which were distributed predominantly near stop codons. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of common m6A peaks in nuclear genes revealed that these m6A-related transcripts were associated with crucial signaling pathways. Comparative transcriptome analysis showed that 1221 differential expressed m6A peaks were identified between TEST and CON, indicating that m6A modification is regulated following BmNPV infection. GO and KEGG pathway analysis of the differentially expressed m6A peaks showed their association with signal transduction, translation, and degradation. To understand further the effect of the m6A machinery on virus infection, expression levels of m6A-related genes were altered in silencing and overexpression experiments. Expression of viral structural protein VP39 was increased in BmN cells by siRNA-mediated depletion of methyltransferase-like (METTL) enzyme genes (BmMETTL3, BmMETTL14) and cytoplasmic YTH-domain family 3 (BmYTHDF3), while the reverse results were found after overexpression of the m6A-related enzymes in BmN cells. Overall, m6A modification might be a novel epigenetic mechanism that regulation BmNPV infection and interference with this mechanism may provide a novel antiviral strategy for preventing BmNPV disease.
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Affiliation(s)
- Xing Zhang
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China.,Institute of Agricultural Biotechnology and Ecological Research, Soochow University, Suzhou, China
| | - Yunshan Zhang
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Kun Dai
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Zi Liang
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Min Zhu
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Jun Pan
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Mingtian Zhang
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Bingyu Yan
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Hanxue Zhu
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Ziyao Zhang
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Yaping Dai
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Manman Cao
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Yuchao Gu
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Renyu Xue
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China.,Institute of Agricultural Biotechnology and Ecological Research, Soochow University, Suzhou, China
| | - Guangli Cao
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China.,Institute of Agricultural Biotechnology and Ecological Research, Soochow University, Suzhou, China
| | - Xiaolong Hu
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China.,Institute of Agricultural Biotechnology and Ecological Research, Soochow University, Suzhou, China
| | - Chengliang Gong
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China.,Institute of Agricultural Biotechnology and Ecological Research, Soochow University, Suzhou, China
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26
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Li B, Li Z, Lu C, Chang L, Zhao D, Shen G, Kusakabe T, Xia Q, Zhao P. Heat Shock Cognate 70 Functions as A Chaperone for the Stability of Kinetochore Protein CENP-N in Holocentric Insect Silkworms. Int J Mol Sci 2019; 20:ijms20235823. [PMID: 31756960 PMCID: PMC6929194 DOI: 10.3390/ijms20235823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/18/2019] [Accepted: 11/18/2019] [Indexed: 01/09/2023] Open
Abstract
The centromere, in which kinetochore proteins are assembled, plays an important role in the accurate congression and segregation of chromosomes during cell mitosis. Although the function of the centromere and kinetochore is conserved from monocentric to holocentric, the DNA sequences of the centromere and components of the kinetochore are varied among different species. Given the lack of core centromere protein A (CENP-A) and CENP-C in the lepidopteran silkworm Bombyx mori, which possesses holocentric chromosomes, here we investigated the role of CENP-N, another important member of the centromere protein family essential for kinetochore assembly. For the first time, cellular localization and RNA interference against CENP-N have confirmed its kinetochore function in silkworms. To gain further insights into the regulation of CENP-N in the centromere, we analyzed the affinity-purified complex of CENP-N by mass spectrometry and identified 142 interacting proteins. Among these factors, we found that the chaperone protein heat shock cognate 70 (HSC70) is able to regulate the stability of CENP-N by prohibiting ubiquitin-proteasome pathway, indicating that HSC70 could control cell cycle-regulated degradation of CENP-N at centromeres. Altogether, the present work will provide a novel clue to understand the regulatory mechanism for the kinetochore activity of CENP-N during the cell cycle.
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Affiliation(s)
- Bingqian Li
- Biological Science Research Center, Southwest University, Chongqing 400715, China; (B.L.); (C.L.); (L.C.); (D.Z.); (G.S.); (Q.X.); (P.Z.)
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
| | - Zhiqing Li
- Biological Science Research Center, Southwest University, Chongqing 400715, China; (B.L.); (C.L.); (L.C.); (D.Z.); (G.S.); (Q.X.); (P.Z.)
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
- Correspondence:
| | - Chenchen Lu
- Biological Science Research Center, Southwest University, Chongqing 400715, China; (B.L.); (C.L.); (L.C.); (D.Z.); (G.S.); (Q.X.); (P.Z.)
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
| | - Li Chang
- Biological Science Research Center, Southwest University, Chongqing 400715, China; (B.L.); (C.L.); (L.C.); (D.Z.); (G.S.); (Q.X.); (P.Z.)
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
| | - Dongchao Zhao
- Biological Science Research Center, Southwest University, Chongqing 400715, China; (B.L.); (C.L.); (L.C.); (D.Z.); (G.S.); (Q.X.); (P.Z.)
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
| | - Guanwang Shen
- Biological Science Research Center, Southwest University, Chongqing 400715, China; (B.L.); (C.L.); (L.C.); (D.Z.); (G.S.); (Q.X.); (P.Z.)
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
| | - Takahiro Kusakabe
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka 819-0395, Japan;
| | - Qingyou Xia
- Biological Science Research Center, Southwest University, Chongqing 400715, China; (B.L.); (C.L.); (L.C.); (D.Z.); (G.S.); (Q.X.); (P.Z.)
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
| | - Ping Zhao
- Biological Science Research Center, Southwest University, Chongqing 400715, China; (B.L.); (C.L.); (L.C.); (D.Z.); (G.S.); (Q.X.); (P.Z.)
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
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27
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Li Z, Zhao P, Xia Q. Epigenetic Methylations on N6-Adenine and N6-Adenosine with the same Input but Different Output. Int J Mol Sci 2019; 20:ijms20122931. [PMID: 31208067 PMCID: PMC6627651 DOI: 10.3390/ijms20122931] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 12/15/2022] Open
Abstract
Epigenetic modifications on individual bases in DNA and RNA can encode inheritable genetic information beyond the canonical bases. Among the nucleic acid modifications, DNA N6-methadenine (6mA) and RNA N6-methyladenosine (m6A) have recently been well-studied due to the technological development of detection strategies and the functional identification of modification enzymes. The current findings demonstrate a wide spectrum of 6mA and m6A distributions from prokaryotes to eukaryotes and critical roles in multiple cellular processes. It is interesting that the processes of modification in which the methyl group is added to adenine and adenosine are the same, but the outcomes of these modifications in terms of their physiological impacts in organisms are quite different. In this review, we summarize the latest progress in the study of enzymes involved in the 6mA and m6A methylation machinery, including methyltransferases and demethylases, and their functions in various biological pathways. In particular, we focus on the mechanisms by which 6mA and m6A regulate the expression of target genes, and we highlight the future challenges in epigenetic regulation.
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Affiliation(s)
- Zhiqing Li
- Biological Science Research Center, Southwest University, Chongqing 400715, China.
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China.
| | - Ping Zhao
- Biological Science Research Center, Southwest University, Chongqing 400715, China.
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China.
| | - Qingyou Xia
- Biological Science Research Center, Southwest University, Chongqing 400715, China.
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China.
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