5-Methylcytosine （m^5C） is a well-characterized DNA modification, and is also predominantly reported in abundant non-coding RNAs in both prokaryotes and eukaryotes. However, the distribution and biological functions...5-Methylcytosine （m^5C） is a well-characterized DNA modification, and is also predominantly reported in abundant non-coding RNAs in both prokaryotes and eukaryotes. However, the distribution and biological functions of m^5C in plant mRNAs remain largely unknown. Here, we report transcriptome-wide profiling of RNA m^5C in Arabidopsis thaliana by applying m^5C RNA immunoprecipitation followed by a deep- sequencing approach （m^5C-RIP-seq）. LC-MS/MS and dot blot analyses reveal a dynamic pattern of m^5C mRNA modification in various tissues and at different developmental stages, m^5C-RIP-seq analysis identified 6045 m^5C peaks in 4465 expressed genes in young seedlings. We found that m^5C is enriched in coding sequences with two peaks located immediately after start codons and before stop codons, and is associated with mRNAs with low translation activity. We further demonstrated that an RNA （cytosine-5）-methyl- transferase, tRNA-specific methyltransferase 4B （TRM4B）, exhibits m^5C RNA methyltransferase activity. Mutations in TRM4B display defects in root development and decreased m^5C peaks. TRM4B affects the transcript levels of the genes involved in root development, which is positively correlated with their mRNA stability and m^5C levels. Our results suggest that m^5C in mRNA is a new epitranscriptome marker inArabidopsis, and that regulation of this modification is an integral part of gene regulatory networks underlying plant development.展开更多
Exposure of airborne particulate matter(PM)with an aerodynamic diameter less than 2.5μm(PM2.5)is epidemiologically associated with lung dysfunction and respiratory symptoms,including pulmonary fibrosis.However,whethe...Exposure of airborne particulate matter(PM)with an aerodynamic diameter less than 2.5μm(PM2.5)is epidemiologically associated with lung dysfunction and respiratory symptoms,including pulmonary fibrosis.However,whether epigenetic mechanisms are involved in PM2.5-induced pulmonary fibrosis is currently poorly understood.Herein,using a PM2.5-induced pulmonary fibrosis mouse model,we found that PM2.5 exposure leads to aberrant mRNA5-methylcytosine(m5C)gain and loss in fibrotic lung tissues.Moreover,we showed the m5C-mediated regulatory map of gene functions in pulmonary fibrosis after PM2.5 exposure.Several genes act as m5C gain-upregulated factors,probably critical for the development of PM2.5-induced fibrosis in mouse lungs.These genes,including Lcn2,Mmp9,Chi3l1,Adipoq,Atp5j2,Atp5l,Atpif1,Ndufb6,Fgr,Slc11 a1,and Tyrobp,are highly related to oxidative stress response,inflammatory responses,and immune system processes.Our study illustrates the first epitranscriptomic RNA m5C profile in PM2.5-induced pulmonary fibrosis and will be valuable in identifying biomarkers for PM2.5 exposure-related lung pathogenesis with translational potential.展开更多
5-Methylcytosine(m^(5)C)is one of the most prevalent internal modifications of messenger RNA(mRNA)in higher eukaryotes.Here we report that Y box protein 2(YBX2)serves as a novel mammalian m^(5)C binding protein to und...5-Methylcytosine(m^(5)C)is one of the most prevalent internal modifications of messenger RNA(mRNA)in higher eukaryotes.Here we report that Y box protein 2(YBX2)serves as a novel mammalian m^(5)C binding protein to undergo liquid-liquid phase separation(LLPS)both in vivo and in vitro,and this YBX2-dependent LLPS is enhanced by m^(5)C marked RNA.Furthermore,the crystal structure assay revealed that W100,as a distinct m^(5)C binding site of YBX2,is critical in mediating YBX2 phase separation.Our study resolved the relationship between RNA m^(5)C and phase separation,providing a clue for a new regulatory layer of epigenetics.展开更多
After implantation,complex and highly specialized molecular events render functionally distinct organ formation,whereas how the epigenome shapes organ-specific development remains to be fully elucidated.Here,nano-hmC-...After implantation,complex and highly specialized molecular events render functionally distinct organ formation,whereas how the epigenome shapes organ-specific development remains to be fully elucidated.Here,nano-hmC-Seal,RNA bisulfite sequencing(RNA-BisSeq),and RNA sequencing(RNA-Seq)were performed,and the first multilayer landscapes of DNA 5-hydroxymethylcytosine(5hmC)and RNA 5-methylcytosine(m^(5)C)epigenomes were obtained in the heart,kidney,liver,and lung of the human foetuses at 13-28 weeks with 123 samples in total.We identified 70,091 and 503 organ-and stage-specific differentially hydroxymethylated regions(DhMRs)and m^(5)C-modified mRNAs,respectively.The key transcription factors(TFs),T-box transcription factor 20(TBX20),paired box 8(PAX8),krueppel-like factor 1(KLF1),transcription factor 21(TCF21),and CCAAT enhancer binding protein beta(CEBPB),specifically contribute to the formation of distinct organs at different stages.Additionally,5hmC-enriched Alu elements may participate in the regulation of expression of TF-targeted genes.Our integrated studies reveal a putative essential link between DNA modification and RNA methylation,and illustrate the epigenetic maps during human foetal organogenesis,which provide a foundation for an in-depth understanding of the epigenetic mechanisms underlying early development and birth defects.展开更多
5-Methylcytosine (5mC) is a dynamic and reversible epigenetic modification in genomic DNA of higher eukaryotes.It has been well-established that the demethylation of 5mC occurs through the ten-eleven translocation (TE...5-Methylcytosine (5mC) is a dynamic and reversible epigenetic modification in genomic DNA of higher eukaryotes.It has been well-established that the demethylation of 5mC occurs through the ten-eleven translocation (TET)-mediated oxidation of 5mC followed by thymine DNA glycosylase (TDG)-initiated base excision repair (BER).Recent findings also have identified an alternative pathway of DNA demethylation.In this pathway,TET enzymes directly oxidize 5mC to form 5-formylcytosine (5fC) or 5-carboxylcytosine (5caC).These modified bases can undergo direct deformylation or decarboxylation,respectively.Additionally,DNA demethylation can also occur through the deamination of 5mC and 5hmC,resulting in the production of thymine and 5-hydroxymethyluracil (5hmU),respectively.Various DNA demethylation pathways possess critical functional implications and roles in biological processes.This Recent Advances article will focus on the studies of mechanisms and biological functions of DNA demethylation,shedding light on the reversible nature of the epigenetic modification of 5mC.展开更多
Among over 170 different types of chemical modifications on RNA nucleobases identified so far,RNA methylation is the major type of epitranscriptomic modifications existing on almost all types of RNAs,and has been demo...Among over 170 different types of chemical modifications on RNA nucleobases identified so far,RNA methylation is the major type of epitranscriptomic modifications existing on almost all types of RNAs,and has been demonstrated to participate in the entire process of RNA metabolism,including transcription,pre-mRNA alternative splicing and maturation,mRNA nucleus export,mRNA degradation and stabilization,mRNA translation.Attributing to the development of high-throughput detection technologies and the identification of both dynamic regulators and recognition proteins,mechanisms of RNA methylation modification in regulating the normal development of the organism as well as various disease occurrence and developmental abnormalities upon RNA methylation dysregulation have become increasingly clear.Here,we particularly focus on three types of RNA methylations:N^(6)-methylcytosine(m^(6)A),5-methylcytosine(m^(5)C),and N^(7)-methyladenosine(m^(7)G).We summarize the elements related to their dynamic installment and removal,specific binding proteins,and the development of high-throughput detection technologies.Then,for a comprehensive understanding of their biological significance,we also overview the latest knowledge on the underlying mechanisms and key roles of these three mRNA methylation modifications in gametogenesis,embryonic development,immune system development,as well as disease and tumor progression.展开更多
More than 160 types of post-transcriptional RNA modifications have been reported;there is substantial variation in modification type,abundance,site,and function across species,tissues,and RNA type.The recent developme...More than 160 types of post-transcriptional RNA modifications have been reported;there is substantial variation in modification type,abundance,site,and function across species,tissues,and RNA type.The recent development of high-throughput detection technology has enabled identification of diverse dynamic and reversible RNA modifications,including N6,2′-O-dimethyladenosine(m6Am),N1-methyladenosine(m1A),5-methylcytosine(m5C),N6-methyladenosine(m6A),pseudouridine(Ψ),and inosine(I).In this review,we focus on eukaryotic mRNA modifications.We summarize their biogenesis,regulatory mechanisms,and biological functions,as well as highthroughput methods for detection of mRNA modifications.We also discuss challenges that must be addressed in mRNA modification research.展开更多
Advances in the detection and mapping of messenger RNA(mRNA)N^6-methyladenosine(m 6A)and 5-methylcytosine(m 5C),and DNA N^6-methyldeoxyadenosine(6mA)redefined our understanding of these modifications as additional tie...Advances in the detection and mapping of messenger RNA(mRNA)N^6-methyladenosine(m 6A)and 5-methylcytosine(m 5C),and DNA N^6-methyldeoxyadenosine(6mA)redefined our understanding of these modifications as additional tiers of epigenetic regulation.In plants,the most prevalent internal mRNA modifications,m^6A and m^5C,play crucial and dynamic roles in many processes,including embryo development,stem cell fate determination,trichome branching,leaf morphogenesis,floral transition,stress responses,fruit ripening,and root development.The newly identified and widespread epigenetic marker 6mA DNA methylation is associated with gene expression,plant development,and stress responses.Here,we review the latest research progress on mRNA and DNA epigenetic modifications,including the detection,dynamics,distribution,functions,regulatory proteins,and evolution,with a focus on m^6A,m^5C,and 6mA.We also provide some perspectives on future research of the newly identified and unknown epigenetic modifications of mRNA and DNA in plants.展开更多
The advent of high-throughput sequencing technol- ogies coupled with new detection methods of RNA modifica- tions has enabled investigation of a new layer of gene regulation - the epitranscriptome. With over loo known...The advent of high-throughput sequencing technol- ogies coupled with new detection methods of RNA modifica- tions has enabled investigation of a new layer of gene regulation - the epitranscriptome. With over loo known RNA modifications, understanding the repertoire of RNA modifications is a huge undertaking. This review summarizes what is known about RNA modifications with an emphasis on discoveries in plants. RNA ribose modifications, base methyl- ations and pseudouridylation are required for normal develop- ment in Arabidopsis, as mutations in the enzymes modifying them have diverse effects on plant development and stress responses. These modifications can regulate RNA structure, turnover and translation. Transfer RNA and ribosomal RNA modifications have been mapped extensively and their functions investigated in many organisms, including plants. Recent work exploring the locations, functions and targeting of N6-methyladenosine （m^6A）, 5-methylcytosine （m^5C）, pseudour- idine （up）, and additional modifications in mRNAs and ncRNAs are highlighted, as well as those previously known on tRNAs and rRNAs. Many questions remain as to the exact mechanisms of targeting and functions of specific modified sites and whether these modifications have distinct functions in the different classes of RNAs.展开更多
文摘5-Methylcytosine （m^5C） is a well-characterized DNA modification, and is also predominantly reported in abundant non-coding RNAs in both prokaryotes and eukaryotes. However, the distribution and biological functions of m^5C in plant mRNAs remain largely unknown. Here, we report transcriptome-wide profiling of RNA m^5C in Arabidopsis thaliana by applying m^5C RNA immunoprecipitation followed by a deep- sequencing approach （m^5C-RIP-seq）. LC-MS/MS and dot blot analyses reveal a dynamic pattern of m^5C mRNA modification in various tissues and at different developmental stages, m^5C-RIP-seq analysis identified 6045 m^5C peaks in 4465 expressed genes in young seedlings. We found that m^5C is enriched in coding sequences with two peaks located immediately after start codons and before stop codons, and is associated with mRNAs with low translation activity. We further demonstrated that an RNA （cytosine-5）-methyl- transferase, tRNA-specific methyltransferase 4B （TRM4B）, exhibits m^5C RNA methyltransferase activity. Mutations in TRM4B display defects in root development and decreased m^5C peaks. TRM4B affects the transcript levels of the genes involved in root development, which is positively correlated with their mRNA stability and m^5C levels. Our results suggest that m^5C in mRNA is a new epitranscriptome marker inArabidopsis, and that regulation of this modification is an integral part of gene regulatory networks underlying plant development.
基金supported by the State Key Program of the National Natural Science Foundation of China(Grant No.91643206)the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDB14030300)the Chinese Academy of Sciences/State Administration of Foreign Experts Affairs(CAS/SAFEA)International Partnership Program for Creative Research Teams of China
文摘Exposure of airborne particulate matter(PM)with an aerodynamic diameter less than 2.5μm(PM2.5)is epidemiologically associated with lung dysfunction and respiratory symptoms,including pulmonary fibrosis.However,whether epigenetic mechanisms are involved in PM2.5-induced pulmonary fibrosis is currently poorly understood.Herein,using a PM2.5-induced pulmonary fibrosis mouse model,we found that PM2.5 exposure leads to aberrant mRNA5-methylcytosine(m5C)gain and loss in fibrotic lung tissues.Moreover,we showed the m5C-mediated regulatory map of gene functions in pulmonary fibrosis after PM2.5 exposure.Several genes act as m5C gain-upregulated factors,probably critical for the development of PM2.5-induced fibrosis in mouse lungs.These genes,including Lcn2,Mmp9,Chi3l1,Adipoq,Atp5j2,Atp5l,Atpif1,Ndufb6,Fgr,Slc11 a1,and Tyrobp,are highly related to oxidative stress response,inflammatory responses,and immune system processes.Our study illustrates the first epitranscriptomic RNA m5C profile in PM2.5-induced pulmonary fibrosis and will be valuable in identifying biomarkers for PM2.5 exposure-related lung pathogenesis with translational potential.
基金the National Natural Science Foundation of China(Grants No.32030058,91940302,91940304,91940000 and 92053115)the fellowship of China Postdoctoral Science Foundation(Grant No.2020M670986)+3 种基金the National Key R&D Program of China(Grants No.2018YFA0109700,2019YFA0801702 and 2019YFA0802201)Beijing Nova Program(Grant No.Z201100006820104)the Youth Innovation Promotion Association of Chinese Academy of Sciences(Grant No.CAS2018133)the Open Research Fund of the National Center for Protein Sciences at Peking University in Beijing.We thank the National Center for Protein Science Shanghai for their instrumental support and technical assistance.We thank the staff from the BL18U1 beamline at Shanghai Synchrotron Radiation Facility for assistance during data collection.
文摘5-Methylcytosine(m^(5)C)is one of the most prevalent internal modifications of messenger RNA(mRNA)in higher eukaryotes.Here we report that Y box protein 2(YBX2)serves as a novel mammalian m^(5)C binding protein to undergo liquid-liquid phase separation(LLPS)both in vivo and in vitro,and this YBX2-dependent LLPS is enhanced by m^(5)C marked RNA.Furthermore,the crystal structure assay revealed that W100,as a distinct m^(5)C binding site of YBX2,is critical in mediating YBX2 phase separation.Our study resolved the relationship between RNA m^(5)C and phase separation,providing a clue for a new regulatory layer of epigenetics.
基金supported by the National Key R&D Program of China(Grant Nos.2019YFA0110900,2019YFA0802202,2019YFA0802200 and 2020YFA0803401)the National Natural Science Foundation of China(Grant Nos.31870817 and 32170819)+2 种基金the Scientific and Technological Innovation Talent Project of Universities of Henan Province,China(Grant No.20HASTIT045)the Shanghai Municipal Science and Technology Major Project,China(Grant No.2017SHZDZX01)the China Postdoctoral Science Foundation(Grant No.2021M692927).
文摘After implantation,complex and highly specialized molecular events render functionally distinct organ formation,whereas how the epigenome shapes organ-specific development remains to be fully elucidated.Here,nano-hmC-Seal,RNA bisulfite sequencing(RNA-BisSeq),and RNA sequencing(RNA-Seq)were performed,and the first multilayer landscapes of DNA 5-hydroxymethylcytosine(5hmC)and RNA 5-methylcytosine(m^(5)C)epigenomes were obtained in the heart,kidney,liver,and lung of the human foetuses at 13-28 weeks with 123 samples in total.We identified 70,091 and 503 organ-and stage-specific differentially hydroxymethylated regions(DhMRs)and m^(5)C-modified mRNAs,respectively.The key transcription factors(TFs),T-box transcription factor 20(TBX20),paired box 8(PAX8),krueppel-like factor 1(KLF1),transcription factor 21(TCF21),and CCAAT enhancer binding protein beta(CEBPB),specifically contribute to the formation of distinct organs at different stages.Additionally,5hmC-enriched Alu elements may participate in the regulation of expression of TF-targeted genes.Our integrated studies reveal a putative essential link between DNA modification and RNA methylation,and illustrate the epigenetic maps during human foetal organogenesis,which provide a foundation for an in-depth understanding of the epigenetic mechanisms underlying early development and birth defects.
基金supported by the National Natural Science Foundation of China(22074110)Guangdong Basic and Applied Basic Research Foundation(2022A1515110550)+2 种基金Central Public-interest Scientific Institution Basal Research Fund,South China Sea Fisheries Research institute,CAFS(No.2021TS02)Guangzhou Basic and Applied Basic Research Foundation(2023A04J1337)Central Public-interest Scientific Institution Basal Research Fund,CAFS(No.2023TD78).
文摘5-Methylcytosine (5mC) is a dynamic and reversible epigenetic modification in genomic DNA of higher eukaryotes.It has been well-established that the demethylation of 5mC occurs through the ten-eleven translocation (TET)-mediated oxidation of 5mC followed by thymine DNA glycosylase (TDG)-initiated base excision repair (BER).Recent findings also have identified an alternative pathway of DNA demethylation.In this pathway,TET enzymes directly oxidize 5mC to form 5-formylcytosine (5fC) or 5-carboxylcytosine (5caC).These modified bases can undergo direct deformylation or decarboxylation,respectively.Additionally,DNA demethylation can also occur through the deamination of 5mC and 5hmC,resulting in the production of thymine and 5-hydroxymethyluracil (5hmU),respectively.Various DNA demethylation pathways possess critical functional implications and roles in biological processes.This Recent Advances article will focus on the studies of mechanisms and biological functions of DNA demethylation,shedding light on the reversible nature of the epigenetic modification of 5mC.
基金supported by the National Natural Science Foundation of China(32121001,32201213)。
文摘Among over 170 different types of chemical modifications on RNA nucleobases identified so far,RNA methylation is the major type of epitranscriptomic modifications existing on almost all types of RNAs,and has been demonstrated to participate in the entire process of RNA metabolism,including transcription,pre-mRNA alternative splicing and maturation,mRNA nucleus export,mRNA degradation and stabilization,mRNA translation.Attributing to the development of high-throughput detection technologies and the identification of both dynamic regulators and recognition proteins,mechanisms of RNA methylation modification in regulating the normal development of the organism as well as various disease occurrence and developmental abnormalities upon RNA methylation dysregulation have become increasingly clear.Here,we particularly focus on three types of RNA methylations:N^(6)-methylcytosine(m^(6)A),5-methylcytosine(m^(5)C),and N^(7)-methyladenosine(m^(7)G).We summarize the elements related to their dynamic installment and removal,specific binding proteins,and the development of high-throughput detection technologies.Then,for a comprehensive understanding of their biological significance,we also overview the latest knowledge on the underlying mechanisms and key roles of these three mRNA methylation modifications in gametogenesis,embryonic development,immune system development,as well as disease and tumor progression.
基金the Ministry of Science and Technology of China(2019YFA0110902,2019YFA0802201)。
文摘More than 160 types of post-transcriptional RNA modifications have been reported;there is substantial variation in modification type,abundance,site,and function across species,tissues,and RNA type.The recent development of high-throughput detection technology has enabled identification of diverse dynamic and reversible RNA modifications,including N6,2′-O-dimethyladenosine(m6Am),N1-methyladenosine(m1A),5-methylcytosine(m5C),N6-methyladenosine(m6A),pseudouridine(Ψ),and inosine(I).In this review,we focus on eukaryotic mRNA modifications.We summarize their biogenesis,regulatory mechanisms,and biological functions,as well as highthroughput methods for detection of mRNA modifications.We also discuss challenges that must be addressed in mRNA modification research.
基金This work was supported by funding from the National Transgenic Major Program of China(2019ZX08010-002)to X.G.the National Natural Sci ence Foundation of China(31871606,31671670)toX.G.,and the Recruit ment Program of Global Youth Expert of China to X.G.
文摘Advances in the detection and mapping of messenger RNA(mRNA)N^6-methyladenosine(m 6A)and 5-methylcytosine(m 5C),and DNA N^6-methyldeoxyadenosine(6mA)redefined our understanding of these modifications as additional tiers of epigenetic regulation.In plants,the most prevalent internal mRNA modifications,m^6A and m^5C,play crucial and dynamic roles in many processes,including embryo development,stem cell fate determination,trichome branching,leaf morphogenesis,floral transition,stress responses,fruit ripening,and root development.The newly identified and widespread epigenetic marker 6mA DNA methylation is associated with gene expression,plant development,and stress responses.Here,we review the latest research progress on mRNA and DNA epigenetic modifications,including the detection,dynamics,distribution,functions,regulatory proteins,and evolution,with a focus on m^6A,m^5C,and 6mA.We also provide some perspectives on future research of the newly identified and unknown epigenetic modifications of mRNA and DNA in plants.
基金supported by ARC grants DP110103805 and FT13100525 awarded to I.S.and an APA and a GRDC PhD topup scholarship awarded to A.B.
文摘The advent of high-throughput sequencing technol- ogies coupled with new detection methods of RNA modifica- tions has enabled investigation of a new layer of gene regulation - the epitranscriptome. With over loo known RNA modifications, understanding the repertoire of RNA modifications is a huge undertaking. This review summarizes what is known about RNA modifications with an emphasis on discoveries in plants. RNA ribose modifications, base methyl- ations and pseudouridylation are required for normal develop- ment in Arabidopsis, as mutations in the enzymes modifying them have diverse effects on plant development and stress responses. These modifications can regulate RNA structure, turnover and translation. Transfer RNA and ribosomal RNA modifications have been mapped extensively and their functions investigated in many organisms, including plants. Recent work exploring the locations, functions and targeting of N6-methyladenosine （m^6A）, 5-methylcytosine （m^5C）, pseudour- idine （up）, and additional modifications in mRNAs and ncRNAs are highlighted, as well as those previously known on tRNAs and rRNAs. Many questions remain as to the exact mechanisms of targeting and functions of specific modified sites and whether these modifications have distinct functions in the different classes of RNAs.
