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Association between mitochondrial DNA haplotype compatibility and increased efficiency of bovine intersubspecies cloning

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Journal of Genetics and Genomics 2011年第1期38卷 21-28页

作者： Hao Yan Zhonghai Yan Qingwen Ma Fei Jiao Shuzhen Huang Fanyi Zeng Yitao Zeng Shanghai Institute of Medical Genetics Shanghai Jiao Tong University 24/1400 West Beijing Road Shanghai 200040 China The Key Lab of Embryo Molecular Biology Ministry of Health China and Shanghai Lab of Embryo and Reproduction Engineering 24/1400 West Beijing Road Shanghai 200040 China Institute of Medical Science Shanghai Jiao Tong University School of Medicine 280 South Chongqing Road Shanghai 200025 China

Reconstructed embryos derived from intersubspecies somatic cell nuclear transfer （SCNT） have poorer developmental potential than those from intrasubspecies SCNT. Based on our previous study that Holstein dairy bovine （HD） mitochondrial DNA （mtDNA） haplotype compatibility between donor karyoplast and recipient cytoplast is crucial for SCNT embryo development, we performed intersubspecies SCNT using HD as donor karyoplast and Luxi yellow heifer （LY） as recipient cytoplast according to mtDNA haplotypes determined by polymerase chain reaction- restriction fragment length polymorphism （PCR-RFLP） analysis. The results demonstrated that intersubspecies mtDNA homotype SCNT embryos had higher pre- and post-implantation developmental competence than intrasubspecies mtDNA heterotype embryos as well as improved blastocyst reprogramming status, including normal H3K9 dimethylation pattern and promoter hypomethylation of pluripotent genes such as Oct4 and Sox2, suggesting that intersubspecies SCNT using LY oocytes maintains HD cloning efficiency and may reprogram HD nuclei to develop into a normal cloned animal ultimately. Our results indicated that karyoplast-cytoplast interactions and mtDNA haplotype compatibility may affect bovine intersubspecies SCNT efficiency. This study on bovine intersubspecies SCNT is valuable for understanding the mechanisms of mtDNA haplotype compatibility between karyoplast and cytoplast impacting the bovine SCNT efficiency, and provides an alternative and economic resource for HD cloning.

关键词： Somatic cell nuclear transfer (SCNT) Mitochondria mtDNA haplotype epigenetic modification Bovine Intersubspecis Intrasubspecis Developmental competence

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Decoding the plant genome: From epigenome to 3D organization

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Journal of Genetics and Genomics 2020年第8期47卷 425-434页

作者： Weizhi Ouyang Zhilin Cao Dan Xiong Guoliang Li Xingwang Li National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan430070China Department of Resources and Environment Henan University of EngineeringZhengzhou451191China Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data Huazhong Agricultural UniversityWuhan430070China

The linear genome of eukaryotes is partitioned into diverse chromatin states and packaged into a threedimensional(3D)structure,which has functional implications in DNA replication,DNA repair,and transcriptional *** the past decades,research on plant functional genomics and epigenomics has made great progress,with thousands of genes cloned and molecular mechanisms of diverse biological processes ***,3D genome research has gradually attracted great attention of many plant ***,we briefly review the progress in genomic and epigenomic research in plants,with a focus on Arabidopsis and rice,and summarize the currently used technologies and advances in plant 3D genome organization *** also discuss the relationships between onedimensional linear genome sequences,epigenomic states,and the 3D chromatin *** review provides basis for future research on plant 3D genomics.

关键词： Plant genomics epigenetic modification Chromatin three-dimensional structures Genomic methods

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Large-scale long terminal repeat insertions produced a significant set of novel transcripts in cotton

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Science China(Life Sciences) 2023年第8期66卷 1711-1724页

作者： Yan Yang Xingpeng Wen Zhiguo Wu Kun Wang Yuxian Zhu Institute for Advanced Studies Wuhan UniversityWuhan 430072China College of Life Sciences Wuhan UniversityWuhan 430072China Hubei Hongshan Laboratory Wuhan 430072China TaiKang Center for Life and Medical Sciences RNA InstituteRemin HospitalWuhan UniversityWuhan 430072China

Genomic analysis has revealed that the 1,637-Mb Gossypium arboreum genome contains approximately 81%transposable elements(TEs),while only 57%of the 735-Mb *** genome is occupied by *** this study,we investigated whether there were unknown transcripts associated with TE or TE fragments and,if so,how these new transcripts were evolved and *** sequence depths increased from 4 to 100 G,a total of 10,284 novel intergenic transcripts(intergenic genes)were *** average,approximately 84%of these intergenic transcripts possibly overlapped with the long terminal repeat(LTR)insertions in the otherwise untranscribed intergenic regions and were expressed at relatively low *** of these intergenic transcripts possessed no transcription activation markers,while the majority of the regular genic genes possessed at least one such *** without transcription activation markers formed their+1 and-1 nucleosomes more closely(only(117±1.4)bp apart),while twice as big spaces(approximately(403.5±46.0)bp apart)were detected for genes with the activation *** analysis of 183 previously assembled genomes across three different kingdoms demonstrated systematically that intergenic transcript numbers in a given genome correlated positively with its LTR *** analysis revealed that genic genes originated during one of the whole-genome duplication events around 137.7million years ago(MYA)for all eudicot genomes or 13.7 MYA for the Gossypium family,respectively,while the intergenic transcripts evolved around 1.6 MYA,resultant of the last LTR *** characterization of these low-transcribed intergenic transcripts can facilitate our understanding of the potential biological roles played by LTRs during speciation and diversifications.

关键词： RNA-seq intergenic transcripts long terminal repeat epigenetic modification nucleosomes

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Rice SUVH Histone Methyltransferase Genes Display Specific Functions in Chromatin modification and Retrotransposon Repression

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Molecular Plant 2010年第4期3卷 773-782页

作者： Fu-Jun Qin Qian-Wen Sun Li-Min Huang Xiang-Song Chen Dao-Xiu Zhou National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University 430070 Wuhan China Institut de Biotechnologie des Plantes UMR8618 CNRS Universite Paris sud 11 91405 Orsay France

Histone lysine methylation plays an important role in heterochromatin formation and reprogramming of gene expression. SET-domain-containing proteins are shown to have histone lysine methyltransferase activities. A large number of SET-domain genes are identified in plant genomes. The function of most SET-domain genes is not known. In this work, we studied the 12 rice （Oryza sativa） homologs of Su（var）3-9, the histone H3 lysine 9 （H3K9） methyltransferase identified in Drosophila. Several rice SUVHs （i.e. SDG714, SDG727, and SDG710） were found to have an antagonistic func- tion to the histone H3K9 demethylase JMJ706, as down-regulation of these genes could partially complement the jmj706 phenotype and reduced histone H3K9 methylation. Down-regulation of a rice Su（var）3-9 homolog （SUVH）, namely SDG728, decreased H3K9 methylation and altered seed morphology. Overexpression of the gene increased H3K9 methylation. SDG728 and other SUVH genes were found to be involved in the repression of retrotransposons such as Tos17 and a Tyl-copia element. Analysis of histone methylation suggested that SDG728-mediated H3K9 methylation may play an important role in retrotransposon repression.

关键词： Plant histone methyltransferases SET domain demethylases DNA methylation retrotransposon epigenetic modification rice chromatin.

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Id2 epigenetically controls CD8^(+)T-cell exhaustion by disrupting the assembly of the Tcf3-LSD1 complex

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Cellular & Molecular Immunology 2024年第3期21卷 292-308页

作者： Yiming Li Mingwei Han Haolin Wei Wan Huang Zhinan Chen Tianjiao Zhang Meirui Qian Lin Jing Gang Nan Xiuxuan Sun Shuhui Dai Kun Wang Jianli Jiang Ping Zhu Liang Chen Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital Fourth Military Medical UniversityXi’anShaanxi 710032China State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases GanzhouJiangxi341000Xi’anShaanxi 710032China School of Medicine Shanghai UniversityShanghai 200444China

CD8^(+)T-cell exhaustion is a state of dysfunction that promotes tumor progression and is marked by the generation of Slamf6^(+)progenitor exhausted(Tex^(prog))and Tim-^(3+)terminally exhausted(Tex^(term))*** of DNA binding protein 2(Id2)has been shown to play important roles in T-cell development and CD8^(+)T-cell ***,the role of Id2 in CD8^(+)T-cell exhaustion is ***,we found that Id2 transcriptionally and epigenetically regulates the generation of Texprog cells and their conversion to Texterm *** deletion of Id2 dampens CD8^(+)T-cell-mediated immune responses and the maintenance of stem-like CD8^(+)T-cell subpopulations,suppresses PD-1 blockade and increases tumor ***,through its HLH domain,Id2 binds and disrupts the assembly of the Tcf3-Tal1 transcriptional regulatory complex,and thus modulates chromatin accessibility at the Slamf6 promoter by preventing the interaction of Tcf3 with the histone lysine demethylase ***,Id2 increases the abundance of the permissive H3K4me2 mark on the Tcf3-occupied E-boxes in the Slamf6 promoter,modulates chromatin accessibility at the Slamf6 promoter and epigenetically regulates the generation of Slamf6+Texprog *** LSD1 inhibitor GSK2879552 can rescue the Id2 knockout phenotype in tumor-bearing *** of LSD1 increases the abundance of Slamf6^(+)Tim-3^(−)Tex^(prog) cells in tumors and the expression level of Tcf1 in Id2-deleted CD8+T *** study demonstrates that Id2-mediated transcriptional and epigenetic modification drives hierarchical CD8^(+)T-cell exhaustion,and the mechanistic insights gained may have implications for therapeutic intervention with tumor immune evasion.

关键词： Id2 T-cell exhaustion epigenetic modification Immune evasion

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Photoelectrochemical Biosensor for 5-Formylcytosine Based on WS_(2)/Bi/Bi_(2)O_(2)CO_(3) Nanocomposite and Rolling Circle Amplification

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Chinese Journal of Chemistry 2022年第2期40卷 247-255页

作者： Qian Wang Huanshun Yin Yunlei Zhou Lulu Cao Zhengkun Yu Yamin Xu Shiyun Ai College of Chemistry and Material Science Food Safety Analysis and Test Engineering Technology Research Center of Shandong ProvinceShandong Agricultural UniversityTaianShandong 271018China

As a key epigenetic modification,5-formylcytosine(5fC)controls many important cell functions,such as gene expression and cell ***,5fC exists in mammalian tissues and cells with low content,and its structure is highly similar to 5-methylcytosine(5mC),5-hydroxymethylcytosine(5hmC)and 5-carboxycytosine(5caC), which requires the detection method for detecti ng 5fC with high sensitivity and *** this experiment,WS_(2)/Bi/Bi_(2)O_(2)CO_(3) was used as the photoactive material,5fC antibody was used as the target molecule recog nition reage nt,and rolling amplification(RCA)was employed as the signal amplification strategy to con struct a no vel photoelectrochemical biose nsor for detecti ng 5-formylcytosi ne deox ynu cleotide(SfdCTP).

关键词： Semicon ductors Photoelectrochemistry Biosensor epigenetic modification Toxicology

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DNA methylation polymorphism in flue-cured tobacco and candidate markers for tobacco mosaic virus resistance

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2011年第11期12卷 935-942页

作者： Jie-hong ZHAO Ji-shun ZHANG Yi WANG Ren-gang WANG Chun WU Long-jiang FAN Xue-liang REN Guizhou Institute of Tobacco Science Guiyang 550081 China Department of Agronomy Zhejiang University Hangzhou 310029 China

DNA methylation plays an important role in the epigenetic regulation of gene expression during plant growth,development,and ***,there is still no distinct evidence in tobacco regarding the distribution of the methylation pattern and whether it contributes to qualitative *** studied the levels and patterns of methylation polymorphism at CCGG sites in 48 accessions of allotetraploid flue-cured tobacco,Nicotiana tabacum,using a methylation-sensitive amplified polymorphism(MSAP) *** results showed that methylation existed at a high level among tobacco accessions,among which 49.3% sites were methylated and 69.9% allelic sites were polymorphic.A cluster analysis revealed distinct patterns of geography-specific *** addition,three polymorphic sites significantly related to tobacco mosaic virus(TMV) resistance were *** suggests that tobacco breeders should pay more attention to epigenetic traits.

关键词： Methylation-sensitive amplified polymorphism epigenetic modification Tobacco mosaic virus (TMV)resistance Flue-cured tobacco

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The regulatory role of m^(6)A modification in the maintenance and differentiation of embryonic stem cells

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Genes & Diseases 2024年第5期11卷 126-139页

作者： Jin Zhang Lingling Tong Yuchen Liu Xiang Li Jiayi Wang Ruoxin Lin Ziyu Zhou Yunbing Chen Yanxi Chen Yirong Liu Di Chen Center for Reproductive Medicine of the Second Affiliated Hospital Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute(ZJU-UoE Institute)Zhejiang University School of MedicineZhejiang UniversityHangzhouZhejiang 310003China Zhejiang University-University of Edinburgh Institute(ZJU-UoE Institute) Zhejiang University School of MedicineZhejiang UniversityHangzhouZhejiang 310003China College of Materials and Chemical Engineering Minjiang UniversityFuzhouFujian 350108China National Key Laboratory of Biobased Transportation Fuel Technology HainingZhejiang 314400China

As the most prevalent and reversible internal epigenetic modification in eukaryotic mRNAs,N6-methyladenosine(m^(6)A)post-transcriptionally regulates the processing and metabolism of mRNAs involved in diverse biological processes.m^(6)A modification is regulated by m^(6)A writers,erasers,and *** evidence suggests that m^(6)A modification plays essential roles in modulating the cell-fate transition of embryonic stem *** investigation of embryonic stem cell maintenance and differentiation is critical for understanding early embryonic development,which is also the premise for the application of embryonic stem cells in regenerative *** review highlights the current knowledge of m^(6)A modification and its essential regulatory contribution to the cell fate transition of mouse and human embryonic stem cells.

关键词： Cell-fate transition Embryonic stem cell epigenetic modification m^(6)A modification Post-transcriptional regulation

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Transcriptional changes in epigenetic modifiers associated with gene silencing in the intestine of the sea cucumber,Apostichopus japonicus(Selenka),during aestivation

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Chinese Journal of Oceanology and Limnology 2011年第6期29卷 1267-1274页

作者：王天明杨红生赵欢陈慕雁王兵 Institute of Oceanology Chinese Academy of Sciences Graduate University of Chinese Academy of Sciences

The sea cucumber, Apostichopusjaponicus, undergoes aestivation to improve survival during periods of high-temperature. During aestivation, the metabolic rate is depressed to reduce the consumption of reserved energy. We evaluated the role of epigenetic modification on global gene silencing during metabolic rate depression in the sea cucumber. We compared the expression of epigenetic modifiers in active and aestivating sea cucumbers. The expression of three genes involved in DNA methylation and chromatin remodeling （DNA （cytosine-5）-methyltransferase l, Methyl-CpG-binding domain protein 2）, and Chromodomain-helicase-DNA-binding protein 5） was significantly higher during aestivation （Days 20 and 40）. Similarly, we observed an increase in the expression of genes involved in histone acetylation （Histone deacetylase 3） and Histone-binding protein RBBP4） during the early （Days 5 and 10） and late phases （Days 20 and 40） of aestivation. There was no change in the expression of KAT2B, a histone acetyltransferase. However, the expression of histone methylation associated modifiers （Histone-arginine methyltransferase CARMER and Histone-lysine N-methyltransferase MLL5） was significantly higher after 5 d in the aestivating group. The results suggest that the expression of epigenetic modifiers involved in DNA methylation, chromatin remodeling, histone acetylation, and histone methylation is upregulated during aestivation. We hypothesize that these changes regulate global gene silencing during aestivation in A. japonicus.

关键词： Apostichopus japonicus aestivation epigenetic modification gene silencing mRNAexpression

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Coordinated transcriptional and post-transcriptional epigenetic regulation during skeletal muscle development and growth in pigs

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Journal of Animal Science and Biotechnology 2023年第2期14卷 564-577页

作者： Du Zhang Shumei Wu Xinxin Zhang Shuqiang Ren Zhonglin Tang Fei Gao Genome Analysis Laboratory of the Ministry of Agriculture Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518000China College of Animal Sciences South China Agricultural UniversityGuangdong Provincial Key Lab of Agro-animal Genomics and Molecular BreedingNational Engineering Research Center for Breeding Swine IndustryGuangzhou 510642China Kunpeng Institute of Modern Agriculture at Foshan Chinese Academy of Agricultural SciencesFoshan 528226China GuangXi Engineering Centre for Resource Development of Bama Xiang Pig Bama 547500China Comparative Pediatrics and Nutrition Department of Veterinary and Animal SciencesFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark.

Background:N6-methyladenosine(m^(6)A)and DNA 5-methylcytosine(5mC)methylation plays crucial roles in diverse biological processes,including skeletal muscle development and *** studies unveiled a potential link between these two systems,implicating the potential mechanism of coordinated transcriptional and post-transcrip-tional regulation in porcine prenatal myogenesis and postnatal skeletal muscle ***:Immunofluorescence and co-IP assays were carried out between the 5mC writers and m^(6)A writers to investigate the molecular basis ***-scale in-house transcriptomic data were compiled for applying weighted correlation network analysis(WGCNA)to identify the co-expression patterns of m^(6)A and 5mC regulators and their potential role in pig ***-genome bisulfite sequencing(WGBS)and methylated RNA immu-noprecipitation sequencing(MeRIP-seq)were performed on the skeletal muscle samples from Landrace pigs at four postnatal growth stages(days 30,60,120 and 180).Results:Significantly correlated expression between 5mC writers and m^(6)A writers and co-occurrence of 5mC and m^(6)A modification were revealed from public datasets of C2C12 *** protein-protein interactions between the DNA methylase and the m^(6)A methylase were observed in mouse myoblast ***,by analyzing tran-scriptome data comprising 81 pig skeletal muscle samples across 27 developmental stages,we identified a 5mC/m^(6)A epigenetic module eigengene and decoded its potential functions in pre-or post-transcriptional regulation in postnatal skeletal muscle development and growth of *** integrative multi-omics analyses on the WGBS methylome data and MeRIP-seq data for both m^(6)A and gene expression profiles revealed a genome/transcriptome-wide correlated dynamics and co-occurrence of 5mC and m^(6)A modifications as a consequence of 5mC/m^(6)A crosstalk in the postnatal myogenesis progress of ***,we identified a group of myogenesis-relat

关键词： DNA methylation epigenetic modification Epigenomic analysis 5mC regulators m^(6)A methylation m^(6)A regulators Myogenesis

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