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Unraveling the 3D Genome Architecture in Plants:Present and Future 被引量:6
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作者 weizhi ouyang Dan Xiong +1 位作者 Guoliang Li Xingwang Li 《Molecular Plant》 SCIE CAS CSCD 2020年第12期1676-1693,共18页
The eukaryotic genome has a hierarchicalthree-dimensional(3D)organization with functional implications for DNA replication,DNA repair,and transcriptional regulation.Over the past decade,scientists have endeavored to e... The eukaryotic genome has a hierarchicalthree-dimensional(3D)organization with functional implications for DNA replication,DNA repair,and transcriptional regulation.Over the past decade,scientists have endeavored to elucidate the spatial characteristics and functions of plant genome architecture using high-throughput chromatin conformation capturing technologies such as Hi-C,ChlA-PET,and HiChIP.Here,we systematically review current understanding of chromatin organization in plants at multiple scales.We also discuss the emerging opinions and concepts in 3D genome research,focusing on state-of-the-art 3D genome techniques,RNA-chromatin interactions,liquid-liquid phase separation,and dynamic chromatin alterations.We propose the application of single-cell/single-molecule multi-omics,multiway(DNA-DNA,DNA-RNA,and RNA-RNA interactions)chromatin conformation capturing methods,and proximity ligation-independent 3D genome-mapping technologies to explore chromatin organization structure and function in plants.Such methods could reveal the spatial interactions between trait-related SNPs and their target genes at various spatiotemporal resolutions,and elucidate the molecular mecha-nisms of the interactions among DNA elements,RNA molecules,and protein factors during the formation of key traits in plants. 展开更多
关键词 3D genomic methods plant 3D genome dynamic chromatin organization liquid-liquid phase separation RNA-chromatin interaction
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Asymmetric epigenome maps of subgenomes reveal imbalanced transcription and distinct evolutionary trends in Brassica napus 被引量:4
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作者 Qing Zhang Pengpeng Guan +17 位作者 Lun Zhao Meng Ma Liang Xie Yue Li Ruiqin Zheng weizhi ouyang Shunyao Wang Hongmeijuan Li Ying Zhang Yong Peng Zhilin Cao Wei Zhang Qin Xiao Yuanling Xiao Tingdong Fu Guoliang Li Xingwang Li Jinxiong Shen 《Molecular Plant》 SCIE CAS CSCD 2021年第4期604-619,共16页
The complexity of the epigenome landscape and transcriptional regulation is significantly increased during plant polyploidization,which drives genome evolution and contributes to the increased adaptability to diverse ... The complexity of the epigenome landscape and transcriptional regulation is significantly increased during plant polyploidization,which drives genome evolution and contributes to the increased adaptability to diverse environments.However,a comprehensive epigenome map of Brassica napus is still unavailable.In this study,we performed integrative analysis of five histone modifications,RNA polymerase Ⅱ CCU-pancy,DNA methylation,and transcriptomes in two B.napus lines(2063A and B409),and established global maps of regulatory elements,chromatin states,and their dynamics for the whole genome(including the An and Cn subgenomes)in four tissue types(young leaf,flower bud,silique,and root)of these two lines.Approximately 65.8% of the genome was annotated with different epigenomic signals.Compared with the Cn subgenome,the An subgenome possesses a higher level of active epigenetic marks and lower level of repressive epigenetic marks.Genes from subgenome-unique regions contribute to the major differences between the An and Cn subgenomes.Asymmetric histone modifications between homeologous gene pairs reflect their biased expression patterns.We identified a novel bivalent chromatin state(with H3K4me1 and H3K27me3)in B.napus that is associated with tissue-specific gene expression.Furthermore,we observed that different types of duplicated genes have discrepant patterns of histone modification and DNA methylation levels.Collectively,our findings provide a valuable epigenetic resource for allopolyploid plants. 展开更多
关键词 Brassica napus EPIGENOME ChlP-seq gene expression
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Decoding the plant genome: From epigenome to 3D organization
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作者 weizhi ouyang Zhilin Cao +2 位作者 Dan Xiong Guoliang Li Xingwang Li 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2020年第8期425-434,共10页
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 regula... 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 regulation.Over 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 elucidated.Recently,3D genome research has gradually attracted great attention of many plant researchers.Herein,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 studies.We also discuss the relationships between onedimensional linear genome sequences,epigenomic states,and the 3D chromatin architecture.This review provides basis for future research on plant 3D genomics. 展开更多
关键词 Plant genomics Epigenetic modification Chromatin three-dimensional structures Genomic methods
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