Dear Editor,The transition from the vegetative to the reproductive phase of plant development,known as the floral transition,plays important roles in the plant life cycle.Flowering is a vulnerable but crucial phase fo...Dear Editor,The transition from the vegetative to the reproductive phase of plant development,known as the floral transition,plays important roles in the plant life cycle.Flowering is a vulnerable but crucial phase for building crop yield,and proper timing of this period is therefore vital for obtaining optimal yields(Jung and Muller,2009).Analysis of flowering time is currently an important research topic in several fields,including plant molecular genetics,evolutionary biology,ecology,and crop breeding(Huang et al.,2011).展开更多
Dear Editor,Rice(Oryza sativa)is one of the most important crops in the worldand a common model plant for genomic research.The genomesofXian/IndicaandGeng/Japonicahave been completelysequenced and annotated with accur...Dear Editor,Rice(Oryza sativa)is one of the most important crops in the worldand a common model plant for genomic research.The genomesofXian/IndicaandGeng/Japonicahave been completelysequenced and annotated with accurate genome information.Over the past few years,epigenomic information,including DNAmethylation,histone modification,and chromatin accessibility,has been characterized in theXian/IndicaandGeng/Japonicage-nomes(Zhao et al.,2020).Quite a few rice three-dimensionalgenome studies have been published in the meantime(Zhaoet al.,2019).However,it is still a big challenge for many groupsthat lack dedicated bioinformatic personnel or sufficientcomputational resources to utilize such epigenetic data.展开更多
Integration of human papillomavirus(HPV)DNA into the human genome is a reputed key driver of cervical cancer.However,the effects of HPV integration on chromatin structural organization and gene expression are largely ...Integration of human papillomavirus(HPV)DNA into the human genome is a reputed key driver of cervical cancer.However,the effects of HPV integration on chromatin structural organization and gene expression are largely unknown.We studied a cohort of 61 samples and identified an integration hot spot in the CCDC106 gene on chromosome 19.We then selected fresh cancer tissue that contained the unique integration loci at CCDC106 with no HPV episomal DNA and performed whole-genome,RNA,chromatin immunoprecipitation and high-throughput chromosome conformation capture(Hi-C)sequencing to identify the mechanisms of HPV integration in cervical carcinogenesis.Molecular analyses indicated that chromosome 19 exhibited significant genomic variation and differential expression densities,with correlation found between three-dimensional(3D)structural change and gene expression.Importantly,HPV integration divided one topologically associated domain(TAD)into two smaller TADs and hijacked an enhancer from PEG3 to CCDC106,with a decrease in PEG3 expression and an increase in CCDC106 expression.This expression dysregulation was further confirmed using 10 samples from our cohort,which exhibited the same HPV-CCDC106 integration.In summary,we found that HPV-CCDC106 integration altered local chromosome architecture and hijacked an enhancer via 3D genome structure remodeling.Thus,this study provides insight into the 3D structural mechanism underlying HPV integration in cervical carcinogenesis.展开更多
基金supported by the National Key R&D Program of China (2022YFF1001400)the National Natural Science Foundation of China (32322061 and 32070559)Fundamental Research Funds for the Central University HZAU (2662023XXPY001).
文摘Dear Editor,The transition from the vegetative to the reproductive phase of plant development,known as the floral transition,plays important roles in the plant life cycle.Flowering is a vulnerable but crucial phase for building crop yield,and proper timing of this period is therefore vital for obtaining optimal yields(Jung and Muller,2009).Analysis of flowering time is currently an important research topic in several fields,including plant molecular genetics,evolutionary biology,ecology,and crop breeding(Huang et al.,2011).
基金This work was supported by the National Key Research and DevelopmentProgram of China(2016YFD0100904 to X.L.,2018YFC1604000 to G.L.)the National Natural Science Foundation of China(31771422 to X.L.,31771402 to G.L.,and 31701163 to L.Z.)the Huazhong AgriculturalUniversity Independent Scientific&Technological Innovation Foundation(2662018py033 to X.L.).
文摘Dear Editor,Rice(Oryza sativa)is one of the most important crops in the worldand a common model plant for genomic research.The genomesofXian/IndicaandGeng/Japonicahave been completelysequenced and annotated with accurate genome information.Over the past few years,epigenomic information,including DNAmethylation,histone modification,and chromatin accessibility,has been characterized in theXian/IndicaandGeng/Japonicage-nomes(Zhao et al.,2020).Quite a few rice three-dimensionalgenome studies have been published in the meantime(Zhaoet al.,2019).However,it is still a big challenge for many groupsthat lack dedicated bioinformatic personnel or sufficientcomputational resources to utilize such epigenetic data.
基金supported by the National Natural Science Foundation of China(81630060 to P.W.,31771402 to G.L.,81830074 and 81772786 to H.W.,81572569 to G.C.,and 81772775 to J.W.)National Science and Technology Major Project(2019YFC1005202 and 2019YFC1005201 to K.L.,and 2018ZX10301402-002 to Q.G.)the research-oriented clinician funding program of Tongji Medical College,Huazhong University of Science and Technology for P.W
文摘Integration of human papillomavirus(HPV)DNA into the human genome is a reputed key driver of cervical cancer.However,the effects of HPV integration on chromatin structural organization and gene expression are largely unknown.We studied a cohort of 61 samples and identified an integration hot spot in the CCDC106 gene on chromosome 19.We then selected fresh cancer tissue that contained the unique integration loci at CCDC106 with no HPV episomal DNA and performed whole-genome,RNA,chromatin immunoprecipitation and high-throughput chromosome conformation capture(Hi-C)sequencing to identify the mechanisms of HPV integration in cervical carcinogenesis.Molecular analyses indicated that chromosome 19 exhibited significant genomic variation and differential expression densities,with correlation found between three-dimensional(3D)structural change and gene expression.Importantly,HPV integration divided one topologically associated domain(TAD)into two smaller TADs and hijacked an enhancer from PEG3 to CCDC106,with a decrease in PEG3 expression and an increase in CCDC106 expression.This expression dysregulation was further confirmed using 10 samples from our cohort,which exhibited the same HPV-CCDC106 integration.In summary,we found that HPV-CCDC106 integration altered local chromosome architecture and hijacked an enhancer via 3D genome structure remodeling.Thus,this study provides insight into the 3D structural mechanism underlying HPV integration in cervical carcinogenesis.
