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

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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Direct Observation of Histone-Induced DNA Shortening

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Chinese Physics Letters 2006年第2期23卷 504-507页

作者：冉诗勇王晓玲付文博赖振华王渭池刘晓晴麦振洪李明 Belting National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Sciences Beijing 100080 Life Science College Capital Normal University Beijjng 100037

We construct a system of magnetic tweezers and apply it to study the interaction between histones and DNA. The condensation of DNA by purified histones at low ionic strengths is directly monitored by recording the length of the DNA as a function of elapsed time. It is found that DNA condensates in a dynamic manner. The binding of hist, ones to DNA is energetically favoured, but the ten,sion applied on DNA tends to unravel the DNA-histone complex, The competition between the two processes determiners the rate of the DNA condensation.

关键词： SINGLE CHROMATIN FIBERS SUPERCOILED DNA RNA-POLYMERASE STRANDED-DNA MOLECULES ELASTICITY FORCE nucleosomes RESOLUTION TWEEZERS

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Nuclear actin switch of the IN080 remodeler

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Journal of Molecular Cell Biology 2019年第5期11卷 343-344页

作者： Jun Wu Yimin Lao Bing Li Department of Biochemistry and Molecular Cell Biology Shanghai Jiao Tong University School of Medicine Shanghai 200025 China Department of Laboratory Medicine Shanghai General Hospital Shanghai Jiao Tong University Shanghai 200080 China

Eukaryotic DNA is wrapped in nucleosomes, which impede the access of transcription factors and regulatory proteins to template DNA. Chromatin remodelers utilize the energy from ATP hydrolysis to drive histone movement relative to nucleosomal DNA and nucleosome editing. Thus, they play critical roles in transcription, DNA replication, and damage repair, and their dysfunctions are often associated with diseases including cancers (Klages-Mundt et al., 2018). Chromatin remodelers can be generally categorized into IN080, SWI/SNF, CHD, and ISWI subfamilies, which share conserved catalytic ATPasetranslocase motors. However, how other auxiliary components of these multi-subunit machinery control their genomic recruitment and actions of DNA translocation remains as a major challenge of the field.

关键词： Eukaryotic DNA nucleosomes of the field

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Heparin resistance in severe thermal injury:a prospective cohort study

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Burns & Trauma 2021年第1期9卷 157-169页

作者： Liam D Cato Benjamin Bailiff Joshua Price Christos Ermogeneous Jon Hazeldine William Lester Gillian Lowe Christopher Wearn Jonathan RB Bishop Janet M Lord Naiem Moiemen Paul Harrison Scar Free Foundation Birmingham Centre for Burns Research University Hospitals Birmingham Foundation TrustQueen Elizabeth Hospital BirminghamMindelsohn WayBirminghamB152WBUK Department of Haematology University Hospitals Birmingham Foundation TrustMindelsohnWayBirminghamB152WBUK Institute of Inflammation and Ageing University of BirminghamBirminghamB152TTUK NIHR Surgical Reconstruction and Microbiology Research Centre University Hospitals Birmingham Foundation TrustMindelsohn WayBirminghamB152WBUK

Background:Low molecular-weight heparin(LMWH)is routinely administered to burn patients for *** studies have reported heparin resistance,yet the mechanism(s)and prevalence have not been systematically *** hypothesized that nucleosomes,composed of histone structures with associated DNA released from injured tissue and activated immune cells in the form of neutrophil extracellular traps(NETs or NETosis),neutralize LMWH resulting in suboptimal anticoagulation,assessed by reduction in anti-factor Xa ***:Blood was sampled from>15%total body surface area(TBSA)burn patients receiving LMWH on days 5,10 and *** anti-factor Xa(AFXa)activity,anti-thrombin(ATIII)activity,cellfree DNA(cfDNA)levels and nucleosome levels were *** effects regression was adjusted for multiple confounders,including injury severity and ATIII activity,and was used to test the association between nucleosomes and ***:A total of 30 patients with severe burns were *** TBSA 43%(SD 17).Twentythree(77%)patients were affected by heparin resistance(defined by AFXa activity<0.2 IU/mL).Mean peak AFXa activity across samples was 0.18 IU/mL(SD 0.11).Mean ATIII was 81.9%activity(SD 20.4).Samples taken at higher LWMH doses were found to have significantly increased AFXa activity,though the effect was not observed at all doses,at 8000 IU no samples were heparin *** levels were negatively correlated with AFXa(r=−0.29,p=0.050)consistent with the *** final model,with peak AFXa as the response variable,was adjusted for nucleosome levels(p=0.0453),ATIII activity(p=0.0053),LMWH dose pre-sample(p=0.0049),drug given(enoxaparin or tinzaparin)(p=0.03),and other confounders including severity of injury,age,gender,time point of ***:Heparin resistance is a prevalent issue in severe *** levels were increased post-burn,and showed an inverse association with AFXa consistent with the hypothesis that they ma

关键词： Burn Heparin resistance Low molecular-weight heparin nucleosomes Neutrophil extracellular traps Factor-Xa Thrombosis Enoxaparin NETosis

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10-bp periodicity as an indicator of nucleosome position

10-bp periodicity as an indicator of nucleosome position

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第四届全国生物信息学与系统生物学学术大会

作者：刘宏德黄焕段学野孙啸东南大学生物电子学国家重点实验室

In this study,fast Fourier transformation(FFT) was used to directly detect 10-bp periodicity of AA-TT-AT/GC in the human *** demonstrated that the 10-bp periodicity signal decreases near transcription start sites(TSSs),which correspond to nucleosome free regions(NFR). Moreover,the 10-bp periodicity signal in promoters negatively correlates with gene expression *** results indicate that 10-bp periodicity is closely associated with nucleosome positioning and can be an indicator of the presence of nucleosomes.

关键词： 10-bp periodicity nucleosomes gene expression

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Dynamic nucleosome positioning in human CD4+ T cell

Dynamic nucleosome positioning in human CD4+ T cell

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第四届全国生物信息学与系统生物学学术大会

作者：刘宏德黄焕段学野孙啸东南大学生物电子学国家重点实验室

In this study,dynamic nucleosome positioning in human CD4+ T cell was *** explained that nucleosome level in the region of～200-bp upstream of TSS behaves like a lighthouse that determines whether a gene can express. And nucleosome dynamic change of promoters is different from other *** considered that there is a different pattern of nucleosome dynamic regulation between promoters and other important regions.

关键词： dynamic regulation nucleosomes gene expression

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