检索结果-南通市图书馆

Evolutionary rewiring and reprogramming of bacterial transcription regulation

在线全文

学校读者我要写书评

暂无评论

Journal of Genetics and Genomics 2011年第7期38卷 279-288页

作者： Li Wang State Key Laboratory of Plant Genomics Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China National Plant Gene Research Center Beijing 100101 China Graduate University of the Chinese Academy of Sciences Beijing 100049 China

Rewiring and reprogramming of transcriptional regulation took place during bacterial speciation. The mechanistic alterations among tran- scription factors, cis-regulatory elements and target genes confer bacteria novel ability to adapt to stochastic environmental changes. This process is critical to their survival, especially for bacterial pathogens subjected to accelerated evolution. In the past two decades, the investigators not only completed the sequences of numerous bacterial genomes, but also made great progress in understanding the molecular basis of evolution. Here we briefly reviewed the current knowledge on the mechanistic changes among orthologous, paralogous and xenogenic regulatory circuits, which were caused by genetic recombinations such as gene duplication, horizontal gene transfer, transposable elements and different genetic contexts. We also discussed the potential impact of this area on theoretical and applied studies of microbes.

关键词： Evo-Devo transcription regulation Rewiring Reprogramming Molecular evolution

transcription factor ZmNAC126 plays an important role in transcriptional regulation of maize starch synthesis-related genes

在线全文

学校读者我要写书评

暂无评论

The Crop Journal 2021年第1期9卷 192-203页

作者： Qianlin Xiao Yayun Wang Hui Li Chunxia Zhang Bin Wei Yongbin Wang Huanhuan Huang Yangping Li Guowu Yu Hanmei Liu Junjie Zhang Yinghong Liu Yufeng Hu Yubi Huang State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China Sichuan Agricultural UniversityChengdu 611130SichuanChina College of Agronomy and Biotechnology Southwest UniversityChongqing 400716China College of Agronomy Sichuan Agricultural UniversityChengdu 611130SichuanChina College of Life Science Sichuan Agricultural UniversityYa'an 625014SichuanChina Maize Research Institute Sichuan Agricultural UniversityChengdu 611130SichuanChina Sichuan Seed Station Chengdu 610041SichuanChina

Maize(Zea mays L.)is one of the most important food crops in the world,and starch is the main component of its *** regulation plays a vital role in starch ***,it is not well understood in *** report the identification of the transcription factor ZmNAC126 and its role in regulation of starch synthesis in *** expression of ZmNAC126 was higher in maize endosperm and kernels than in roots or ***126 shared a similar expression pattern with starch synthesis genes during seed development,and its expression pattern was also consistent with the accumulation of ***126 is a typical transcription factor with a transactivation domain between positions 201 and 227 of the amino acid sequence,is located in the nucleus,and binds to CACG repeats in *** one-hybrid assay revealed that ZmNAC126 bound the promoters of ZmGBSSI,ZmSSIIa,ZmSSIV,ZmISA1,and *** overexpression of ZmNAC126 in maize endosperm increased the activities of promoters pZmSh2,pZmBt2,pZmGBSSI,pZmSSIIIa,and pZmBT1 but inhibited the activities of pZmISA1 and ***126 thus acts in starch synthesis by transcriptionally regulating targeted starch synthesis-related genes in maize kernels.

关键词： Maize Starch synthesis ZmNAC126 Co-expression transcription regulation

TELS: A Novel Computational Framework for Identifying Motif Signatures of Transcribed Enhancers

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2018年第5期16卷 332-341页

作者： Dimitrios Kleftogiannis Haitham Ashoor Vladimir B.Bajic Centre for Evolution and Cancer Division of Molecular PathologyThe Institute of Cancer Research(ICR)London SM2 5NGUnited Kingdom The Jackson Laboratory for Genomic Medicine FarmingtonCT 06032USA Computational Bioscience Research Center(CBRC) ComputerElectrical and Mathematical Sciences and Engineering

In mammalian cells, transcribed enhancers(TrEns) play important roles in the initiation of gene expression and maintenance of gene expression levels in a spatiotemporal manner. One of the most challenging questions is how the genomic characteristics of enhancers relate to enhancer activities. To date, only a limited number of enhancer sequence characteristics have been investigated, leaving space for exploring the enhancers’ DNA code in a more systematic way. To address this problem, we developed a novel computational framework, Transcribed Enhancer Landscape Search(TELS), aimed at identifying predictive cell type/tissue-specific motif signatures of *** a case study, we used TELS to compile a comprehensive catalog of motif signatures for all known TrEns identified by the FANTOM5 consortium across 112 human primary cells and *** results confirm that combinations of different short motifs characterize in an optimized manner cell type/tissue-specific TrEns. Our study is the first to report combinations of motifs that maximize classification performance of TrEns exclusively transcribed in one cell type/tissue from TrEns exclusively transcribed in different cell types/tissues. Moreover, we also report 31 motif signatures predictive of enhancers’ broad activity. TELS codes and material are publicly available at http://***/TELS.

关键词： Sequence analysis Machine learning transcription regulation Transcribed enhancer Motif identification

SEUSS and PIF4 Coordinately Regulate Light and Temperature Signaling Pathways to Control Plant Growth

在线全文

学校读者我要写书评

暂无评论

Molecular Plant 2018年第7期11卷 928-942页

作者： Junling Huai Xinyu Zhang dialong Li Tingting Ma Ping Zha Yanjun Jing Rongcheng Lin Key Laboratory of Photobiology Institute of Botany Chinese Academy of Sciences Beijing 100093 China University of Chinese Academy of Sciences Beijing 100049 China GAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences Beijing 100093 China These authors contribute equally to this article.

Plants continuously monitor environmental conditions （such as light and temperature） and adjust their growth and development accordingly. The transcription factor PHYTOCHROME-INTERACTING FACTOR4 （PIF4） regulates both light and temperature signaling pathways. Here, we identified ENHANCED PHOTOMORPHOGENIC2 （EPP2） as a new repressor of photomorphogenesis in red, far-red, and blue light. Map-based cloning revealed that EPP2 encodes the SEUSS （SEU） transcription regulator. The C terminus of SEU has transcriptional activation activity, and SEU physically interacts with PIF4. Moreover, SEU promotes the expression of many genes, including auxin biosynthetic and responsive genes, and regulates IAA levels in plants. SEU associates with the regulatory regions of INDOLE-3-ACETIC ACID INDUCIBLE6 （IAA6） and IAA 19 in a PIF4-independent manner, whereas the binding of PIF4to these genes requires SEU. Furthermore, muta- tions in SEU affect H3K4me3 methylation at IAA6 and IAA 19, and SEU positively regulates warm temperature- mediated hypocotyl growth together with PIF4. Collectively, our results reveal that SEU acts as a central regulator integrating light and temperature signals to control plant growth by coordinating with PIF4.

关键词： light temperature SEU PIF4 transcription regulation

Histone methylation readers MRG1/MRG2 interact with the transcription factor TCP14 to positively modulate cytokinin sensitivity in Arabidopsis

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Journal of Genetics and Genomics 2023年第8期50卷 589-599页

作者： Fan Wang Xixi Cai Huizhe Wei Linghao Zhang Aiwu Dong Wei Su State Key Laboratory of Genetic Engineering Collaborative Innovation Center for Genetics and DevelopmentDepartment of BiochemistryInstitute of Plant BiologySchool of Life SciencesFudan UniversityShanghai 200438China

Cytokinins influence many aspects of plant growth and *** cytokinin biosynthesis and signaling have been well studied in planta,little is known about the regulatory effects of epigenetic modifications on the cytokinin ***,we reveal that mutations to Morf Related Gene(MRG)proteins MRG1/MRG2,which are readers of trimethylated histone H3 lysine 4 and lysine 36(H3K4me3 and H3K36me3),result in cytokinin hyposensitivity during various developmental processes,including callus induction and root and seedling growth *** to the mrg1 mrg2 mutant,plants with a defective AtTCP14,which belongs to the TEOSINTE BRANCHED,CYCLOIDEA,AND PROLIFERATING CELL FACTOR(TCP)transcription factor family,are insensitive to ***,the transcription of several genes related to cytokinin signaling pathway is ***,the expression of Arabidopsis thaliana HISTIDINE-CONTAINING PHOSPHOTRANSMITTER PROTEIN 2(AHP2)decreases significantly in the mrg1 mrg2 and tcp14-2 *** also confirm the interaction between MRG2 and TCP14 in vitro and in ***,MRG2 and TCP14 can be recruited to AHP2 after recognizing H3K4me3/H3K36me3 markers and promote the histone-4 lysine-5 acetylation to further enhance AHP2 *** summary,our research elucidate a previously unknown mechanism mediating the effects of MRG proteins on the magnitude of the cytokinin response.

关键词： Arabidopsis Cytokinin response Histone methylation reader TCP transcription factors transcription regulation

Roles, Functions, and Mechanisms of Long Non-coding RNAs in Cancer

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2016年第1期14卷 42-54页

作者： Yiwen Fang Melissa J. Fullwood cancer science institute of singapore national university of singapore Singapore 117599 Singapore School of Biological Sciences Nanyang Technological University Singapore 637551 Singapore Institute of Molecular and Cell Biology Agency for Science Technology and Research (A*STAR) Singapore 138673 Singapore Yale-NUS Liberal Arts College Singapore 138527 Singapore

Long non-coding RNAs （ineRNAs） play important roles in cancer. They are involved in chromatin remodeling, as well as transcriptional and post-transcriptional regulation, through a vari- ety of chromatin-based mechanisms and via cross-talk with other RNA species, lncRNAs can func- tion as decoys, scaffolds, and enhancer RNAs. This review summarizes the characteristics of lncRNAs, including their roles, functions, and working mechanisms, describes methods for identi- fying and annotating lncRNAs, and discusses future opportunities for lncRNA-based therapies using antisense oligonucleotides.

关键词： IncRNAS Chromatin transcription regulation Antisense oligonucleotides Cancer

Characterization of a novel regulatory pathway for mannitol metabolism and its coordination with biofilm formation in Mycobacterium smegmatis

在线全文

学校读者我要写书评

暂无评论

Journal of Genetics and Genomics 2018年第9期45卷 477-488页

作者： Jialing Hu Hua Zhang Si Zhou Weihui Li Zheng-Guo He National Key Laboratory of Agricultural Microbiology College of Life Science and TechnologyHuazhong Agricultural University

Biofilm formation has been implicated to be tightly regulated in bacteria. Mycobacterial species possess a unique cell-wall structure; however, the underlying regulation mechanism for their biofilm formation remains largely unclear. In this study, we characterized a hypothetical mannitol metabolism and transportation gene cluster（Ms5571-Ms5576）, designated as mmt operon, whose expression significantly contributes to the biofilm formation in Mycobacterium smegmatis. We showed that in the operon the Ms5575 gene encodes a GntR-like transcriptional repressor and the Ms5576 gene encodes a mannitol2-dehydrogenase which can produce D-mannitol from D-mannose. Strikingly, the D-mannitol molecule can derepress the negative regulation of Ms5575 on the mmt operon to stimulate the operon＇s expression. Consistently, addition of D-mannitol into the medium can obviously induce mycobacterial biofilm formation. Furthermore, we found that Ms0179 positively regulates the mmt operon through its downstream regulator Ms0180. Ms0180 directly binds the mmt operon to positively regulate its expression. Both Ms0179 and Ms0180 significantly affect the mycobacterial biofilm formation. Taken together, we explored a regulatory pathway for the mannitol metabolism and its coordination with the biofilm formation in M. smegmatis. This finding provides novel insights into the unique mechanism of biofilm formation regulation in mycobacteria.

关键词： transcription regulation Biofilm formation Mannitol Mycobacteria

A novel candidate gene CLN8 regulates fat deposition in avian

在线全文

学校读者我要写书评

暂无评论

Journal of Animal Science and Biotechnology 2023年第5期14卷 1895-1908页

作者： Xiaoqin Li Fan Zhang Yunxiao Sun Dandan Sun Fangxi Yang Yongtong Liu Zhuocheng Hou National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics and Breeding College of Animal Science and TechnologyMARAChina Agricultural UniversityNo.2 Yuanmingyuan West RdBeijing 100193China Beijing Nankou Duck Breeding Inc Beijing 100076China

Background The fat deposition has a crucial role in animal meat flavor,and fat deposition-related traits are vital for breeding in the commercial duck *** fat-related traits are typical complex phenotypes,which need a large amount of data to analyze the genetic *** In this study,we performed a new phenotypic analysis of fat traits and genotyped whole-genome varia-tions for 1,246 ducks,and combed with previous GWAS data to reach 1,880 ducks for following *** carcass composition traits,subcutaneous fat weight(SFW),subcutaneous fat percentage(SFP),abdominal fat weight(AFW),abdominal fat percentage(AFP)and the body weight of day 42(BW42)for each duck were *** identified a set of new loci that affect the traits related to fat deposition in *** these loci,ceroid-lipofuscinosis,neuronal 8(CLN8)is a novel candidate gene controlling fat *** investigated its novel function and regulation in avian *** significant SNPs(the most significant SNP,P-value=21.37E-12)and a single haplotype were detected in the upstream of CLN8 for subcutaneous fat ***,luciferase assay demonstrated that 5 linked SNPs in the upstream of the CLN8 gene significantly decreased the transcriptional activity of ***,ATAC-seq analysis showed that transcription factor binding sites were identified in a region close to the haplotype.A set of luciferase reporter gene vectors that contained different deletion fragments of the CLN8 promoter were con-structed,and the core promoter area of CLN8 was finally identified in the-1,884/-1,207 bp region of the 5′flanking sequences,which contains adipogenesis-related transcription factors binding ***,the over-expression of CLN8 can remarkably facilitate adipocyte differentiation in *** with these,the global transcriptome profiling and functional analysis of the over-expressed CLN8 in the cell line further revealed that the lipid biosynthetic process durin

关键词： Avian Adipogenesis CLN8 SNP transcription regulation

Genetic resources and precise gene editing for targeted improvement of barley abiotic stress tolerance

在线全文

学校读者我要写书评

暂无评论

Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2023年第12期24卷 1069-1092页

作者： Sakura KARUNARATHNE Esther WALKER Darshan SHARMA Chengdao LI Yong HAN Western Crop Genetics Alliance College of ScienceHealthEngineering and EducationMurdoch UniversityMurdochWA6150Australia Department of Primary Industries and Regional Development South PerthWA6151Australia

Abiotic stresses, predominately drought, heat, salinity, cold, and waterlogging, adversely affect cereal crops. They limit barley production worldwide and cause huge economic losses. In barley, functional genes under various stresses have been identified over the years and genetic improvement to stress tolerance has taken a new turn with the introduction of modern geneediting platforms. In particular, clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9) is a robust and versatile tool for precise mutation creation and trait improvement. In this review, we highlight the stress-affected regions and the corresponding economic losses among the main barley producers. We collate about 150 key genes associated with stress tolerance and combine them into a single physical map for potential breeding practices. We also overview the applications of precise base editing, prime editing, and multiplexing technologies for targeted trait modification, and discuss current challenges including high-throughput mutant genotyping and genotype dependency in genetic transformation to promote commercial breeding. The listed genes counteract key stresses such as drought, salinity, and nutrient deficiency, and the potential application of the respective gene-editing technologies will provide insight into barley improvement for climate resilience.

关键词： Clustered regularly interspaced short palindromic repeats(CRISPR) Gene function Drought Genetic improvement transcription regulation Breeding