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Use of Rich BHI Medium Instead of Synthetic TMH Medium for gene regulation Study in Yersinia pestis

Biomedical and Environmental Sciences 2012年第6期25卷 639-644页

作者： ZHANG Yi Quan MA Li Zhi WANG Li GAO He TAN Ya Fang GUO Zhao Biao QIU Jing Fu YANG Rui Fu ZHOU Dong Sheng State Key Laboratory of Pathogen and Biosecurity Beo'ing Institute of Microbiology and Epidemiology Beijing 100071 China Department of Emergency Medicine General Hospital of Chinese People's Armed Police Forces Beijing 100039 China Department of Medical Laboratory Chongqing Medical University Chongqing 400016 China State Key Laboratory for Infectious Disease Prevention and Control National Institute for Communicable Disease Control and Prevention Chinese Centre for Disease Control and Prevention Beijing 102206 China

Objective This study is to verify the use of rich BHI medium to substitute synthetic media for gene regulation studies in Yersinia pestis. Methods The transcriptional regulation of rovA by PhoP or via temperature upshift, and that of pla by CRP were investigated when Y. pestis was cultured in BHI. After cultivation under 26 ~C, and with temperature shifting from 26 to 37 ~C, the wild-type （WT） strain or its phoP or crp null mutant （AphoP or Acrp, respectively） was subject to RNA isolation, and then the promoter activity of rovA or plo in the above strains was detected by the primer extension assay. The rovA promoter-proximal region was cloned into the pRW50 containing a promoterless lacZ gene. The recombinant LacZ reporter plasmid was transformed into WT and AphoP to measure the promoter activity of rovA in these two strains with the ^-Galactosidase enzyme assay system. Results When Y. pestis was cultured in BHI, the transcription of rovA was inhibited by PhoP and upon temperature upshift while that ofpla was stimulated by CRP. Conclusion The rich BHI medium without the need for modification to be introduced into the relevant stimulating conditions （which are essential to triggering relevant gene regulatory cascades）, can be used in lieu of synthetic TMH media to cultivate Y. pestis for gene regulation studies.

关键词： Yersinia pestis BHI TMH gene regulation

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SWR1 Chromatin-Remodeling Complex Subunits and H2A.Z Have Non-overlapping Functions in Immunity and gene regulation in Arabidopsis

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Molecular Plant 2016年第7期9卷 1051-1065页

作者： Souha Berriri Sreeramaiah N Gangappa and S Vinod Kumar Cell and Developmental Biology Department John Innes Centre Norwich NR4 7UH UK

Incorporation of the histone variant H2A.Z into nucleosomes by the SWR1 chromatin remodeling complex is a critical step in eukaryotic gene regulation. In Arabidopsis, SWRlc and H2A.Z have been shown to con- trol gene expression underlying development and environmental responses. Although they have been implicated in defense, the specific roles of the complex subunits and H2A.Z in immunity are not well under- stood. In this study, we analyzed the roles of the SWRlc subunits, PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 （PIE1）, ACTIN-RELATED PROTEIN6 （ARP6）, and SWR1 COMPLEX 6 （SWC6）, as well as H2A.Z, in defense and gene regulation. We found that SWRlc components play different roles in resistance to different pathogens. Loss of PIE1 and SWC6 function as well as depletion of H2A.Z led to reduced basal resistance, while loss of ARP6 fucntion resulted in enhanced resistance. We found that mutations in PIE1 and SWC6 resulted in impaired effector-triggered immunity. Mutation in SWRlc components and H2A.Z also resulted in compromised jasmonic acid/ethylene-mediated immunity. Genome-wide expres- sion analyses similarly reveal distinct roles for H2A.Z and SWRlc components in gene regulation, and sug- gest a potential role for PIE1 in the regulation of the cross talk between defense signaling pathways. Our data show that although they are part of the same complex, Arabidopsis SWRlc components could have non-redundant functions in plant immunity and gene regulation.

关键词： arabidopsis SWR1 chromatin remodeling H2A.Z immunity gene regulation

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The Change-Over of Yin-yang and gene regulation in Kidney Deficiency Syndromes

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Journal of Traditional Chinese Medicine 2009年第3期29卷 237-239页

作者：董飞侠何立群 Shuguang Hospital Affiliated to Shanghai University of Chinese Medicine E-institute of TCM Internal Medicine of Shanghai Municipal Education Commission

The present paper studies gene regulation in kidney deficiency syndromes from the simple Nephrotic Syndrome and with the principle of positive-negative regulation to control the change-over ofyin-yang, the modem molecular biological techniques can be used, such as gene chip, representational difference analysis （RDA） and gene sequence analysis, so as to investigate the inner relationship between the genes and kidney deficiency syndromes and prove the effect given by these genes on the pathophysiological status of change-over ofyin-yang in kidney deficiency syndromes. This philosophical approach and method can also be adopted for studies of the related genes in other TCM syndromes.

关键词： nephritic syndrome kidney-deficiency syndrome change-over ofyin and yang gene regulation

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PRMT5 in gene regulation and hematologic malignancies

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genes & Diseases 2019年第3期6卷 247-257页

作者： Fen Zhu Lixin Rui Department of Medicine and Carbone Cancer Center University of Wisconsin School of Medicine and Public HealthMadisonWI53792USA

Arginine methylation is a common posttranslational modification that governs important cellular processes and impacts development,cell growth,proliferation,and *** methylation is catalyzed by protein arginine methyltransferases(PRMTs),which are classified as type I and type II enzymes responsible for the formation of asymmetric and symmetric dimethylarginine,***5 is the main type II enzyme that catalyzes symmetric dimethylarginine of histone proteins to induce gene silencing by generating repressive histone marks,including H2AR3me2s,H3R8me2s,and ***5 can also methylate nonhistone proteins such as the transcription factors p53,E2F1 and *** of these proteins by PRMT5 are involved in diverse cellular processes,including transcription,translation,DNA repair,RNA processing,and metabolism.A growing literature demonstrates that PRMT5 expression is upregulated in hematologic malignancies,including leukemia and lymphoma,where PRMT5 regulates gene expression to promote cancer cell *** PRMT5 by specific inhibitors has emerged as a potential therapeutic strategy to treat these diseases.

关键词： gene regulation Hematologic malignancies Metabolism Pathogenesis PRMT5

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Nucleosomal Context of Binding Sites Influences Transcription Factor Binding Affinity and gene regulation

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Genomics, Proteomics & Bioinformatics 2009年第4期7卷 155-162页

作者： Zhiming Dai Xianhua Dai Qian Xiang Jihua Feng Electronic Department Sun Yat-Sen University Guangzhou 510006 China.

Transcription factor （TF） binding to its DNA target site plays an essential role in gene regulation. The location, orientation and spacing of transcription factor binding sites （TFBSs） also affect regulatory function of the TF. However, how nucleosomal context of TFBSs influences TF binding and subsequent gene regulation remains to be elucidated. Using genome-wide nucleosome positioning and TF binding data in budding yeast, we found that binding affinities of TFs to DNA tend to decrease with increasing nucleosome occupancy of the associated binding sites. We further demonstrated that nucleosomal context of binding sites is correlated with gene regulation of the corresponding TF. Nucleosome-depleted TFBSs are linked to high gene activity and low expression noise, whereas nucleosome-covered TFBSs are associated with low gene activity and high expression noise. Moreover, nucleosome-covered TFBSs tend to disrupt coexpression of the corresponding TF target genes. We conclude that nucleosomal context of binding sites influences TF binding affinity, subsequently affecting the regulation of TFs on their target genes. This emphasizes the need to include nucleosomal context of TFBSs in modeling gene regulation.

关键词： gene regulation nucleosome transcription factor binding site

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Toward an understanding of the relation between gene regulation and 3D genome organization

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Quantitative Biology 2020年第4期8卷 295-311页

作者： Hao Tian Ying Yang Sirui Liu Hui Quan Yi Qin Gao Beijing National Laboratory for Molecular Sciences College of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871China Biomedical Pioneering Innovation Center(BIOPIC) Peking UniversityBeijing 100871China Beijing Advanced Innovation Center for Genomics(ICG) Peking UniversityBeijing 100871China

Background:High-order chromatin structure has been shown to play a vital role in gene *** we identified two types of sequence domains,CGI(CpG island)forest and CGI prairie,which tend to spatially segregate,but to different extent in different *** we aim to further quantify the association of domain segregation with gene regulation and therefore ***:By means of the published RNA-seq and Hi-C data,we identified tissue-specific genes and quantitatively investigated how their regulation is relevant to chromatin ***,two types of gene networks were constructed and the association between gene pair co-regulation and genome organization is ***:We show that compared to forests,tissue-specific genes tend to be enriched in *** specific genes also tend to cluster according to their functions in a relatively small number of ***,tissue-specific forest-prairie contact formation was associated with the regulation of tissue-specific genes,in particular those in the prairie domains,pointing to the important role of gene positioning,in the linear DNA sequence as well as in 3D chromatin structure,in gene regulatory network ***:We investigated how gene regulation is related to genome organization from the perspective of forest-prairie spatial *** unlike compartments A and B,forest and prairie are identified solely based on sequence ***,the simple and uniform framework(forest-prairie domain segregation)provided here can be utilized to further understand the chromatin structure changes as well as the underlying biological significances in different stages,such as tumorgenesis.

关键词： CGI forest CGI prairie domain segregation chromatin structure gene regulation

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Reprogramming the endogenous type I CRISPR-Cas system for simultaneous gene regulation and editing in Haloarcula hispanica

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mLife 2022年第1期1卷 40-50页

作者： Kaixin Du Luyao Gong Ming Li Haiying Yu Hua Xiang State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijingChina University of Chinese Academy of Sciences BeijingChina CAS Key Laboratory of Microbial Physiological and Metabolic Engineering Institute of MicrobiologyChinese Academy of SciencesBeijingChina

The type I system is the most widely distributed CRISPR-Cas system identified so ***,we have revealed the natural reprogramming of the type I CRISPR effector for gene regulation with a crRNA-resembling RNA in halophilic ***,we conducted a comprehensive study of the impact of redesigned crRNAs with different spacer lengths on gene regulation with the native type I-B CRISPR system in Haloarcula *** the spacer targeting the chromosomal gene was shortened from 36 to 28 bp,transformation efficiencies of the spacer-encoding plasmids were improved by over three orders of magnitude,indicating a significant loss of ***,by conducting whole-genome sequencing and measuring the growth curves of the hosts,we still detected DNA cleavage and its influence on cell ***,when the spacer was shortened to 24 bp,the transcription of the target gene was downregulated to 10.80%,while both interference and primed adaptation *** modifying the lengths of the spacers,the expression of the target gene could be suppressed to varying ***,by designing crRNAs with different spacer lengths and targeting different genes,we achieved simultaneous gene editing(cdc6E)and gene regulation(crtB)for the first time with the endogenous type I CRISPR-Cas system.

关键词： CRISPR-Cas system gene editing gene regulation type I

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Role of long non-coding RNAs in gene regulation and oncogenesis

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Chinese Medical Journal 2011年第15期124卷 2378-2383页

作者： PAN Yan-feng FENG Lei ZHANG Xian-qiang SONG Li-jie LIANG Hong-xia LI Zhi-qin TAO Feng-bao Department of Infectious Disease the First Hospital Affiliated to Zhengzhou University Zhengzhou Henan 450000 China

Objective This article aims to review recent studies on the biological characteristics of long non-coding RNAs （IncRNAs）, transcription regulation by IncRNAs, and the results of recent studies on the mechanism of action of IncRNAs in tumor development. Data sources The data cited in this review were mainly obtained from the articles listed in PubMed and HighWire that were published from January 2002 to June 2010. The search terms were ＂long non-coding RNA＂, ＂gene regulation＂, and ＂tumor＂. Study selection The mechanism of IncRNAs in gene expression regulation, and tumors concerned with IncRNAs and the role of IncRNAs in oncogenesis. Results IncRNAs play an important role in transcription control, and post-transcriptional controlling. IncRNAs are suppressing and promoting factors. regulation by controlling chromatin remodeling, transcriptional involved in many kinds of tumors and play key roles as both Conclusion IncRNAs could perfectly regulate the balance of gene expression system and play important roles in oncogenic cellular transformation.

关键词： long non-coding RNA gene regulation cancer

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LncRNA-guided chromatin remodeling and gene regulation

LncRNA-guided chromatin remodeling and gene regulation

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中国生物化学与分子生物学会2019年全国学术会议暨学会成立四十周年

作者： He Zhang School of Life Science and Technology Tongji University

Residing in the physical heart of the cell, the nucleus has now fully shed its once one-dimensional reputation as the repository for genetic information toward a more dynamic three-dimensional view of chromatin biology. As an important regulatory factor, long non-coding RNAs(lncRNAs) has exhibited its critical role in chromosomal architecture and gene expression, we thus carried out a series of research to shed light on lncRNA-guided chromatin remodeling and gene regulation. We firstly delineated a novel mechanism by which a kcnq1 ot1 lncRNA directly builds an intrachromosomal interaction complex to establish allele-specific transcriptional gene silencing over a large chromosomal domain. In addition, we also proposed a novel mechanism by which ROR lncRNA may serve as a decoy oncoRNA that blocks binding surfaces, preventing the recruitment of histone modifying enzymes, thereby specifying a new pattern of histone modifications that promote tumorigenesis. Moreover, we further revealed a novel GAU1 lncRNA was initially activated by an open chromatin status, triggering recruitment of the transcription elongation factor TCEA1 at the oncogene GALNT8 promoter and cis-activated the expression of GALNT8. Collectively, these studies will provide better understanding of a novel lncRNA-guided dynamic mechanism of chromatin tuning.

关键词： lncRNA chromatin remodeling gene regulation

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gene Expression and regulation of Blastocyst Formation

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Developmental and Reproductive Biology 2002年第1期11卷 75-81页

作者：陈瑛张玉兰张秋野哈尔滨医科大学附属二院妇产科哈尔滨150086

Blastocyst formation is a crucial stage of early embryo *** junction proteins and cell adhesion associated proteins are involved in the establishment of cell junction,and subsequently induce cell compaction,blastocyst formation,differentiation of trophectoderm and maintenance of blastocyst *** regulating development and differentiation participate in embryo development and differentiation of inner cell mass and trophectoderm,which controls the transition from the undifferentiation to differentiation ***,cytokine and growth factor have influence on the proliferation of cells of inner cell *** a word,many proteins and factors are involved in the gene expression and regulation of blastocyst formation.

关键词： blastocyst gene expression gene regulation

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