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mRNA alternative polyadenylation (APA) in regulation of gene expression and diseases

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genes & Diseases 2023年第1期10卷 165-174页

作者： Siyao Guo Shuibin Lin Center for Translational Medicine Precision Medicine InstituteThe First Affiliated HospitalSun Yat-sen UniversityGuangzhouGuangdong 510080China State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer CenterGuangzhouGuangdong510060China

The mRNA polyadenylation plays essential function in regulation of mRNA ***-regulations of mRNA polyadenylation are frequently linked with aberrant gene expression and disease *** the action of polyadenylate polymerase,poly(A)tail is synthesized after the polyadenylation signal(PAS)sites on the *** polyadenylation(APA)often occurs in mRNAs with multiple poly(A)sites,producing different 3'ends for transcript variants,and therefore plays important functions in gene expression *** this review,we first summarize the classical process of mRNA 3'-terminal formation and discuss the length control mechanisms of poly(A)innucleus and *** review the research progress on alternative polyadenylation regulation and the APA site selection ***,we summarize the functional roles of APA in the regulation of gene expression and diseases including cancers.

关键词： Alternative polyadenylation(APA) Cancer gene expression mRNA polyadenylation Poly(A)

Effects of pyraclostrobin on growth,oxidative stress,and gene expression in relation to stress and ATP-binding cassette transporters in Tetrahymena thermophila

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Journal of Oceanology and Limnology 2024年第1期42卷 150-162页

作者： Yang LIU Jiale ZHANG Peng XIAO Xin LIU Yisifu MA Jing ZHANG Bangjun ZHANG Henan International Joint Laboratory of Aquatic Ecotoxicology and Health Protection Xinxiang 453007China College of Life Sciences Henan Normal UniversityXinxiang 453007China Journal of Henan Normal University Xinxiang 453007China College of Life and Environmental Science Wenzhou UniversityWenzhou 325035China Department of Ecosystem Studies School of Environmental ScienceUniversity of Shiga PrefectureShiga 522-8533Japan

Pyraclostrobin(PYR),a widely used fungicide,has negative effects on fish and algae,but its toxicity in protozoa remains *** this study,the effects of PYR on the growth,oxidative stress,and gene expression related to stress and ATP-binding cassette(ABC)transporters in Tetrahymena thermophila were *** result showed that the 96-h IC_(50)of PYR against *** was 17.2 mg/***,PYR inhibited the growth of *** in concentration-or time-dependent manner.A morphological study revealed that the shape and size of *** changed,and damage of cell membrane surface was observed by scanning electron microscopy after 96 h of PYR *** activities of superoxide dismutase(SOD)and catalase(CAT)increased throughout the *** contrast,the glutathione(GSH)content was increased at 24 h and 48 h of exposure and decreased at 96 ***,a significant increase in malondialdehyde(MDA)level was observed in *** after96 h of ***,PYR upregulated the HSP703,HSP705,GPx2,and ABAC15 gene expression in the 0.1–5-mg/L groups and downregulated the HSP704,HSP90,TGR,and ABCC52 mRNA levels at 96 h of *** results suggest that PYR may exert adverse effects on *** by inducing oxidative stress and changing the gene expression related to ABC transporters and stress,which may enrich the understanding of the toxicity mechanism of PYR in aquatic organisms and provide reference data for aquatic ecological risk assessments.

关键词： pyraclostrobin Tetrahymena thermophila growth oxidative stress gene expression

Homeobox protein A1-like and DNA methylation regulate embryo-specific Zinc finger protein 615 gene expression and embryonic development in the silkworm Bombyx mori

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Insect Science 2023年第4期30卷 1063-1080页

作者： Yu-Lin Tian Tong-Yu Fu Qi-En Zhong Yi-Guang Lin Si-Chun Zheng Guan-Feng Xu Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology Guangzhou Key Laboratory of Insect Development Regulation and Applied ResearchInstitute of Insect Science and TechnologySchool of Life SciencesSouth China Normal UniversityGuangzhouChina

DNA methylation and transcription factors play roles in gene expression and animal *** insects,DNA methylation modifies gene bodies,but how DNA methylation and transcription factors regulate gene expression is *** this study,we investigated the mechanism that regulates the expression of Bombyx mori Zinc finger pro-tein 615(ZnF 615),which is a downstream gene of DNA methyltransferase 1(Dnmt1),and its effects on the regulation of embryonic *** progressively truncating the ZnF 615 promoter,it was found that the-223 and-190 nt region,which contains homeobox(Hox)protein cis-regulatory elements(CREs),had the greatest impact on the transcription of ZnF *** interference(RNAi)-mediated knockdown and overexpres-sion of Hox family genes showed that Hox A1-like can enhance the messenger RNA level of ZnF *** studies showed that Hox A1-like regulates ZnF 615 expression by directly binding to the-223 and-190 nt region of its *** RNAi-mediated knockdown or overexpression of Hox A1-like and Dnmtl significantly inhibited or enhanced the regulatory effect of either gene alone on ZnF 615 expression,suggesting that both DNA methylation of gene bodies and binding of transcription factors to pro-moters are essential for gene ***-mediated knockdown of Hox A1-like and Dnmtl showed that the embryonic development was retarded and the hatching rate was *** together,these data suggest that Hox A1-like and DNA methylation en-hance the expression of ZnF 615,thereby affecting the development of *** embryos.

关键词： Bombyx mori DNA methylation embryo gene expression Hox Al-like ovary

Inositol and Phosphatidylinositol Mediated Glucose Derepression, gene expression and Invertase Secretion in Yeasts

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Acta Biochimica et Biophysica Sinica 2004年第7期36卷 443-449页

作者： Zhen-Ming CHI*, Jun-Feng LI, Xiang-Hong WANG, and Shu-Min YAOUNESCO Chinese Center of Marine Biotechnology, Ocean University of China, Qingdao 266003, China UNESCO Chinese Center of Marine Biotechnology Ocean University of China

Glucose repression occurs in many yeast species and some filamentous fungi, and it represses the expression and secretion of many intracellular and extracellular proteins. In recent years, it has been found that many biochemical reactions in yeast cells are mediated by phosphatidylinositol (PI)-type signaling pathway. However, little is known about the relationships between PI-type signaling and glucose repression, gene expression and invertase secretion in yeasts. Many evidences in our previous studies showed that glucose repression, invertase secretion, gene expression and cell growth were mediated by inositol and PI in Saccharomyces and Schizosaccharomyces. The elucidation of the new regulatory mechanisms of protein secretion, gene expression and glucose repression would be an entirely new aspect of inositol and PI-type signaling regulation in yeasts.

关键词： glucose repression PI-type signaling pathway invertase secretion gene expression

Time-series gene expression prof iles in AGS cells stimulated with Helicobacter pylori

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World Journal of Gastroenterology 2010年第11期16卷 1385-1396页

作者： You, Yuan-Hai Song, Yan-Yan Meng, Fan-Liang He, Li-Hua Zhang, Mao-Jun Yan, Xiao-Mei Zhang, Jian-Zhong Chinese Ctr Dis Control & Prevent Natl Inst Communicable Dis Control & Prevent Beijing 102206 Peoples R China

AIM: To extend the knowledge of the dynamic interaction between Helicobacter pylori (H. pylori) and host mucosa. METHODS: A time-series cDNA microarray was performed in order to detect the temporal gene expression prof iles of human gastric epithelial adenocarcinoma cells infected with H. pylori. Six time points were selected to observe the changes in the model. A differential expression prof ile at each time point was obtained by comparing the microarray signal value with that of 0 h. Real-time polymerase chain reaction was subsequently performed to evaluate the data quality. RESULTS: We found a diversity of gene expression patterns at different time points and identifi ed a group of genes whose expression levels were significantly correlated with several important immune response and tumor related pathways. CONCLUSION: Early infection may trigger some important pathways and may impact the outcome of the infection.

关键词： Helicobacter pylori gene expression Microarray Time-series

The nucleolus as a genomic safe harbor for strong gene expression in Nannochloropsis oceanica

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Molecular Plant 2022年第2期15卷 340-353页

作者： Christian Südfeld Ana Pozo-Rodríguez Sara A.Manjavacas Díez RenéH.Wijffels Maria J.Barbosa Sarah D'Adamo Wageningen University Bioprocess EngineeringPO Box 166700 AA WageningenNetherlands Faculty of Biosciences and Aquaculture Nord University8049 BodøNorway

Microalgae are used in food and feed,and they are considered a potential feedstock for sustainably pro-duced chemicals and ***,production of microalgal-derived chemicals is not yet economically *** engineering could bridge the gap to industrial application and facilitate the production of novel products from ***,we report the discovery of a novel gene expression system in the oleaginous microalga Nannochloropsis that exploits the highly efficient transcriptional activity of RNA po-lymerase I and an internal ribosome entry site for *** identified the nucleolus as a genomic safe harbor for Pol I transcription and used it to construct transformant strains with consistently strong trans-gene *** new expression system provides an outstanding tool for genetic and metabolic en-gineering of microalgae and thus will probably make substantial contributions to microalgal research.

关键词： Nannochloropsis gene expression nucleolus RNA polymerase I IRES aIRES

Designing artificial synthetic promoters for accurate,smart,and versatile gene expression in plants

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Plant Communications 2023年第4期4卷 12-29页

作者： Erum Yasmeen Jin Wang Muhammad Riaz Lida Zhang Kaijing Zuo Single Cell Research Center School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China Biotechnology Research Institute Chinese Academy of Agricultural SciencesBeijingChina

With the development of high-throughput biology techniques and artificial intelligence,it has become increasingly feasible to design and construct artificial biological parts,modules,circuits,and even whole *** overcome the limitations of native promoters in controlling gene expression,artificial promoter design aims to synthesize short,inducible,and conditionally controlled promoters to coordinate the expression of multiple genes in diverse plant metabolic and signaling *** promoters are versatile and can drive gene expression accurately with smart responses;they show potential for enhancing desirable traits in crops,thereby improving crop yield,nutritional quality,and food *** review first illustrates the importance of synthetic promoters,then introduces promoter architecture and thoroughly summarizes advances in synthetic promoter *** to the development of synthetic promoters and future applications of such promoters in synthetic plant biology and crop improvement are also discussed.

关键词： plants synthetic promoter cis element gene expression

Clinical significance of CD34^(+)CD117^(dim)/CD34^(+)CD117^(bri) myeloblast-associated gene expression in t(8;21)acute myeloid leukemia

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Frontiers of Medicine 2021年第4期15卷 608-620页

作者： Xueping Li Yuting Dai Bing Chen Jinyan Huang Saijuan Chen Lu Jiang Shanghai Institute of Hematology State Key Laboratory of Medical GenomicsNational Research Center for Translational Medicine at ShanghaiRuijin Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai 200025China School of Life Sciences and Biotechnology Shanghai Jiao Tong UniversityShanghai 200240China

OriginalTranslation t(8;21)(q22;q22)acute myeloid leukemia(AML)is a highly heterogeneous hematological malignancy with a high relapse rate in *** leukemic myeloblast populations(CD34^(+)CD117^(dim) and CD34^(+)CD117^(bri))were previously identified in t(8;21)AML,and CD34^(+)CD117^(dim) cell proportion was determined as an independent factor for this disease ***,we examined the impact of CD34^(+)CD117^(dim)/CD34^(+)CD117^(bri) myeloblast-associated gene expression on t(8;21)AML clinical *** this study,85 patients with t(8;21)AML were *** mRNA expression levels of CD34^(+)CD117^(dim)-associated genes(LGALS1,EMP3,and CRIP1)and CD34^(+)CD117^(bri)-associated genes(TRH,PLAC8,and IGLL1)were measured using quantitative reverse transcription *** between gene expression and clinical outcomes were determined using Cox regression *** showed that patients with high LGALS1,EMP3,or CRIP1 expression had significantly inferior overall survival(OS),whereas those with high TRH or PLAC8 expression showed relatively favorable *** analysis revealed that CD19,CD34^(+)CD117^(dim) proportion,KIT mutation,minimal residual disease(MRD),and expression levels of LGALS1,EMP3,CRIP1,TRH and PLAC8 were associated with *** analysis indicated that KIT mutation,MRD and CRIP1 and TRH expression levels were independent prognostic variables for *** the clinical relevance of CD34^(+)CD117^(dim)/CD34^(+)CD117^(bri) myeloblast-associated gene expression may provide new clinically prognostic markers for t(8;21)AML.

关键词： t(8 21)(q22 q22)AML CD34^(+)CD117^(dim)/CD344^(+)CD117^(bri)cell population gene expression prognosis

Transcriptome profiling reveals phase-specific gene expression in the developing barley inflorescence

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The Crop Journal 2020年第1期8卷 71-86页

作者： Huiran Liu Gang Li Xiujuan Yang Hendrik N.J.Kuijer Wanqi Liang Dabing Zhang Joint International Research Laboratory of Metabolic&Developmental Sciences Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and HealthState Key Laboratory of Hybrid RiceSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China School of Agriculture Food and WineThe University of AdelaideSouth Australia 5064Australia

The shape of an inflorescence varies among cereals,ranging from a highly branched panicle in rice to a much more compact spike in barley(Hordeum vulgare L.)and wheat(Triticum aestivum L.).However,little is known about the molecular basis of cereal inflorescence *** profiled transcriptomes at three developmental stages of the barley main shoot apex—spikelet initiation,floral organ differentiation,and floral organ growth—and compared them with those from vegetative seedling *** analyses identified 3688 genes differentially transcribed between the three meristem stages,with a further 1394 genes preferentially expressed in reproductive compared with vegetative *** assembly and gene Ontology analysis classified these 4888 genes into 28 clusters,revealing distinct patterns for genes such as transcription factors,histone modification,and cell-cycle progression specific for each stage of inflorescence *** also compared expression patterns of VRS(SIX-ROWED SPIKE)genes and auxin-,gibberellic acid-and cytokinin-associated genes between two-rowed and six-rowed barley to describe regulators of lateral spikelet *** findings reveal barley inflorescence phase-specific gene expression,identify new candidate genes that regulate barley meristem activities and flower development,and provide a new genetic resource for further dissection of the molecular mechanisms of spike development.

关键词： Inflorescence meristem Transcriptome gene expression Hormones Barley