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Expression and responses to dehydration and salinity stresses of V-PPase gene members in wheat

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Journal of Genetics and genomics 2009年第12期36卷 711-720页

作者： Yuezhi Wang Haibin Xu Guangxiang Zhang Huilan Zhu Lixia Zhang Zhengzhi Zhang Caiqin Zhang Zhengqiang Ma The Applied Plant genomics laboratory Crop Genomics and Bioinformatics Center & National Key Lab of Crop Genetics and Germplasm Enhancement Nanjing Agricultural University Nanjing 210095 China

Vacuolar H^＋-translocating pyrophosphatase （V-PPase） is a key enzyme related to plant growth as well as abiotic stress tolerance. In this work, wheat V-PPase genes TaVP1, TaVP2 and TaVP3 were identified. TaVP1 and TaVP2 are more similar to each other than to TaVP3. Their deduced polypeptide sequences preserve the topological structure and essential residues of V-PPases. Phylogenetic studies suggested that monocot plants, at least monocot grasses, have three VP paralogs. TaVP3 transcripts were only detected in developing seeds, and no TaVP2 transcripts were found in germinating seeds. TaVP2 was mainly expressed in shoot tissues and down-regulated in leaves under dehydration. Its expression was up-regulated in roots under high salinity. TaVP1 was relatively more ubiquitously and evenly expressed than TaVP2. Its expression level in roots was highest among the tissues examined, and was inducible by salinity stress. These results indicated that the V-PPase gene paralogs in wheat are differentially regulated spatially and in response to dehydration and salinity stresses.

关键词： vacuolar H^+-pyrophosphatase abiotic stress phylogenetic analysis

Identification and Validation of Single Nucleotide Polymorphisms in Poplar Using Publicly Expressed Sequence Tags

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Journal of Integrative Plant Biology 2005年第12期47卷 1493-1499页

作者： Bo ZHANG Yan ZHOU Liang ZHANG Qiang ZHUGE Ming-Xiu WANG Min-Ren HUANG Forest Genetics and Gene Engineering laboratory Nanjing Forestry University Nanjing 210037 China genomics and bioinformatics Institute Hangzhou 310008 China

By using assembled expressed sequence tags （ESTs） from 14 different eDNA libraries that contain 84 132 sequences reads, 556 Populus candidate single nucleotide polymorphisms （SNPs） were identified. Because traces were not available from dbEST （http：//***/dbEST/***）, stringent filters were used to identify reliable candidate SNPs. Sequences analysis indicated that the main types of substitutions among candidate SNPs were A/G and T/C transitions, which accounted for 22.0% and 30.8%, respectively. One hundred and ten candidate SNPs were tested. As a result, 38 candidate SNPs were confirmed by directed sequencing of PCR products amplified from six different individuals. Thirteen new SNPs in intron regions were found and multiple SNPs were found to be located in both intron and exon regions of four contigs. Heterozygosis was found in all 47 candidate sites and five SNP sites were heterozygous in all six samples. This is the first report of SNP identification in a tree species which reveals that assembled ESTs from multiple libraries of the public database may provide a rich source of comparative sequences for an SNP search in the poplar genome.

关键词： expressed sequence tag poplar single nucleotide polymorphism.

The Non-Coding RNA Llme23 Drives the Malignant Property of Human Melanoma Cells

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Journal of Genetics and genomics 2013年第4期40卷 179-188页

作者： Chuan-Fang Wu Guang-Hong Tan Cheng-Chuan Ma Ling Li Center for Functional genomics and bioinformatics Ministry of EducationKey Laboratory for Bio-Resource and Eco-EnvironmentCollege of Life ScienceSichuan University Hainan Provincial Key laboratory of Tropical Medicine Hainan Medical College Center for Functional genomics and bioinformatics Ministry of EducationKey Laboratory for Bio-Resource and Eco-EnvironmemCollege of Life ScienceSichuan University

Several lines of evidence support the notion that increased RNA-binding ability of polypyrimidine tract-binding（PTB） proteinassociated splicing factor（PSF） and aberrant expression of long non-coding RNAs（IncRNAs） are associated with mouse and human *** identify the PSF-binding IncRNA involved in human oncogenesis,we screened a nuclear RNA repertoire of human melanoma cell line,YUSAC,through RNA-SELEX affinity chromatography.A previously unreported IncRNA,termed as Llme23,was found to bind immobilized PSF *** specific binding of Llme23 to both recombinant and native PSF protein was confirmed in vitro and in vivo. The expression of PSF-binding Llme23 is exclusively detected in human melanoma *** down Llme23 remarkably suppressed the malignant property of YUSAC cells,accompanied by the repressed expression of proto-oncogene *** results may indicate that Llme23 can function as an oncogenic RNA and directly associate the PSF-binding IncRNA with human melanoma.

关键词： LncRNA Llme23 PSF Melanoma Rab23

Predicting disease genes for familial dilated cardiomyopathy based on the codon usage bias

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Chinese Science Bulletin 2005年第18期50卷 2028-2032页

作者： ZHOU Yanhong ZHOU Quanxiong LIU Huailan WAN Honghui Center for bioinformatics Huazhong University of Science and Technology Wuhan 430074 China Hubei bioinformatics and Molecular Imaging Key laboratory Wuhan 430074 China laboratory of bioinformatics Maryland Institute of Dynamic Genomics Silver Spring MD 20906. USA

Familial dilated cardiomyopathy (FDC) is a common monogenic disease mostly with autosomal dominant inheritance. Fifteen different loci for autosomal dominant FDC have been mapped; however, only eight FDC genes have been found, and it is still a big challenge to identify ad-ditional seven FDC genes in their chromosomal regions. We found that the codon usage frequencies in most of known FDC gene sequences are consistently biased, and significantly different from the average codon usage frequencies of human genes. This unique feature of codon usage was used to de-velop a novel approach to predicting FDC genes. Leave-one- out cross-validation results demonstrate that this approach can effectively detect FDC genes from numbers of genes in their chromosomal regions. Another advantage of this ap-proach is that it is solely based on DNA sequences and there-fore has the ability to identify potential FDC genes whose functions are completely unknown. Further, this approach has been used to analyze the seven FDC loci in which the FDC genes are still unknown. Both the detailed prediction results and the prediction program are available at http:// ***, which might provide help for relevant experimental researches to find new FDC genes.

关键词：疾病因子心肌病家族疾病密码 FDC

Comparative analysis of the pig BAC sequence involved in the regulation of myostatin gene

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Science China(Life Sciences) 2005年第2期48卷 168-180页

作者： YU Zhengquan1,LI Yan2,MENG Qingyong1,YUAN Jing1,ZHAO Zhihui1,LI Wei2,HU Xiaoxiang1,YAN Bingxue1,FAN Baoliang1,YU Shuyang1 & LI Ning1 1.State Key laboratory for Agrobiotechnology,China Agricultural University,Beijing 100094,China 2.Beijing genomics Institute / genomics and bioinformatics Center,Institute of Genetics and Development Biology,Chinese Academy of Sciences,Beijing 100101,China State Key laboratory for Agrobiotechnology China Agricultural University Beijing China Beijing genomics Institute / genomics and bioinformatics Center Institute of Genetics and Development Biology Chinese Academy of Sciences Beijing China

Myostatin (GDF8, MSTN) is a member of the transforming growth factor beta su- perfamily that is essential for proper regulation of skeletal muscle mass. In order to study its ex- pression and regulatory mechanism deeply, we have presented a comparative analysis of about 170-kb pig BAC sequence containing the myostatin gene among pig, human and mouse. The genomic region is characterized by high interspersed repeats and low G+C content. As for the myostatin gene, a higher sequence similarity is found between human and pig than between these species and the mouse. One striking feature is that the structure of two TATA-boxes in the nearby downstream of CCAAT-box is identified in the promoter. Further analysis reveals that the TATA-box1 is responsible for the transcription in pig and human, but the TATA-box2 acts on the transcription in mouse. The other interesting feature is that two polyadenylation signal sequences (AATAAA) exist in 3′UTR of the pig myostatin gene. Moreover, a large number of potential tran- scription factor-binding sites are also identified in evolutionary conserved regions (ECRs), which may be associated with the regulation of myostatin. Many putative transcription factors play an important role in the muscle development, and the complex interaction between myostatin and these factors may be required for proper muscle development.

关键词： myostatin, comparative analysis, transcriptional factors, muscle development.

Database Commons:A Catalog of Worldwide Biological Databases

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genomics, Proteomics & bioinformatics 2023年第5期21卷 1054-1058页

作者： Lina Ma Dong Zou Lin Liu Huma Shireen Amir AAbbasi Alex Bateman Jingfa Xiao Wenming Zhao Yiming Bao Zhang Zhang National genomics Data Center Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China CAS Key laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China National Center for bioinformatics Programme of Comparative and Evolutionary GenomicsFaculty of Biological SciencesQuaid-i-Azam UniversityIslamabad 45320Pakistan European Molecular Biology laboratory European Bioinformatics Institute(EMBL-EBI)HinxtonCambridge CB101SDUnited Kingdom

Biological databases serve as a global fundamental infrastructure for the worldwide scientific community,which dramatically aid the transformation of big data into knowledge discovery and drive significant innovations in a wide range of research *** the rapid data production,biological databases continue to increase in size and *** build a catalog of worldwide biological databases,we curate a total of 5825 biological databases from 8931 publications,which are geographically distributed in 72 countries/regions and developed by 1975 institutions(as of September 20,2022).We further devise a z-index,a novel index to characterize the scientific impact of a database,and rank all these biological databases as well as their hosting institutions and countries in terms of citation and ***,we present a series of statistics and trends of worldwide biological databases,yielding a global perspective to better understand their status and impact for life and health *** up-to-date catalog of worldwide biological databases,as well as their curated meta-information and derived statistics,is publicly available at Database Commons(https://***/databasecommons/).

关键词： Biological database Catalog Database Commons Citation z-index

Systematic identification and annotation of multiple-variant compound effects at transcription factor binding sites in human genome

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Journal of Genetics and genomics 2018年第7期45卷 373-379页

作者： Si-Jin Cheng Shuai Jiang Fang-Yuan Shi Yang Ding Ge Gao State Key laboratory of Protein and Plant Gene Research School of Life SciencesCenter for BioinformaticsPeking University Beijing Advanced Innovation Center for genomics Peking University

Understanding the functional effects of genetic variants is crucial in modern genomics and genetics. Transcription factor binding sites （TFBSs） are one of the most important cis-regulatory elements. While multiple tools have been developed to assess functional effects of genetic variants at TFBSs, they usually assume that each variant works in isolation and neglect the potential ＂interference＂ among multiple variants within the same TFBS. In this study, we presented COPE-TFBS （Context-Oriented Predictor for variant Effect on Transcription Factor Binding Site）, a novel method that considers sequence context to accurately predict variant effects on TFBSs. We systematically re-analyzed the sequencing data from both the 1000 Genomes Project and the Genotype-Tissue Expression （GTEx） Project via COPE-TFBS, and identified numbers of novel TFBSs, transformed TFBSs and discordantly annotated TFBSs resulting from multiple variants, further highlighting the necessity of sequence context in accurately annotating genetic variants.

关键词： Compound effect Transcription factor binding site Variant annotation bioinformatics Genetic variants

Identification and fine mapping of PmNJ3946 for powdery mildew resistance in einkorn wheat

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The Crop Journal 2023年第6期11卷 1846-1851页

作者： Peisi Wang Jun Huang Na Li Jie Zhang Caimei Gu Yang Yuan Ziruo Wen Haiyan Jia Zhongxin Kong Zhengqiang Ma Crop genomics and bioinformatics Center and National Key laboratory of Crop Genetics and Germplasm Enhancement Nanjing Agricultural UniversityNanjing 210095JiangsuChina Zhongshan Biological Breeding laboratory Nanjing 210014JiangsuChina

Powdery mildew caused by Blumeria graminis ***(Bgt)is a destructive wheat *** it can be easily overcome by deployment of resistance genes,the resistance is often quickly compromised by pathogen ***,exploration and characterization of new resistance genes is always *** NJ3946 derived from a cross of einkorn wheat accessions TA2032 and M389 showed resistance to powdery *** analysis of an F2 population derived from a cross of NJ3946 and M389 suggested that the resistance was conferred by a dominant *** polymorphic markers identified through bulked segregant analysis(BSA),this gene was mapped to a novel locus on chromosome 3A,and was designated as *** segregant RNA-seq analysis(BSR-seq)was conducted to obtain more closely linked markers,which allowed delimitation of the PMNJ3946 locus to a 0.9 cM interval covering a physical distance of less than 1 ***3946 was flanked by Xwgrc5153 and SNP-derived marker CHS21_3A008915069,and co-segregated with SNP-derived markers CHS21_3A008939814 and CHS21_*** PmNJ3946 discovery expands the diversity of powdery mildew resistance genes and is useful for wheat breeding.

关键词： Powdery mildew Disease resistance Genetic mapping Triticum monococcum PmNJ3946

Non-coding Transcripts from Enhancers:New Insights into Enhancer Activity and Gene Expression Regulation

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genomics, Proteomics & bioinformatics 2017年第3期15卷 201-207页

作者： Hongjun Chen Guangshi Du Xu Song Ling Li Center for Functional genomics and bioinformatics Key Laboratory of Bio-Resources and Eco-Environment of Ministry of EducationCollege of Life ScienceSichuan University State Key laboratory of Biotherapy West China HospitalSichuan University

Long non-coding RNAs （lncRNAs） have gained widespread interest in the past decade owing to their enormous amount and surprising functions implicated in a variety of biological pro- cesses. Some lncRNAs exert function as enhancers, i.e., activating gene transcription by serving as the cis-regulatory molecules. Furthermore, recent studies have demonstrated that many enhancer elements can be transcribed and produce RNA molecules, which are termed as enhancer RNAs （eRNAs）. The eRNAs are not merely the by-product of the enhancer transcription. In fact, many of them directly exert or regulate enhancer activity in gene activation through diverse mechanisms. Here, we provide an overview of enhancer activity, transcription of enhancer itself, characteristics of eRNAs, as well as their roles in regulating enhancer activity and gene expression.

关键词： LncRNA Enhancer transcriptioneRNA Enhancer activity Gene expression