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Duplication and expression analysis of multicopy miRNA gene family members in Arabidopsis and rice

Cell research 2006年第5期16卷 507-518页

作者： Danhua Jiang~(1,2. Changsong Yin~1 Aiping Yu~(1,3) Xiaofan Zhou~1 Wanqi Liang~(1,4) Zheng Yuan~1 Yun Xu~1 Qingbo Yu~1 Tieqiao Wen~2.Dabing Zhang~(1,4) ~1SJTU-SIBS-PSU Joint center for Life sciences,School of Life Science and Biotechnology,{2. Jiao Tong University 800 Dongchuan Road,{2. 2.02.0, china ~2.chool of Life Science,{2. University,99 Shangda Road,{2. 2.0444,china ~3College of Life and Environment sciences,{2. Normal University,100 Guilin Road, {2. 2.02.4,china ~4Key Laboratory of Agricultural {12.tics and Breeding,Agro-biotech research center,{2. academy of Agricultural sciences,2.01 Beidi Road,{2. 2.1106,china SJTU-SIBS-PSU Joint center for Life sciences School of Life Science and Biotechnology Shanghai Jiao Tong University Shanghai China School of Life Science Shanghai University Shanghai China College of Life and Environment sciences Shanghai Normal University Shanghai China Key Laboratory of Agricultural genetics and Breeding Agro-biotech Research Center Shanghai Academy of Agricultural Sciences Shanghai China

To understand the expansion of multicopy microRNA (miRNA) families in plants,we localized the reported miRNAgenes from Arabidopsis and rice to their chromosomes,respectively,and observed that 37% of 117 miRNA genes fromArabidopsis and 35% of 173 miRNA genes from rice were segmental duplications in the *** order to characterizewhether the expression diversification has occurred among plant multicopy miRNA family members,we designed PCRprimers targeting 48 predicted miRNA precursors from 10 families in Arabidopsis and *** from RT-PCR datasuggest that the transcribed precursors of members within the same miRNA family were present at different *** addition,although miR160 and miR162.sequences were conserved in Arabidopsis and rice,we found that theexpression patterns of these genes differed between the two *** data suggested that expression diversifica-tion has occurred in multicopy miRNA families,increasing our understanding of the expression regulation of miRNAsin plants.

关键词： gene duplication microRNA multicopy

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Seasonal water storage change of the Yangtze River basin detected by GRACE

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Science china Earth sciences 2006年第5期49卷 483-491页

作者： HU Xiaogong1, CHEN Jianli1,2. ZHOU Yonghong1, HUANG Cheng1 & LIAO Xinhao1 1. center for Astro-geodynamics research, {2. Astronomical Observatory, national Astronomical Observatories, {2. 2.0030, china 2. center for Space research, University of Texas at Austin, 392. W. Braker Lane, Suite 2.0, Austin, TX78750, USA center for Astro-geodynamics research Shanghai Astronomical Observatory National Astronomical Observatories Shanghai China center for Space research University of Texas at Austin Austin USA

US-Germany co-sponsered satellite gravimetry mission GRACE (Gravity Recovery And Climate Experiment), launched in March 2.02. has been producing monthly time series of Earth gravity models up to degree and order of 12.. The GRACE mission consists of two identical satellites flying on an almost polar orbit with an altitude of about 300-500 km and satelite-to-satellite ranging of about 2.0 km. Thanks to the payloads of space-borne GPS receivers, accelerometers and high-precision K-band satelite-to-satellite ranging mesurements, GRACE gravity models are expected to achieve more than one order of magnitude of improvement over previous models at spatial scales of a few hundred kilometers or larger. Recovery of surface mass re-distribution based on GRACE’s time-varying gravity models is applied to studies in solid Earth geophysics, oceanography, climatology and geodesy. At secular time scales, GRACE is expected to provide valuable information on global ice changes, whose variations have profound influences on global climate, and in particular, on sea level changes. At seasonal time scales, GRACE is expected to reveal surface water changes with an ac- curacy of less than 1 cm, or ocean bottom pressure changes with an accuracy of less than 1 mbar (1 mbar =102.Pa). These surface mass redistribution measurements would impove our understanding of the global and regional mass and energy cycles that are critical to human life. Using 15 GRACE monthly gravity models covering the period from April 2.02.to December 2.03, this study compares seasonal water storage changes recovered from GRACE data and hydrology models at global and regional scales, with particular focus on the Yangtze River basin of china. Annual amplitude of 3.4 cm of equivalent water height change is found for the Yangtze River basin with maximum in Spring and Autumn, agreeing with two state-of-the-art hydrology models. The differences between GRACE re- sults and model predictions are less than 1-2.cm. We conclude

关键词： GRACE, earth gravity, water storage, Yangtze River basin.

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Mechanisms of microRNA-mediated gene regulation

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Science china(Life sciences) 2009年第12期52卷 1111-1116页

作者： ZHAO Shuang & LIU Mo-Fang· State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, shanghai Institutes for Biological sciences, the{2., shanghai 2.0031, china State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences the Chinese Academy of Sciences Shanghai China

microRNAs (miRNAs) are identified as a class of non-protein regulators and a new source for broad control of gene expression in eukaryotes. The past years have witnessed substantial progress in understanding miRNA functions and mechanisms, although a few controversies remain. Various hypotheses and models have been suggested for the mechanisms of miRNA repression, including translational inhibition at the level of initiation or elongation, rapid degradation of the nascent peptide, mRNA degradation, and mRNA sequestration into P bodies (processing bodies) and SGs (stress granules) for degradation or/and storage. Recently, some noncanonical miRNA regulation, such as miRNA activation and de-repression of miRNA inhibition, have been uncovered. This review discusses some recent advances about how miRNAs regulate their targets and various modes of miRNA function.

关键词： miRNA repression activation de-repression processing bodies stress granules

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Embryonic stem cells generated by nuclear transfer of human somatic nuclei into rabbit oocytes

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Cell research 2003年第4期13卷 251-263页

作者： YING CHEN, ZHI Xu HE, AILIAN LIU, KAI WANG, WEN WEI MAO, JIAN XIN CHU, YONG LU, ZHENG Fu FANG, YING TANG SHI, QING ZHANG YANG, DA YUAN CHEN, MIN RANG WANG, JIN SONG LI, SHAO LIANG HUANG, XIANG YIN KONG, YAO ZHOU SHI, Zm QIANG WANG, JIA HuI XIA, ZHI GAO LONG, ZHI GANG XUE, WEN XIANG DING, HuI ZHEN SHENG center for Developmental Biology, shanghai Second Medical University, shanghai 200092, china Laboratory of Stem Cell Biology, Institute of Biochemistry and Cell Biology, shanghai Institutes for Biological sciences, chinese academy of sciences, 1665 Kong Jiang Road, shanghai 200092, china center for Stem Cell research, the Second Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510120,china State Key Laboratory of Reproductive Biology, Institute of Zoology, chinese academy of sciences, 19 Zhong-guan Cun Road, Haidian District, Beijing 100080, china Health Science center, shanghai Institutes of Biological sciences, chinese academy of sciences and shanghai Second Medical University, shanghai 200025, china national Laboratory of Medical genetics, Central South University, 88 Xiangya Road, Changsha 410078, china Xinhua Hospital, shanghai Second Medical University, 1665 Kong Jiang Road, shanghai 200092, china center for Developmental Biology Shanghai Second Medical University Shanghai 200092 China Laboratory of Stem Cell Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 1665 Kong Jiang Road Shanghai 200092 China center for Stem Cell research the Second Affiliated Hospital Sun Yat-Sen University Guangzhou 510120 China State Key Laboratory of Reproductive Biology Institute of Zoology Chinese Academy of Sciences 19 Zhong-guan Cun Road Haidian District Beijing 100080 China Health Science center Shanghai Institutes of Biological Sciences Chinese Academy of Sciences and Shanghai Second Medical University Shanghai 200025 China national Laboratory of Medical genetics Central South University 88 Xiangya Road Changsha 410078 China Xinhua Hospital Shanghai Second Medical University 1665 Kong Jiang Road Shanghai 200092 China

To solve the problem of immune incompatibility, nuclear transplantation has been envisaged as a means to produce cells or tissues for human autologous transplantation. Here we have derived embryonic stem cells by the transfer of human somatic nuclei into rabbit oocytes. The number of blastocysts that developed from the fused nuclear transfer was comparable among nuclear donors at ages of 5, 42. 52.and 60 years, and nuclear transfer (NT) embryonic stem cells (ntES cells) were subsequently derived from each of the four age groups. These results suggest that human somatic nuclei can form ntES cells independent of the age of the donor. The derived ntES cells are human based on karyotype, isogenicity, in situ hybridization, PCR and immunocytochemistry with probes that distinguish between the various species. The ntES cells maintain the capability of sustained growth in an undifferentiated state, and form embryoid bodies, which, on further induction, give rise to cell types such as neuron and muscle, as well

关键词： nuclear transfer (NT) somatic cell nuclear transfer (SCNT) embryonic stem cells (ES cell) therapeutic cloning rabbit oocyte.

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水稻基因组中MITEs的偏爱位置

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生物化学与生物物理学报 2000年第3期32卷 223-228页

作者：张显亮洪国藩中国科学院国家基因研究中心!上海2.02.3

已知微型倒转重复转座因子 (MITEs)广泛分布于真核生物基因附近的非编码区。为探讨MITEs在基因组一级结构中的分布规律 ,通过对 82.b的水稻BAC克隆l1 3 3 2.序列分析 ,精确鉴定了 1 0个蛋白质编码基因的位置和转录方向以及 7个MITEs的... 详细信息

已知微型倒转重复转座因子 (MITEs)广泛分布于真核生物基因附近的非编码区。为探讨MITEs在基因组一级结构中的分布规律 ,通过对 82.b的水稻BAC克隆l1 3 3 2.序列分析 ,精确鉴定了 1 0个蛋白质编码基因的位置和转录方向以及 7个MITEs的位置 ,毫无例外的观察到 ,MITEs只要存在 ,总是位于最近的基因的上游 ,不管该基因与之相距多远、转录方向如何。另外还发现 ,1个MITE被 2.基因共享。由于MITEs易于鉴定 ,因而这种位置模式可以用作探测其下游基因存在的工具。

关键词：水稻基因组位置模式微型倒转重复转座因子基因5′侧区

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Identification and Characterization of a Rat Novel gene RSEP4 Expressed Specifically in Central Nervous System

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Acta Biochimica et Biophysica Sinica 2004年第7期36卷 501-507页

作者： Xi-Dao WANG1,2. Ling-Wei KONG1, Zhi-Qin XIE1, Yu-Qiu ZHANG3, Zhi-Xin LIN2. Zhi-Qi ZHAO3,Lei YU4, and Nai-He JING1* 1 Laboratory of Molecular Cell Biology, Laboratory of Stem Cell Biology, Institute of Biochemistry and Cell Biology, shanghai Institutes for Biological sciences,{2., Graduate School of the{2., shanghai 2.0031, china School of Life Science and Biotechnology, 2. shanghai Jiaotong University, shanghai 2.0030, china Institute of Neurobiology, Fudan University, shanghai 2.0433, china 3 4 Department of Cell Biology, Neurobiology and Anatomy, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA Laboratory of Molecular Cell Biology Laboratory of Stem Cell Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of SciencesShanghai 200031 China School of Life Science and Biotechnology Shanghai Jiaotong UniversityShanghai 200030 China Institute of Neurobiology Fudan UniversityShanghai 200433 China Department of Cell Biology Neurobiology and Anatomy College of Medicine University of CincinnatiCincinnati Ohio USA

The low-abundantly expressed genes composed the majorities of the mRNAs expressed in the central nervous system (CNS), and were thought to be important for the normal brain functions. Through differential screening a low-abundance cDNA sublibrary with mRNA from neuropathic pain of chronic constriction injury (CCI) model, we have identified a novel rat gene, rat spinal-cord expression protein 4 gene (RSEP4). The total length of RSEP4 cDNA is 2.06 bp, with a 501 nucleotide open reading frame (ORF) that encodes a 167 amino acid polypeptide. Northern blot revealed that RSEP4 was expressed specifically in the CNS. In situ hybridization showed that the mRNA of RSEP4 was strongly expressed in the CA1, CA2. CA3 and DG regions of hippocampus, the Purkinje cells of cerebellum, and the small sensory neurons of dorsal horn and large motor neurons of ventral horn of spinal cord. Over-expression of RSEP4-EGFP fusion protein in the human embryonic kidney 2.3T cells showed that RSEP4 protein was mainly localized in the cell cytoplasm. These results suggest that RSEP4 may play some roles in the CNS.

关键词： central nervous system (CNS) rat Northern blot in situ hybridization

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Biological networks to the analysis of microarray data

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Progress in Natural Science:Materials International 2006年第12期16卷 1242-1251页

作者： FANG Zhuo~1, LUO Qingming~1**, ZHANG Guoqing~1 and LI Yixue~2.*(1. Hubei Bioinformatics and Molecular Imaging Key Laboratory,Huazhong University of Science and Technology, Wuhan 430074, china 2. shanghai {2. for Bioinformation and Technology, shanghai 2.02.5, china) Hubei Bioinformatics and Molecular Imaging Key Laboratory Huazhong University of Science and Technology Wuhan 430074 China shanghai center for Bioinformation and Technology Shanghai 200235 China

Microarray technology, which permits rapid and large-scale screening for patterns of gene expressions, usually generates a large amount of data. How to mine the biological meanings under these data is one of the main challenges in bioinformatics. Compared to the pure mathematical techniques, those methods incorporated with some prior biological knowledge generally bring better interpretations. Recently, a new analysis, in which the knowledge of biological networks such as metabolic network and protein interaction network is introduced, is widely applied to microarray data analysis. The microarray data analysis based on biological networks contains two main research aspects: identification of active components in biological networks and assessment of gene sets significance. In this paper, we briefly review the progress of these two categories of analyses, especially some representative methods.

关键词： biological networks microarray data analysis subnetwork gene set.

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Genome-wide linkage disequilibrium and recombination map in rice

Genome-wide linkage disequilibrium and recombination map in ...

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第十三届全国植物基因组学大会

作者： Kunyan Liu,Bin Han~* national center For {2. research,Institute of Plant Physiology and Ecology,shanghai Institute For Biological sciences,chinese academy of sciences,shanghai 2.02.3,china

Linkage disequilibrium(LD),the nonrandom association between alleles at different loci,is a noticeable feature of the organization of genetic variations in natural *** knowledge of LD facilitates the determination of ...

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一种使用混合PCR筛选技术高效延伸水稻BAC-重叠群的方法(英文)

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生物化学与生物物理学报 2002年第3期34卷 358-364页

作者：胡昊李滔穆洁韩斌洪国藩中国科学院上海生命科学研究院国家基因研究中心中国科学院上海生命科学研究院国家基因研究中心上海2.02.3

使用“克隆连克隆 (clonebyclone)”战略进行水稻基因组测序需要依赖于构建好的基因组物理图。工作着眼于水稻籼稻广陆矮 4号 (OryzasativaindicaGuangLuAi4)第四号染色体长臂上 5 6 .1～ 6 8cM的区域 ,采用PCR方法筛选BAC全库来延伸重... 详细信息

使用“克隆连克隆 (clonebyclone)”战略进行水稻基因组测序需要依赖于构建好的基因组物理图。工作着眼于水稻籼稻广陆矮 4号 (OryzasativaindicaGuangLuAi4)第四号染色体长臂上 5 6 .1～ 6 8cM的区域 ,采用PCR方法筛选BAC全库来延伸重叠群 ,构建物理图。通过参照特异遗传探针定位的BAC克隆 (seedBAC)末端序列设计了 14对引物 ,按特定规则分成 3组 ,分别以代表水稻BAC库 (共 2.2.36 8个BAC )的 2.33个BACpool为模板进行PCR反应 ,一共获得了 6 5个阳性BAC克隆 ,通过末端测序、酶切杂交等方法确定了其中 2.9个BAC克隆作为有效延伸的克隆 ,延伸了 8个重叠群。通过酶切杂交、末端测序等方法还获知阳性BAC的延伸方向、延伸长度以及与seedBAC之间的重叠长度。8个重叠群总的延伸长度达到5 10kb。与实验室原用于作物理图的其他方法如指纹图、点杂交等相比 ,该方法有高效率、高灵敏度、专一性好、可重复使用等优点。创新之处在于通过引物的合理分组和PCR实验条件的改进降低了假阳性和假阴性率

关键词：水稻细菌人工染色体(BAC) PCR 重叠群

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Identification of a NF-кB site in the negative regulatory element (ε-NRAII) of human ε-globin gene and its binding protein NF-кB p50 in the nuclei of K562.cells

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Cell research 2002年第1期12卷 79-82页

作者： CHUN Hui HOU, JIAN HUANG, Ruo LAN QIAN Group of Globin gene Expression and Regulation, State Key Labortory of Molecular Biology, Institute of Biochemistry and Cell Biology, shanghai Institutes for Biological {2., chinese academy of sciences, shanghai Group of Globin gene Expression and Regulation Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences State Key Labortory of Molecular Biology 上海 200031 Group of Globin gene Expression and Regulation Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences State Key Labortory of Molecular Biology 上海 200031

The developmental control of the human e-globin gene expression is mediated by transcription regulatory elements in the 5’ flanking DNA of this gene. Sequence analysis has revealed a DNA motif (GGGGAATTTGCT) similar to NF-кB consensus sequence resides in the negative regulatory element (-302.bp～ -2.02.p, termed ε-NRAII) 5’ to the cap site of this gene. NRF DNA fragment (-3010bp～ -2.86bp) containing the NF-кB motif similar sequence was synthesized and used in electrophoresis mobility shift assay (EMSA) and competitive analysis. Data showed that a protein factor from nuclear extracts of K562.cells specifically interacted with NRF DNA fragment. The synthetic NF DNA fragment (containing NF-кB consensus sequence) could competed for the protein binding, but MNF DNA fragment (mutated NF-кB motif) could not, suggesting that the binding protein is a member of NF-кB/Rel family. Western blot assay demonstrated that the molecular weight of NF-кB protein in the nuclei of K562.cells is 50ku. We suggested that NF-кB p50 may play an important role in the regulation of human c-globin gene expression.

关键词： Human ε-globin gene negative regulatory element NE-кB p50.

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