RNA和RNA组学(RNomics)

nullRNA和RNA组学（RNomics) 研究进展RNA和RNA组学（RNomics) 研究进展nullReference: An expanding universe of noncoding RNA. 2002. Science. 296:1260-1263 (www.sciencemag.org) Glimpses of a tiny RNA world. 2001. Science. 294:797-799. Non-coding RNAs: the architects of eukaryotic complexity. 2001. EMBO Reports. 2(11):986-991. (embo-reports.oupjournals.org)nullnull蛋白质编码基因数量nullRNA的种类及主要功能Ribosomal RNAs (rRNAs): translation Transfer RNAs (tRNAs): translation Messenger RNAs (mRNAs): protein template Noncoding RNAs(ncRNAs): various types and functionsnullmRNA、tRNA、rRNA的功能null多聚核糖体的电镜和示意图null原核生物核糖体的大亚基和小亚基null原核和真核生物的核糖体null原核和真核生物核糖体的装配null原核和真核生物的转录和翻译过程null核糖体的解聚与重新装配null蛋白质的翻译过程null翻译过程中的转位null翻译过程的终止null基因的三联密码null三联密码子按简并性排列nulltRNA中参与氨酰tRNA合成酶 的识别因子null酵母丙氨酸tRNA的一级结构nulltRNA的氨酰化反应nulltRNA的氨酰化反应nullThe Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å Resolution Science. 2000. 289:905-919. Nenad Ban,1* Poul Nissen,1* Jeffrey Hansen,1 Peter B. Moore,1, 2 Thomas A. Steitz1, 2, 3 1 Department of Molecular Biophysics & Biochemistry, and 2 Department of Chemistry, Yale University, and 3 Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA. *   These two authors contributed equally to this work. null核糖体的电子密度图null核糖体大亚基旋转花冠图null23S rRNA的二级结构null核糖体大亚基RNA的四级和二级结构null核糖体大亚基RNA的四级和二级结构（续）null23S rRNA的保守和扩展序列null大亚基核糖体蛋白质骨架结构null核糖体大亚基表面的蛋白质null蛋白质延伸入RNA和 多域的相互作用nullThe Structural Basis of Ribosome Activity in Peptide Bond Synthesis Science. 2000. 289:920-930. Poul Nissen,1* Jeffrey Hansen,1* Nenad Ban,1* Peter B. Moore,1, 2 Thomas A. Steitz1, 2, 3 1 Department of Molecular Biophysics and Biochemistry and 2 Department of Chemistry, Yale University, and 3 Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA. *   These authors contributed equally to this work. null肽基转移酶底物和类似物的化学结构null底物类似物的相位电子密度图氧：红 磷：黄 氮：兰 碳：绿 底物：灰nullA-和P-位点结合的组合模型null23S\5S rRNA、蛋白质和组合CCA的填空模型null域5活性位点区的立体图nullThe closest approach of polypeptides to the peptidyl transferase active site marked by the Yarus inhibitor, CCdA-p-PuronullConserved nucleotides in the peptidyl transferase region with bound CCdA-p-Puronull肽基转移酶活性位点的催化装置null多肽的出口通道nullCrystal Structure of the Ribosome at 5.5 Å Resolution Science. 2001. 292:883-896. Marat M. Yusupov,1* Gulnara Zh. Yusupova,1* Albion Baucom,1 Kate Lieberman,1 Thomas N. Earnest,2 J. H. D. Cate,3 Harry F. Noller1 1 Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California at Santa Cruz, Santa Cruz, CA 95064, USA. 2 Berkeley Center for Structural Biology, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. 3 Whitehead Institute, Cambridge, MA 01242, USA. nullElectron density of tRNAMetf bound to the P site of the 70S ribosome, at 5.5 Å resolutionnull70S核糖体的结构nullSecondary and tertiary structures of 16S, 23S, and 5S rRNAsnullConformational differences between rRNAs in 70S ribosomes and 30S and 50S subunitsnull亚基间桥null亚基间桥（续）nulltRNA-ribosome interactionsnullTwo views of the A-tRNA anticodon stem loop bound to its codon in the 30S subunit A sitenull Interaction of E-tRNA with the ribosome. Secondary structures of 16S and 23S rRNA, showing molecular contacts with A-tRNA (gold), P-tRNA (orange), and E-tRNA (red)nullStructural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution Science. 2001. 292:1863-1876. Patrick Cramer,* David A. Bushnell, Roger D. Kornberg Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA. nullRefined Pol II structurenullStructure of Rpb1null(A to D) Structure of Rpb2nullStructure and location of the Rpb3/10/11/12 subassemblynullStructure and location of Rpb5, Rpb6, Rpb8, and Rpb9nullSurface charge distribution and factor binding sitesnullFour mobile modules of the Pol II structurenullActive center. Stereoview from the Rpb2 side toward the clampnullRNA exit and Rpb1 COOH-terminal repeat domain (CTD)nullProposed path for straight DNA in an initiation complexnullSequence identity between RNA polymerasesnullA conserved RNA polymerase core structurenull非编码RNA的结构与功能nullNoncoding RNAs (ncRNAs) in eukaryotes Small RNA (sRNA) in bacteria Small nuclear RNAs (snRNAs) Small nucleolar RNAs (snoRNAs) MicroRNA(miRNA) Small temporal RNAs(stRNAs) Small interfering RNAs(siRNAs) RNA interference (RNAi) Guide RNAs(gRNAs) tRNA/mRNA: tmRNA非编码RNA的名称与缩写符号null克隆ncRNA的方法计算机分析法 基因克隆法 蛋白质-RNA分离法null计算机分析法大致过程：利用计算机软件从已知基因组序列中寻找基因间区中的snoRNA序列，然后模拟其高级结构，引物扩增其序列和克隆，或人工合成其序列，测定其功能。 存在的问：未分析mRNA、rRNA和蛋白质编码基因中的反义链。null小RNA的克隆和鉴定详见：http://exppc01.uni-muenster.de/expath/snmrnas.htm存在问题：基因的特异时空和瞬时表达null蛋白质-RNA复合物分离法分离蛋白质- RNA复合物，除去蛋白质，纯化RNA分子，反转录成cDNA，克隆，测序，结果分析。所得RNA的cDNA克隆必须进行Northern杂交，以确认其转录物大小是否相符。nullNoncoding RNA functions and involving in processes nullncRNA(red)的各种作用方式直接配对 模拟其他核酸结构 形成RNA-蛋白质复合物nullComparison of the prokaryotic and proposed eukaryotic genetic operating systemsnulleRNA在真核生物网状系统中的作用nullRNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. The EMBO J. 2001 20(11):2943-2953 Alexander Hüttenhofer1, Martin Kiefmann, Sebastian Meier-Ewert2,3, John O’Brien2,4, Hans Lehrach2, Jean-Pierre Bachellerie1,5 and Jürgen Brosius1 Institute of Experimental Pathology/Molecular Neurobiology, ZMBE, 48149 Münster, 2Max-Planck-Institute of Molecular Genetics, 14195 Berlin-Dahlem, Germany and 5Laboratoire de Biologie Moléculaire Eucaryote du CNRS, Université Paul-Sabatier, 31062 Toulouse, France 3Present address: GPC Biotech AG, 82152 Plannegg-Martinsried, Germany 4Present address: Department of Clinical Pharmacology, RCSI, Dublin 2, Ireland 1Corresponding authors e-mail: huttenh@uni-muenster.de, brosius@uni-muenster.de or bachel@ibcg.biotoul.fr null测序与结果分析先从2个cDNA文库中随机测序400个克隆 用BLASTN进行数据分析和归类 从富集后的cDNA文库中再测序2500个克隆null随机测序的cDNA类别和比例nullsnoRNA的类别和功能C/D盒snoRNAs: 引导rRNA甲基化 C/D盒snoRNAs: 引导snRNA甲基化 C/D盒snoRNAs: 未鉴定目标 H/ACA盒snoRNAs: 引导rRNA假尿嘧啶化 H/ACA盒snoRNAs: 引导snRNA假尿嘧啶化 H/ACA盒snoRNAs: 未鉴定目标 H/ACA盒和C/D盒snoRNAs: 脑特异性，未鉴定目标 位于mRNA编码区内的RNAs 位于mRNA的5’-或3’-端非编码区的RNAs 类似重复因子的RNAs 未知序列和结构的snmRNAsnullsnoRNAs的引导(A)和产生(B)null鼠H/ACA snoRNA与鼠rRNA(A)或snRNA间的碱基配对nullIdentification of Novel Genes Coding for Small Expressed RNAs Science 2001 294:853-858 Mariana Lagos-Quintana, Reinhard Rauhut, Winfried Lendeckel, Thomas Tuschl* Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.nullSlicing and dicing miRNAsnullExpression of miRNAs Representative examples of Northern blot analysis are depictednullGenomic organization of miRNA gene clustersnullPredicted precursor structures of D. melanogaster miRNAsnullPredicted precursor structures of human miRNAsnullD.melanogaster miRNAsE, embryo; L, larval stage; P, pupa; A, adult; S2, Schneider 2 cellsnullHuman miRNAsnullAn Abundant Class of Tiny RNAs with Probable Regulatory Roles in Caenorhabditis elegans Science 2001 294:858-862 Nelson C. Lau, Lee P. Lim, Earl G. Weinstein, David P. Bartel* Whitehead Institute for Biomedical Research, and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA. nullFold-back secondary structures involving miRNAs (red) and their flanking sequences (black)nullUnique sequence features of the miRNAsnullmiRNA cloned From C.elegansnullExpression of newly found miRNAs and let-7 RNA during C. elegans developmentnullAn Extensive Class of Small RNAs in Caenorhabditis elegans Science 2001 294:858-862 Rosalind C. Lee and Victor Ambros* Dartmouth Medical School, Department of Genetics, Hanover, NH 03755, USA. nullNorthern blots of small RNA transcriptsnullMicroRNA gene products in Caenorhabditis elegansnullPredicted secondary structures of stem-loop precursors of selected C. elegans miRNAsnullnullnullNoncoding RNAs(ncRNAS) Small nucleolar RNAs (snoRNAs): methylation and pseudouridylation in rRNA of vertebrates with about 100 sites per ribosome; mammalian telomerase formation. C/D-box snoRNAs; H/ACA-box RNAs Regulatory RNAs: Xist and roX RNAs tmRNA: guiding incomplete protein degradation in bacteria Splicesomal small nuclear RNAs(snRNAs): U1, U2, U6 Editing guide RNAs: in mitochondria of kinetoplastid protozoans Mini-RNAs: lin-4 and let-7, controlling development