Characterisation of tomato short RNAs involved in fruit development

参与果实发育的番茄短RNA的表征

• 批准号: BB/G006199/1
• 负责人: Graham Seymour
• 金额: $ 0.64万
• 依托单位: University of Nottingham
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2009
• 资助国家: 英国
• 起止时间: 2009 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FG006199%2F1
• 关键词: Characterisation; tomato; short; RNAs; involved

Most of the RNA molecules in cells are involved in protein production (ribosomal, transfer or messenger RNAs), however there are RNA molecules with other functions. A very recently discovered class of non-coding RNAs have been called microRNAs (miRNAs) because they are very short (19-24 nucleotides). These miRNAs can recognise specific mRNAs because they have partially complementary sequences to them. As a result of this interaction between miRNAs and mRNAs, the expression of the targeted mRNAs is significantly reduced. Most plant miRNAs regulate the production of transcription factors required for normal development of plants. Many miRNAs have been identified in arabidopsis and rice and several miRNAs found in one species were absent from the other suggesting that there are miRNAs which are present only in a certain group of plants. We hypothesized that miRNAs could regulate the development of different plant characteristics that are missing from arabidopsis and rice. If this was true, novel miRNAs regulating valuable plant traits could be discovered in other species. We tested this hypothesis on fleshy fruit development because of its agronomic importance. Tomato is the model plant for fleshy fruit development and ripening; therefore we sequenced more than half a million short RNAs from tomato fruit and leaf. We have demonstrated that conserved miRNAs are present in fruit and that one of them targeted a known transcription factor required for fruit ripening. We also identified four novel miRNAs, which are absent from arabidopsis and other plant genomes and showed that one of them targeted a CTR family (genes that are involved in fruit ripening) member. In addition we identified novel candidates of another class of short RNA that are produced through a different biogenesis pathway than miRNAs. These are called ta-siRNAs and are produced in a phased manner from precursor non-coding RNAs. Our preliminary work demonstrated that the process of fleshy fruit development is regulated by miRNAs and we would like to establish the biological role of the two miRNAs we showed to target ripening genes through transgenic tomato plants that produce more miRNAs or target genes that are resistant to miRNA targeting. We also propose to validate and characterise the ta-siRNA candidates. Further deep sequencing work will establish the expression profile of short RNAs during fruit development and ripening and also identify short RNAs that are regulated by known transcription factors involved in fruit development. Finally, we developed a novel technique to generate a library of mRNAs that are cleaved by short RNAs and we will apply this protocol for tomato fruit tissue. This tool will help target prediction and will have a big impact for crop research. Most crop species' genome is not known and this tool will enable researchers to investigate short RNA targets in these species. Understanding this layer of regulation in fruit development and ripening may lead to the improvement of key characteristics of fleshy fruits.

细胞中的大多数 RNA 分子都参与蛋白质生产（核糖体、转移或信使 RNA），但也有一些 RNA 分子具有其他功能。最近发现的一类非编码 RNA 被称为 microRNA (miRNA)，因为它们非常短（19-24 个核苷酸）。这些 miRNA 可以识别特定的 mRNA，因为它们具有与其部分互补的序列。由于 miRNA 和 mRNA 之间的相互作用，目标 mRNA 的表达显着降低。大多数植物 miRNA 调节植物正常发育所需的转录因子的产生。已在拟南芥和水稻中鉴定出许多 miRNA，并且在一个物种中发现的几种 miRNA 在另一个物种中不存在，这表明存在仅存在于某一类植物中的 miRNA。我们假设 miRNA 可以调节拟南芥和水稻所缺失的不同植物特征的发育。如果这是真的，那么可以在其他物种中发现调节有价值的植物性状的新 miRNA。由于其农艺重要性，我们对肉质果实发育的假设进行了检验。番茄是肉质果实发育和成熟的模型植物；因此，我们对番茄果实和叶子中超过 50 万个短 RNA 进行了测序。我们已经证明水果中存在保守的 miRNA，其中一个靶向水果成熟所需的已知转录因子。我们还鉴定了四种新的 miRNA，它们在拟南芥和其他植物基因组中不存在，并表明其中一种靶向 CTR 家族（参与果实成熟的基因）成员。此外，我们还发现了另一类短 RNA 的新候选者，这些短 RNA 是通过与 miRNA 不同的生物发生途径产生的。这些被称为 ta-siRNA，是由前体非编码 RNA 分阶段产生的。我们的初步工作表明，肉质果实的发育过程是由 miRNA 调控的，我们希望通过产生更多 miRNA 或对 miRNA 靶向具有抗性的靶基因的转基因番茄植物来确定我们展示的两种 miRNA 靶向成熟基因的生物学作用。我们还建议验证和表征 ta-siRNA 候选物。进一步的深度测序工作将建立果实发育和成熟过程中短RNA的表达谱，并鉴定受果实发育中已知转录因子调控的短RNA。最后，我们开发了一种新技术来生成被短 RNA 切割的 mRNA 文库，我们将将此协议应用于番茄果实组织。该工具将有助于目标预测，并对作物研究产生重大影响。大多数作物物种的基因组尚不清楚，该工具将使研究人员能够研究这些物种中的短 RNA 靶标。了解水果发育和成熟过程中的这一层调控可能有助于改善肉质水果的关键特性。

项目成果

The tomato genome sequence provides insights into fleshy fruit evolution.

番茄基因组序列提供了对肉质果实进化的见解

• DOI: 10.1038/nature11119
• 发表时间: 2012-05-30
• 期刊: NATURE
• 影响因子: 64.8
• 作者: Sato, Shusei;Tabata, Satoshi;Hirakawa, Hideki;Asamizu, Erika;Shirasawa, Kenta;Isobe, Sachiko;Kaneko, Takakazu;Nakamura, Yasukazu;Shibata, Daisuke;Aoki, Koh;Egholm, Michael;Knight, James;Bogden, Robert;Li, Changbao;Shuang, Yang;Xu, Xun;Pan, Shengkai;Cheng, Shifeng;Liu, Xin;Ren, Yuanyuan;Wang, Jun;Albiero, Alessandro;Dal Pero, Francesca;Todesco, Sara;Van Eck, Joyce;Buels, Robert M.;Bombarely, Aureliano;Gosselin, Joseph R.;Huang, Minyun;Leto, Jonathan A.;Menda, Naama;Strickler, Susan;Mao, Linyong;Gao, Shan;Tecle, Isaak Y.;York, Thomas;Zheng, Yi;Vrebalov, Julia T.;Lee, JeMin;Zhong, Silin;Mueller, Lukas A.;Stiekema, Willem J.;Ribeca, Paolo;Alioto, Tyler;Yang, Wencai;Huang, Sanwen;Du, Yongchen;Zhang, Zhonghua;Gao, Jianchang;Guo, Yanmei;Wang, Xiaoxuan;Li, Ying;He, Jun;Li, Chuanyou;Cheng, Zhukuan;Zuo, Jianru;Ren, Jianfeng;Zhao, Jiuhai;Yan, Liuhua;Jiang, Hongling;Wang, Bao;Li, Hongshuang;Li, Zhenjun;Fu, Fuyou;Chen, Bingtang;Han, Bin;Feng, Qi;Fan, Danlin;Wang, Ying;Ling, Hongqing;Xue, Yongbiao;Ware, Doreen;McCombie, W. Richard;Lippman, Zachary B.;Chia, Jer-Ming;Jiang, Ke;Pasternak, Shiran;Gelley, Laura;Kramer, Melissa;Anderson, Lorinda K.;Chang, Song-Bin;Royer, Suzanne M.;Shearer, Lindsay A.;Stack, Stephen M.;Rose, Jocelyn K. C.;Xu, Yimin;Eannetta, Nancy;Matas, Antonio J.;McQuinn, Ryan;Tanksley, Steven D.;Camara, Francisco;Guigo, Roderic;Rombauts, Stephane;Fawcett, Jeffrey;Van de Peer, Yves;Zamir, Dani;Liang, Chunbo;Spannagl, Manuel;Gundlach, Heidrun;Bruggmann, Remy;Mayer, Klaus;Jia, Zhiqi;Zhang, Junhong;Ye, Zhibiao;Bishop, Gerard J.;Butcher, Sarah;Lopez-Cobollo, Rosa;Buchan, Daniel;Filippis, Ioannis;Abbott, James;Dixit, Rekha;Singh, Manju;Singh, Archana;Pal, Jitendra Kumar;Pandit, Awadhesh;Singh, Pradeep Kumar;Mahato, Ajay Kumar;Dogra, Vivek;Gaikwad, Kishor;Sharma, Tilak Raj;Mohapatra, Trilochan;Singh, Nagendra Kumar;Causse, Mathilde;Rothan, Christophe;Schiex, Thomas;Noirot, Celine;Bellec, Arnaud;Klopp, Christophe;Delalande, Corinne;Berges, Helene;Mariette, Jerome;Frasse, Pierre;Vautrin, Sonia;Zouine, Mohamed;Latche, Alain;Rousseau, Christine;Regad, Farid;Pech, Jean-Claude;Philippot, Murielle;Bouzayen, Mondher;Pericard, Pierre;Osorio, Sonia;Fernandez del Carmen, Asuncion;Monforte, Antonio;Granell, Antonio;Fernandez-Munoz, Rafael;Conte, Mariana;Lichtenstein, Gabriel;Carrari, Fernando;De Bellis, Gianluca;Fuligni, Fabio;Peano, Clelia;Grandillo, Silvana;Termolino, Pasquale;Pietrella, Marco;Fantini, Elio;Falcone, Giulia;Fiore, Alessia;Giuliano, Giovanni;Lopez, Loredana;Facella, Paolo;Perrotta, Gaetano;Daddiego, Loretta;Bryan, Glenn;Orozco, Modesto;Pastor, Xavier;Torrents, David;van Schriek, Keygene N. V. Marco G. M.;Feron, Richard M. C.;van Oeveren, Jan;de Heer, Peter;daPonte, Lorena;Jacobs-Oomen, Saskia;Cariaso, Mike;Prins, Marcel;van Eijk, Michiel J. T.;Janssen, Antoine;van Haaren, Mark J. J.;Jo, Sung-Hwan;Kim, Jungeun;Kwon, Suk-Yoon;Kim, Sangmi;Koo, Dal-Hoe;Lee, Sanghyeob;Hur, Cheol-Goo;Clouser, Christopher;Rico, Alain;Hallab, Asis;Gebhardt, Christiane;Klee, Kathrin;Joecker, Anika;Warfsmann, Jens;Goebel, Ulrike;Kawamura, Shingo;Yano, Kentaro;Sherman, Jamie D.;Fukuoka, Hiroyuki;Negoro, Satomi;Bhutty, Sarita;Chowdhury, Parul;Chattopadhyay, Debasis;Datema, Erwin;Smit, Sandra;Schijlen, Eliog. W. M.;van de Belt, Jose;van Haarst, Jan C.;Peters, Sander A.;van Staveren, Marjo J.;Henkens, Marleen H. C.;Mooyman, Paul J. W.;Hesselink, Thamara;van Ham, Roeland C. H. J.;Jiang, Guoyong;Droege, Marcus;Choi, Doil;Kang, Byung-Cheol;Kim, Byung Dong;Park, Minkyu;Kim, Seungill;Yeom, Seon-In;Lee, Yong-Hwan;Choi, Yang-Do;Li, Guangcun;Gao, Jianwei;Liu, Yongsheng;Huang, Shengxiong;Fernandez-Pedrosa, Victoria;Collado, Carmen;Zuniga, Sheila;Wang, Guoping;Cade, Rebecca;Dietrich, Robert A.;Rogers, Jane;Knapp, Sandra;Fei, Zhangjun;White, Ruth A.;Thannhauser, Theodore W.;Giovannoni, James J.;Angel Botella, Miguel;Gilbert, Louise;Gonzalez, Ramon;Goicoechea, Jose Luis;Yu, Yeisoo;Kudrna, David;Collura, Kristi;Wissotski, Marina;Wing, Rod;Schoof, Heiko;Meyers, Blake C.;Gurazada, Aishwarya Bala;Green, Pamela J.;Mathur, Saloni;Vyas, Shailendra;Solanke, Amolkumar U.;Kumar, Rahul;Gupta, Vikrant;Sharma, Arun K.;Khurana, Paramjit;Khurana, Jitendra P.;Tyagi, Akhilesh K.;Dalmay, Tamas;Mohorianu, Irina;Walts, Brandon;Chamala, Srikar;Barbazuk, W. Brad;Li, Jingping;Guo, Hui;Lee, Tae-Ho;Wang, Yupeng;Zhang, Dong;Paterson, Andrew H.;Wang, Xiyin;Tang, Haibao;Barone, Amalia;Chiusano, Maria Luisa;Ercolano, Maria Raffaella;D'Agostino, Nunzio;Di Filippo, Miriam;Traini, Alessandra;Sanseverino, Walter;Frusciante, Luigi;Seymour, Graham B.;Elharam, Mounir;Fu, Ying;Hua, Axin;Kenton, Steven;Lewis, Jennifer;Lin, Shaoping;Najar, Fares;Lai, Hongshing;Qin, Baifang;Qu, Chunmei;Shi, Ruihua;White, Douglas;White, James;Xing, Yanbo;Yang, Keqin;Yi, Jing;Yao, Ziyun;Zhou, Liping;Roe, Bruce A.;Vezzi, Alessandro;D'Angelo, Michela;Zimbello, Rosanna;Schiavon, Riccardo;Caniato, Elisa;Rigobello, Chiara;Campagna, Davide;Vitulo, Nicola;Valle, Giorgio;Nelson, David R.;De Paoli, Emanuele;Szinay, Dora;de Jong, Hans H.;Bai, Yuling;Visser, Richard G. F.;Lankhorst, Rene M. Klein;Beasley, Helen;McLaren, Karen;Nicholson, Christine;Riddle, Claire;Gianese, Giulio
• 通讯作者: Gianese, Giulio