The complex transcriptional landscape of the anucleate human platelet.
The complex transcriptional landscape of the anucleate human platelet.
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DOI：
10.1186/1471-2164-14-1
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发表时间：
2013-01-16
期刊：
影响因子：
4.4
通讯作者：
Rigoutsos I
中科院分区：
文献类型：
--
作者：
Bray PF;McKenzie SE;Edelstein LC;Nagalla S;Delgrosso K;Ertel A;Kupper J;Jing Y;Londin E;Loher P;Chen HW;Fortina P;Rigoutsos I
人体血小板对于维持正常止血至关重要，血小板功能障碍常常导致出血或血栓形成。使用微阵列对全基因组血小板 RNA 表达的估计提供了对血小板转录组的见解，但受到已知转录本数量的限制。这项工作的目标是对白细胞耗尽的血小板中的 RNA 进行深度测序，以捕获所有表达转录本的复杂特征。我们从总RNA和核糖体RNA耗尽的RNA制剂中，从四个健康个体中的每一个生成了长RNA（≥40个核苷酸）谱，以及短RNA（<40个核苷酸）谱。对约 10 亿条读数的分析表明，编码和非编码血小板转录物跨越了非常宽的动态范围（超出 β-肌动蛋白≥16 个 PCR 循环），我们通过 qRT-PCR 对数十种血小板信使 RNA 验证了这一结果。令人惊讶的是，核糖体 RNA 的消耗对转录本相对丰度的估计产生了显着的不利影响。在已知的蛋白质编码位点中，约 9,500 个存在于人类血小板中。我们观察到通过 RNA-seq 鉴定的 mRNA 与表达良好的 mRNA 的微阵列之间存在很强的相关性，但 RNASeq 鉴定了更多丰度较低的转录本，并允许发现新的转录本。我们的分析揭示了不同类别的非编码 RNA，包括：蛋白质编码位点的普遍反义转录物；大量以前未报道的丰富的 microRNA；逆转录转座子；以及数千个新颖的未注释的长和短内含子转录本，考虑到血小板的无核性质，这是一个有趣的发现。这些数据可通过 UCSC 基因组浏览器的本地镜像获得，并可通过以下网址访问：http://cm.jefferson.edu/platelets_2012/。
Human blood platelets are essential to maintaining normal hemostasis, and platelet dysfunction often causes bleeding or thrombosis. Estimates of genome-wide platelet RNA expression using microarrays have provided insights to the platelet transcriptome but were limited by the number of known transcripts. The goal of this effort was to deep-sequence RNA from leukocyte-depleted platelets to capture the complex profile of all expressed transcripts. From each of four healthy individuals we generated long RNA (≥40 nucleotides) profiles from total and ribosomal-RNA depleted RNA preparations, as well as short RNA (<40 nucleotides) profiles. Analysis of ~1 billion reads revealed that coding and non-coding platelet transcripts span a very wide dynamic range (≥16 PCR cycles beyond β-actin), a result we validated through qRT-PCR on many dozens of platelet messenger RNAs. Surprisingly, ribosomal-RNA depletion significantly and adversely affected estimates of the relative abundance of transcripts. Of the known protein-coding loci, ~9,500 are present in human platelets. We observed a strong correlation between mRNAs identified by RNA-seq and microarray for well-expressed mRNAs, but RNASeq identified many more transcripts of lower abundance and permitted discovery of novel transcripts. Our analyses revealed diverse classes of non-coding RNAs, including: pervasive antisense transcripts to protein-coding loci; numerous, previously unreported and abundant microRNAs; retrotransposons; and thousands of novel un-annotated long and short intronic transcripts, an intriguing finding considering the anucleate nature of platelets. The data are available through a local mirror of the UCSC genome browser and can be accessed at: http://cm.jefferson.edu/platelets_2012/.
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影响因子：
64.8
作者：
通讯作者：
--
影响因子：
14.9
作者：
Belancio VP;Roy-Engel AM;Pochampally RR;Deininger P
通讯作者：
Deininger P
影响因子：
64.5
作者：
Denis, MM;Tolley, ND;Weyrich, AS
通讯作者：
Weyrich, AS
影响因子：
64.8
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Gieger, Christian;Radhakrishnan, Aparna;Cvejic, Ana;Tang, Weihong;Porcu, Eleonora;Pistis, Giorgio;Serbanovic-Canic, Jovana;Elling, Ulrich;Goodall, Alison H.;Labrune, Yann;Lopez, Lorna M.;Maegi, Reedik;Meacham, Stuart;Okada, Yukinori;Pirastu, Nicola;Sorice, Rossella;Teumer, Alexander;Voss, Katrin;Zhang, Weihua;Ramirez-Solis, Ramiro;Bis, Joshua C.;Ellinghaus, David;Goegele, Martin;Hottenga, Jouke-Jan;Langenberg, Claudia;Kovacs, Peter;O'Reilly, Paul F.;Shin, So-Youn;Esko, Toenu;Hartiala, Jaana;Kanoni, Stavroula;Murgia, Federico;Parsa, Afshin;Stephens, Jonathan;van der Harst, Pim;van der Schoot, C. Ellen;Allayee, Hooman;Attwood, Antony;Balkau, Beverley;Bastardot, Francois;Basu, Saonli;Baumeister, Sebastian E.;Biino, Ginevra;Bomba, Lorenzo;Bonnefond, Amelie;Cambien, Francois;Chambers, John C.;Cucca, Francesco;D'Adamo, Pio;Davies, Gail;de Boer, Rudolf A.;de Geus, Eco J. C.;Doering, Angela;Elliott, Paul;Erdmann, Jeanette;Evans, David M.;Falchi, Mario;Feng, Wei;Folsom, Aaron R.;Frazer, Ian H.;Gibson, Quince D.;Glazer, Nicole L.;Hammond, Chris;Hartikainen, Anna-Liisa;Heckbert, Susan R.;Hengstenberg, Christian;Hersch, Micha;Illig, Thomas;Loos, Ruth J. F.;Jolley, Jennifer;Khaw, Kay Tee;Kuehnel, Brigitte;Kyrtsonis, Marie-Christine;Lagou, Vasiliki;Lloyd-Jones, Heather;Lumley, Thomas;Mangino, Massimo;Maschio, Andrea;Leach, Irene Mateo;McKnight, Barbara;Memari, Yasin;Mitchell, Braxton D.;Montgomery, Grant W.;Nakamura, Yusuke;Nauck, Matthias;Navis, Gerjan;Noethlings, Ute;Nolte, Ilja M.;Porteous, David J.;Pouta, Anneli;Pramstaller, Peter P.;Pullat, Janne;Ring, Susan M.;Rotter, Jerome I.;Ruggiero, Daniela;Ruokonen, Aimo;Sala, Cinzia;Samani, Nilesh J.;Sambrook, Jennifer;Schlessinger, David;Schreiber, Stefan;Schunkert, Heribert;Scott, James;Smith, Nicholas L.;Snieder, Harold;Starr, John M.;Stumvoll, Michael;Takahashi, Atsushi;Tang, W. H. Wilson;Taylor, Kent;Tenesa, Albert;Thein, Swee Lay;Toenjes, Anke;Uda, Manuela;Ulivi, Sheila;van Veldhuisen, Dirk J.;Visscher, Peter M.;Voelker, Uwe;Wichmann, H-Erich;Wiggins, Kerri L.;Willemsen, Gonneke;Yang, Tsun-Po;Zhao, Jing Hua;Zitting, Paavo;Bradley, John R.;Dedoussis, George V.;Gasparini, Paolo;Hazen, Stanley L.;Metspalu, Andres;Pirastu, Mario;Shuldiner, Alan R.;van Pelt, L. Joost;Zwaginga, Jaap-Jan;Boomsma, Dorret I.;Deary, Ian J.;Franke, Andre;Froguel, Philippe;Ganesh, Santhi K.;Jarvelin, Marjo-Riitta;Martin, Nicholas G.;Meisinger, Christa;Psaty, Bruce M.;Spector, Timothy D.;Wareham, Nicholas J.;Akkerman, Jan-Willem N.;Ciullo, Marina;Deloukas, Panos;Greinacher, Andreas;Jupe, Steve;Kamatani, Naoyuki;Khadake, Jyoti;Kooner, Jaspal S.;Penninger, Josef;Prokopenko, Inga;Stemple, Derek;Toniolo, Daniela;Wernisch, Lorenz;Sanna, Serena;Hicks, Andrew A.;Rendon, Augusto;Ferreira, Manuel A.;Ouwehand, Willem H.;Soranzo, Nicole
通讯作者：
Soranzo, Nicole
影响因子：
30.8
作者：
Faulkner, Geoffrey J.;Kimura, Yasumasa;Carninci, Piero
通讯作者：
Carninci, Piero