Structured RNAs and synteny regions in the pig genome.
Structured RNAs and synteny regions in the pig genome.
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DOI：
10.1186/1471-2164-15-459
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发表时间：
2014-06-10
期刊：
影响因子：
4.4
通讯作者：
Gorodkin J
中科院分区：
文献类型：
--
作者：
Anthon C;Tafer H;Havgaard JH;Thomsen B;Hedegaard J;Seemann SE;Pundhir S;Kehr S;Bartschat S;Nielsen M;Nielsen RO;Fredholm M;Stadler PF;Gorodkin J
注释哺乳动物基因组的非编码RNA（ncRNA）是不平凡的，因为远不是所有的ncRNA是已知的，计算模型是资源需求。目前，人类基因组拥有最好的哺乳动物ncRNA注释，这是几个小组无数努力的结果。然而，对于越来越多的测序哺乳动物基因组，其中一些，如猪，作为疾病模型和生产动物相关，需要一个更直接的策略。我们提出了一个全面的注释结构RNA在猪的基因组。结合序列和结构相似性搜索以及类别特定方法，我们获得了一个保守集，共有3，391个结构化RNA基因座，其中分别有1，011个和2，314个与现有数据库中的结构化RNA具有很强的序列和结构相似性。RNA基因座包括139个顺式调控元件基因座、58个lncRNA基因座、11个注释冲突和3，183个ncRNA基因。ncRNA基因包括359个miRNA、8个核酶、185个rRNA、638个snoRNA、1，030个snRNA、810个tRNA和153个不属于上述类别的ncRNA基因。当在基因组的本地混洗版本上运行管道时，我们在最高置信水平下没有获得匹配。对来自10种不同猪组织的合并文库的RNA-seq数据的额外分析增加了另外165个miRNA基因座，产生了3，556个结构化RNA基因座的总体注释。这个注释代表了我们在自动化注释方面所做的最大努力。为了进一步提高可靠性，3，556个结构化RNA中的571个通过依赖于RNA类别的方法手动管理，而1，581个被宣布为假基因。我们进一步创建了猪与20种代表性脊椎动物的多重比对，从中RNAz预测了83，859个具有保守RNA结构的从头RNA位点。528个RNAz预测与基于同源性的注释或新型miRNA重叠。我们进一步提出了一个实质性的同线性分析，其中包括1,004个谱系特异性的从头RNA基因座和4个ncRNA基因座，在已知的注释特异性的Laurasiatheria（猪，牛，海豚，马，猫，狗，刺猬）。我们已经获得了哺乳动物基因组结构化ncRNA的最全面的注释之一，这可能在健康建模和生产中发挥核心作用。核心注释可在Ensembl 70中获得，完整的注释可在http://rth.dk/resources/rnannotator/susscr102/version1.02上获得。本文的在线版本（doi：10.1186/1471-2164-15-459）包含补充材料，可供授权用户使用。
Annotating mammalian genomes for noncoding RNAs (ncRNAs) is nontrivial since far from all ncRNAs are known and the computational models are resource demanding. Currently, the human genome holds the best mammalian ncRNA annotation, a result of numerous efforts by several groups. However, a more direct strategy is desired for the increasing number of sequenced mammalian genomes of which some, such as the pig, are relevant as disease models and production animals. We present a comprehensive annotation of structured RNAs in the pig genome. Combining sequence and structure similarity search as well as class specific methods, we obtained a conservative set with a total of 3,391 structured RNA loci of which 1,011 and 2,314, respectively, hold strong sequence and structure similarity to structured RNAs in existing databases. The RNA loci cover 139 cis-regulatory element loci, 58 lncRNA loci, 11 conflicts of annotation, and 3,183 ncRNA genes. The ncRNA genes comprise 359 miRNAs, 8 ribozymes, 185 rRNAs, 638 snoRNAs, 1,030 snRNAs, 810 tRNAs and 153 ncRNA genes not belonging to the here fore mentioned classes. When running the pipeline on a local shuffled version of the genome, we obtained no matches at the highest confidence level. Additional analysis of RNA-seq data from a pooled library from 10 different pig tissues added another 165 miRNA loci, yielding an overall annotation of 3,556 structured RNA loci. This annotation represents our best effort at making an automated annotation. To further enhance the reliability, 571 of the 3,556 structured RNAs were manually curated by methods depending on the RNA class while 1,581 were declared as pseudogenes. We further created a multiple alignment of pig against 20 representative vertebrates, from which RNAz predicted 83,859 de novo RNA loci with conserved RNA structures. 528 of the RNAz predictions overlapped with the homology based annotation or novel miRNAs. We further present a substantial synteny analysis which includes 1,004 lineage specific de novo RNA loci and 4 ncRNA loci in the known annotation specific for Laurasiatheria (pig, cow, dolphin, horse, cat, dog, hedgehog). We have obtained one of the most comprehensive annotations for structured ncRNAs of a mammalian genome, which is likely to play central roles in both health modelling and production. The core annotation is available in Ensembl 70 and the complete annotation is available at http://rth.dk/resources/rnannotator/susscr102/version1.02. The online version of this article (doi:10.1186/1471-2164-15-459) contains supplementary material, which is available to authorized users.
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影响因子：
7
作者：
Harrow J;Frankish A;Gonzalez JM;Tapanari E;Diekhans M;Kokocinski F;Aken BL;Barrell D;Zadissa A;Searle S;Barnes I;Bignell A;Boychenko V;Hunt T;Kay M;Mukherjee G;Rajan J;Despacio-Reyes G;Saunders G;Steward C;Harte R;Lin M;Howald C;Tanzer A;Derrien T;Chrast J;Walters N;Balasubramanian S;Pei B;Tress M;Rodriguez JM;Ezkurdia I;van Baren J;Brent M;Haussler D;Kellis M;Valencia A;Reymond A;Gerstein M;Guigó R;Hubbard TJ
通讯作者：
Hubbard TJ
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
14.9
作者：
Griffiths-Jones, S
通讯作者：
Griffiths-Jones, S
影响因子：
4.4
作者：
Esteve-Codina A;Kofler R;Palmieri N;Bussotti G;Notredame C;Pérez-Enciso M
通讯作者：
Pérez-Enciso M
通过修剪动力学编程矩阵，快速成对的结构RNA对齐。
影响因子：
4.3
作者：
Havgaard, Jakob H.;Torarinsson, Elfar;Gorodkin, Jan
通讯作者：
Gorodkin, Jan