Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements.
Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements.
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DOI：
10.1093/nar/gkn1041
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发表时间：
2009-03
影响因子：
14.9
通讯作者：
Jones SJ
中科院分区：
文献类型：
--
作者：
Sleumer MC;Bilenky M;He A;Robertson G;Thiessen N;Jones SJ
从8种线虫的基因组完全测序的可用性提供了一个机会，以确定新的顺式调控元件的启动子区的秀丽隐杆线虫成绩单使用比较基因组学。我们确定了C. elegans在C.布里格塞角remanei，C. brenneri，C.利用WABA比对算法对日本、太平洋棱纹线虫、马来丝虫和旋毛虫进行比对。我们将C. elegans与其直系同源物的上游区域，并确定了保守的DNA序列元件的从头模体发现。在3847 C上游共发现了158017个新的保守基序。elegans转录本，其中三个或更多的直系同源物是可用的，并确定了82%的44个实验证明的调控元件从ORegAnno。我们将26%的基序注释为与来自ORegAnno、TRANSFAC和JASPAR的转录因子的已知结合序列相似。这是第一个有注释的线虫上游保守元件目录，可用于寻找推定的调控元件，改进基因模型，发现新的RNA基因，并了解线虫门中转录因子及其结合位点的进化。注释的基序为表征的转录因子和表征的哺乳动物转录因子的直向同源物提供了新的结合位点候选物。
The availability of completely sequenced genomes from eight species of nematodes has provided an opportunity to identify novel cis-regulatory elements in the promoter regions of Caenorhabditis elegans transcripts using comparative genomics. We determined orthologues for C. elegans transcripts in C. briggsae, C. remanei, C. brenneri, C. japonica, Pristionchus pacificus, Brugia malayi and Trichinella spiralis using the WABA alignment algorithm. We pooled the upstream region of each transcript in C. elegans with the upstream regions of its orthologues and identified conserved DNA sequence elements by de novo motif discovery. In total, we discovered 158 017 novel conserved motifs upstream of 3847 C. elegans transcripts for which three or more orthologues were available, and identified 82% of 44 experimentally proven regulatory elements from ORegAnno. We annotated 26% of the motifs as similar to known binding sequences of transcription factors from ORegAnno, TRANSFAC and JASPAR. This is the first catalogue of annotated conserved upstream elements for nematodes and can be used to find putative regulatory elements, improve gene models, discover novel RNA genes, and understand the evolution of transcription factors and their binding sites in phylum Nematoda. The annotated motifs provide novel binding site candidates for both characterized transcription factors and orthologues of characterized mammalian transcription factors.
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影响因子：
9.8
作者：
Hillier LW;Miller RD;Baird SE;Chinwalla A;Fulton LA;Koboldt DC;Waterston RH
通讯作者：
Waterston RH
Oreganno：一种开放访问社区驱动的监管注释资源。
影响因子：
14.9
作者：
Griffith OL;Montgomery SB;Bernier B;Chu B;Kasaian K;Aerts S;Mahony S;Sleumer MC;Bilenky M;Haeussler M;Griffith M;Gallo SM;Giardine B;Hooghe B;Van Loo P;Blanco E;Ticoll A;Lithwick S;Portales-Casamar E;Donaldson IJ;Robertson G;Wadelius C;De Bleser P;Vlieghe D;Halfon MS;Wasserman W;Hardison R;Bergman CM;Jones SJ;Open Regulatory Annotation Consortium
通讯作者：
Open Regulatory Annotation Consortium
TransFac及其模块移植：真核生物中的转录基因调节。
影响因子：
14.9
作者：
Matys V;Kel-Margoulis OV;Fricke E;Liebich I;Land S;Barre-Dirrie A;Reuter I;Chekmenev D;Krull M;Hornischer K;Voss N;Stegmaier P;Lewicki-Potapov B;Saxel H;Kel AE;Wingender E
通讯作者：
Wingender E
影响因子：
30.8
作者：
Dieterich, Christoph;Clifton, Sandra W.;Schuster, Lisa N.;Chinwalla, Asif;Delehaunty, Kimberly;Dinkelacker, Iris;Fulton, Lucinda;Fulton, Robert;Godfrey, Jennifer;Minx, Pat;Mitreva, Makedonka;Roeseler, Waltraud;Tian, Huiyu;Witte, Hanh;Yang, Shiaw-Pyng;Wilson, Richard K.;Sommer, Ralf J.
通讯作者：
Sommer, Ralf J.
影响因子：
5.6
作者：
Bando, T;Ikeda, T;Kagawa, H
通讯作者：
Kagawa, H