Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure
作者： Elfar Torarinsson , Milena Sawera , Jakob H Havgaard , Merete Fredholm , Jan Gorodkin
DOI: 10.1101/GR.5226606
关键词:
摘要: Human and mouse genome sequences contain roughly 100,000 regions that are unalignable in primary sequence neighbor corresponding alignable between both organisms. These pairs generally assumed to be nonconserved, although the level of structural conservation these has never been investigated. Owing limitations computational methods, comparative genomics lacking ability compare such nonconserved for conserved RNA elements. We have investigated presence elements by conducting a local alignment, using FOLDALIGN, on subset estimate 1800 common structures. Comparing our results with recent mapping transcribed fragments (transfrags) human, we find high-scoring candidates twice as likely found overlapped transfrags than not transfrags. To verify coexpression predicted human mouse, conducted expression studies RT-PCR Northern blotting candidates, which overlap chromosome 20. confirmed 32 out 36 whereas blots four 12 candidates. Furthermore, many indicate differential different tissues. Hence, findings suggest there expressed non-coding sequence.
genome.org参考文章(17)
Steve Rozen, Helen Skaletsky, Primer3 on the WWW for general users and for biologist programmers. Methods of Molecular Biology. ,vol. 132, pp. 365- 386 ,(2000) , 10.1385/1-59259-192-2:365
Timothy R Hughes, Tomas Babak, Benjamin J Blencowe, A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription BMC Genomics. ,vol. 6, pp. 104- 104 ,(2005) , 10.1186/1471-2164-6-104
Elena Rivas, Sean R Eddy, Noncoding RNA gene detection using comparative sequence analysis BMC Bioinformatics. ,vol. 2, pp. 8- 8 ,(2001) , 10.1186/1471-2105-2-8
Significance of nucleotide sequence alignments: a method for random sequence permutation that preserves dinucleotide and codon usage. Molecular Biology and Evolution. ,vol. 2, pp. 526- 538 ,(1985) , 10.1093/OXFORDJOURNALS.MOLBEV.A040370
Françoise Wyers, Mathieu Rougemaille, Gwenaël Badis, Jean-Claude Rousselle, Marie-Elisabeth Dufour, Jocelyne Boulay, Béatrice Régnault, Frédéric Devaux, Abdelkader Namane, Bertrand Séraphin, Domenico Libri, Alain Jacquier, Cryptic Pol II Transcripts Are Degraded by a Nuclear Quality Control Pathway Involving a New Poly(A) Polymerase Cell. ,vol. 121, pp. 725- 737 ,(2005) , 10.1016/J.CELL.2005.04.030
Christopher Workman, Anders Krogh, No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution Nucleic Acids Research. ,vol. 27, pp. 4816- 4822 ,(1999) , 10.1093/NAR/27.24.4816
S Altschula, Warren Gisha, Webb Millerb, E Meyersc, D Lipmana, None, Basic Local Alignment Search Tool Journal of Molecular Biology. ,vol. 215, pp. 403- 410 ,(1990) , 10.1016/S0022-2836(05)80360-2
Michael J. Holland, Transcript Abundance in Yeast Varies over Six Orders of Magnitude Journal of Biological Chemistry. ,vol. 277, pp. 14363- 14366 ,(2002) , 10.1074/JBC.C200101200
David Sankoff, Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems Siam Journal on Applied Mathematics. ,vol. 45, pp. 810- 825 ,(1985) , 10.1137/0145048
Pea Carninci, T Kasukawa, S Katayama, J Gough, MC Frith, Norihiro Maeda, Rieko Oyama, T Ravasi, B Lenhard, C Wells, Rimantas Kodzius, Kazuro Shimokawa, Vladimir B Bajic, SE Brenner, Serge Batalov, ARR Forrest, Mihaela Zavolan, MJ Davis, Laurens G Wilming, V Aidinis, JE Allen, A Ambesi-Impiombato, R Apweiler, Rajith N Aturaliya, TL Bailey, M Bansal, L Baxter, Kirk W Beisel, T Bersano, H Bono, Alistair M Chalk, KP Chiu, V Choudhary, A Christoffels, DR Clutterbuck, ML Crowe, E Dalla, BP Dalrymple, B De Bono, G Della Gatta, Diego di Bernardo, T Down, P Engstrom, M Fagiolini, G Faulkner, CF Fletcher, T Fukushima, M Furuno, S Futaki, M Gariboldi, P Georgii-Hemming, TR Gingeras, Takashi Gojobori, RE Green, S Gustincich, M Harbers, Yutaka Hayashi, TK Hensch, N Hirokawa, D Hill, L Huminiecki, M Iacono, Kazuho Ikeo, A Iwama, T Ishikawa, M Jakt, A Kanapin, Masaru Katoh, Y Kawasawa, Janet Kelso, H Kitamura, Hiroaki Kitano, G Kollias, SPT Krishnan, A Kruger, SK Kummerfeld, IV Kurochkin, LF Lareau, D Lazarevic, L Lipovich, J Liu, S Liuni, S McWilliam, M Madan Babu, M Madera, Luigi Marchionni, Hideo Matsuda, S Matsuzawa, H Miki, F Mignone, S Miyake, K Morris, Salim Mottagui-Tabar, N Mulder, N Nakano, H Nakauchi, P Ng, R Nilsson, S Nishiguchi, S Nishikawa, F Nori, O Ohara, Y Okazaki, V Orlando, KC Pang, WJ Pavan, G Pavesi, G Pesole, Nikolai Petrovsky, S Piazza, J Reed, JF Reid, Brian Z Ring, M Ringwald, B Rost, Y Ruan, Steven L Salzberg, A Sandelin, C Schneider, C Schonbach, K Sekiguchi, Colin AM Semple, S Seno, L Sessa, Y Sheng, Y Shibata, H Shimada, K Shimada, D Silva, B Sinclair, S Sperling, E Stupka, Koji Sugiura, R Sultana, Yoichi Takenaka, K Taki, K Tammoja, SL Tan, S Tang, MS Taylor, J Tegner, SA Teichmann, HR Ueda, E Van Nimwegen, R Verardo, CL Wei, K Yagi, H Yamanishi, E Zabarovsky, S Zhu, None, The Transcriptional Landscape of the Mammalian Genome Science. ,vol. 309, pp. 1559- 1563 ,(2005) , 10.1126/SCIENCE.1112014