Wed, 20 Aug 2008 21:15:22 BST CiteULike: marcius's Ghosh http://www.citeulike.org/user/marcius/author/Ghosh CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/marcius/article/1336057 <i>Science (17 May 2007), 1138341.</i><br /><br />Significant fractions of eukaryotic genomes give rise to RNA, much of which is unannotated and has reduced protein-coding potential. The genomic origins and the relations of human nuclear and cytosolic polyadenylated RNAs longer than 200 nucleotides and whole-cell RNAs less than 200 nt are investigated in this genome-wide study. Subcellular addresses for nucleotides present in detected RNAs were assigned, and their potential processing into short RNAs was investigated. Taken together, these observations suggest a role for some unannotated RNAs as primary transcripts for the production of short RNAs. Three novel potentially functional classes of RNAs have been identified, two of which are syntenically conserved and correlate with the expression state of protein-coding genes. These data support a highly interleaved organization of the human transcriptome. 10.1126/science.1138341 RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription Philipp Kapranov Jill Cheng Sujit Dike David Nix Radharani Duttagupta Aarron Willingham Peter Stadler Jana Hertel Joerg Hackermueller Ivo Hofacker Ian Bell Evelyn Cheung Jorg Drenkow Erica Dumais Sandeep Patel Gregg Helt Madhavan Ganesh Srinka Ghosh Antonio Piccolboni Victor Sementchenko Hari Tammana Thomas Gingeras doi:10.1126/science.1138341 Science (17 May 2007), 1138341. 2007-05-27T00:42:53-00:00 2007 Science 1138341 classification genome ncrna http://www.citeulike.org/user/marcius/article/341149 <i>Nature Structural & Molecular Biology, Vol. 12, No. 10. (18 September 2005), pp. 886-892.</i><br /><br />Only few instances are known of protein folds that tolerate massive sequence variation for the sake of binding diversity. The most extensively characterized is the immunoglobulin fold. We now add to this the C-type lectin (CLec) fold, as found in the major tropism determinant (Mtd), a retroelement-encoded receptor-binding protein of Bordetella bacteriophage. Variation in Mtd, with its approximately 10(13) possible sequences, enables phage adaptation to Bordetella spp. Mtd is an intertwined, pyramid-shaped trimer, with variable residues organized by its CLec fold into discrete receptor-binding sites. The CLec fold provides a highly static scaffold for combinatorial display of variable residues, probably reflecting a different evolutionary solution for balancing diversity against stability from that in the immunoglobulin fold. Mtd variants are biased toward the receptor pertactin, and there is evidence that the CLec fold is used broadly for sequence variation by related retroelements. The C-type lectin fold as an evolutionary solution for massive sequence variation Stephen Mcmahon Jason Miller Jeffrey Lawton Donald Kerkow Asher Hodes Marc Marti-Renom Sergei Doulatov Eswar Narayanan Andrej Sali Jeff Miller Partho Ghosh doi:10.1038/nsmb992 Nature Structural & Molecular Biology, Vol. 12, No. 10. (18 September 2005), pp. 886-892. 2005-10-04T22:32:23-00:00 2005 Nature Structural & Molecular Biology 1545-9993 12 10 886 892 Nature Publishing Group computational_biology evolution immunology protein_function protein_structure