RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription

Author:

Kapranov Philipp1234,Cheng Jill1234,Dike Sujit1234,Nix David A.1234,Duttagupta Radharani1234,Willingham Aarron T.1234,Stadler Peter F.1234,Hertel Jana1234,Hackermüller Jörg1234,Hofacker Ivo L.1234,Bell Ian1234,Cheung Evelyn1234,Drenkow Jorg1234,Dumais Erica1234,Patel Sandeep1234,Helt Gregg1234,Ganesh Madhavan1234,Ghosh Srinka1234,Piccolboni Antonio1234,Sementchenko Victor1234,Tammana Hari1234,Gingeras Thomas R.1234

Affiliation:

1. Affymetrix Laboratory, Affymetrix, Inc., 3420 Central Expressway, Santa Clara, CA, 95051, USA.

2. University of Leipzig, Department of Computer Science, Leipzig, Germany.

3. Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany.

4. Institute for Theoretical Chemistry, University of Vienna, Austria.

Abstract

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 associations of human nuclear and cytosolic polyadenylated RNAs longer than 200 nucleotides (nt) and whole-cell RNAs less than 200 nt were 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 novel role for some unannotated RNAs as primary transcripts for the production of short RNAs. Three 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.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

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