RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription
Philipp Kapranov,1
Jill Cheng,1
Sujit Dike,1
David A. Nix,1
Radharani Duttagupta,1
Aarron T. Willingham,1
Peter F. Stadler,2
Jana Hertel,2
Jörg Hackermüller,3
Ivo L. Hofacker,4
Ian Bell,1
Evelyn Cheung,1
Jorg Drenkow,1
Erica Dumais,1
Sandeep Patel,1
Gregg Helt,1
Madhavan Ganesh,1
Srinka Ghosh,1
Antonio Piccolboni,1
Victor Sementchenko,1
Hari Tammana,1
Thomas R. Gingeras1*
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.
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.
* To whom correspondence should be addressed. E-mail: tom_gingeras{at}affymetrix.com
