RNA maps reveal new RNA classes and a possible function for pervasive transcription

Kapranov, P., Cheng, J., Dike, S., Nix, D. A., Duttagupta, R., Willingham, A. T., Stadler, P. F., Hertel, J., Hackermüller, J., Hofacker, I. L., Bell, I., Cheung, E., Drenkow, J., Dumais, E., Patel, S., Helt, G., Ganesh, M., Ghosh, S., Piccolboni, A., Sementchenko, V., Tammana, H., Gingeras, T. R. (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science, 316 (5830). pp. 1484-1488. ISSN 00368075 (ISSN)

URL: http://www.ncbi.nlm.nih.gov/pubmed/17510325
DOI: 10.1126/science.1138341

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.

Item Type: Paper
Additional Information:
Uncontrolled Keywords: gene product polyadenylated RNA RNA transcriptome eukaryote gene expression genome protein article cell nucleus cytosol gene mapping genetic conservation genome analysis human human cell priority journal RNA processing RNA transcription Animals Cell Line, Tumor Exons Genome Human Hela Cells Humans Mice Promoter Regions (Genetics) RNA Precursors RNA, Messenger Synteny Terminator Regions (Genetics) Transcription, Genetic Eukaryota
Subjects: bioinformatics > genomics and proteomics > annotation > map annotation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > RNA expression
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > ncRNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > sRNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes
CSHL Authors:
Communities: CSHL labs > Gingeras lab
Depositing User: CSHL Librarian
Date: 2007
Date Deposited: 08 Mar 2012 16:16
Last Modified: 12 Jul 2013 20:08
Related URLs:
URI: http://repository.cshl.edu/id/eprint/25318

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