RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription
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.
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References and Notes
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We thank M. Mittmann, D. Le, and E. Schell for design of tiling arrays; K. Kole, D. Barone, and C. Chen for their help with direct RNA labeling; G. Hannon, K. Fejes-Toth, D. Gerhard, and K. Nussbacher for technical discussion and assistance in manuscript preparation; Mt. Sinai Hospital and A. Nagy, R. Nagy, W. Abramow-Newerly, J. Rossant, and J. Roder for procurement of the R1mES cell line; and M. Brown and D. Menke at Stanford for help in preparation of mouse embryo fibroblasts. This project has been funded in part with funds from the National Cancer Institute, NIH, under contract no. N01-CO-12400 and from the National Human Genome Research Institute, NIH, under grant no. U01HG003147, and by Affymetrix, Inc. The data discussed in this publication have been deposited in National Center for Biotechnology Information's Gene Expression Omnibus (GEO, www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series accession number GSE-7576.
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Science
Volume 316 | Issue 5830
8 June 2007
8 June 2007
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American Association for the Advancement of Science.
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Received: 4 December 2006
Accepted: 24 April 2007
Published in print: 8 June 2007
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