DOI: 10.1126/science.1138341. RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription

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

10.1126/science.1138341

Crossref journal-article

American Association for the Advancement of Science (AAAS)

Science (221)

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.

Bibliography

Kapranov, P., Cheng, J., Dike, S., Nix, D. A., Duttagupta, R., Willingham, A. T., Stadler, P. F., Hertel, J., HackermuÌller, J., Hofacker, I. L., Bell, I., Cheung, E., Drenkow, J., Dumais, E., Patel, S., Helt, G., Ganesh, M., Ghosh, S., Piccolboni, A., â¦ Gingeras, T. R. (2007). RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription. Science, 316(5830), 1484â1488.

Authors 22

Philipp Kapranov (first)
Jill Cheng (additional)
Sujit Dike (additional)
David A. Nix (additional)
Radharani Duttagupta (additional)
Aarron T. Willingham (additional)
Peter F. Stadler (additional)
Jana Hertel (additional)
Jörg Hackermüller (additional)
Ivo L. Hofacker (additional)
Ian Bell (additional)
Evelyn Cheung (additional)
Jorg Drenkow (additional)
Erica Dumais (additional)
Sandeep Patel (additional)
Gregg Helt (additional)
Madhavan Ganesh (additional)
Srinka Ghosh (additional)
Antonio Piccolboni (additional)
Victor Sementchenko (additional)
Hari Tammana (additional)
Thomas R. Gingeras (additional)

References 15 Referenced 2,103

10.1126/science.1108625
ENCODE-Project-Consortium in preparation.
10.1126/science.1068597
10.1016/j.cell.2006.06.009
10.1101/gr.6036807
Data available at http://transcriptome.affymetrix.com/hs_whole_genome; www.ncbi.nlm.nih.gov/geo/; http://genome.ucsc.edu/.
Materials and methods are available as supporting material on Science Online.
10.1261/rna.5206304
10.1038/ng1789
10.1073/pnas.0507783103
10.1038/nature05519
10.1126/science.165.3891.349
10.1016/S0022-2836(61)80072-7
10.1016/0959-437X(94)90066-3
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.

Dates

Type	When
Created	18 years, 3 months ago (May 18, 2007, 1:13 p.m.)
Deposited	1 year, 7 months ago (Jan. 10, 2024, 3:36 a.m.)
Indexed	1 day, 10 hours ago (Aug. 31, 2025, 6:15 a.m.)
Issued	18 years, 2 months ago (June 8, 2007)
Published	18 years, 2 months ago (June 8, 2007)
Published Print	18 years, 2 months ago (June 8, 2007)

Funders 0

None

BibTeX

@article{Kapranov_2007, title={RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription}, volume={316}, ISSN={1095-9203}, url={http://dx.doi.org/10.1126/science.1138341}, DOI={10.1126/science.1138341}, number={5830}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Kapranov, Philipp and Cheng, Jill and Dike, Sujit and Nix, David A. and Duttagupta, Radharani and Willingham, Aarron T. and Stadler, Peter F. and Hertel, Jana and Hackermüller, Jörg and Hofacker, Ivo L. and Bell, Ian and Cheung, Evelyn and Drenkow, Jorg and Dumais, Erica and Patel, Sandeep and Helt, Gregg and Ganesh, Madhavan and Ghosh, Srinka and Piccolboni, Antonio and Sementchenko, Victor and Tammana, Hari and Gingeras, Thomas R.}, year={2007}, month=jun, pages={1484–1488} }

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