Published online 4 October 2005
Article |
Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts
Department of Medicine, Section of Hematology/Oncology, University of Chicago 5841 S. Maryland Avenue, MC2115, Chicago, IL 60637, USA 1Department of Biology and Biochemistry, University of Bath Somerset, BA2 7AY, UK 2Department of Genetics and Developmental Biology, University of Connecticut Health Center Farmington, CT 06030-3301, USA
*To whom correspondence should be addressed. Tel: +1 773 795 5474; Fax: +1 773 702 3002; Email: jchen{at}medicine.bsd.uchicago.edu
Received June 3, 2005. Revised August 4, 2005. Accepted September 5, 2005.
Although both the 5'- and 3'-untranslated regions (5'- and 3'-UTRs) of eukaryotic mRNAs may play a crucial role in posttranscriptional gene regulation, we observe that cis-encoded natural antisense RNAs have a striking preferential complementarity to the 3'-UTRs of their target genes in mammalian (human and mouse) genomes. A null neutral model, evoking differences in the rate of 3'-UTR and 5'-UTR extension, could potentially explain high rates of 3'-to-3' overlap compared with 5'-to-5' overlap. However, employing a simulation model we show that this null model probably cannot explain the finding that 3'-to-3' overlapping pairs have a much higher probability (>5 times) of conservation in both mouse and human genomes with the same overlapping pattern than do 5'-to-5' overlaps. Furthermore, it certainly cannot explain the finding that overlapping pairs seen in both genomes have a significantly higher probability of having co-expression and inverse expression (i.e. characteristic of sense–antisense regulation) than do overlapping pairs seen in only one of the two species. We infer that the function of many 3'-to-3' overlaps is indeed antisense regulation. These findings underscore the preference for, and conservation of, 3'-UTR-targeted antisense regulation, and the importance of 3'-UTRs in gene regulation.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  M. Carlile, P. Nalbant, K. Preston-Fayers, G. S. McHaffie, and A. Werner Processing of naturally occurring sense/antisense transcripts of the vertebrate Slc34a gene into short RNAs Physiol Genomics, June 10, 2008; 34(1): 95 - 100. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Zhang, B. Raghavan, M. Kotur, J. Cheatham, D. Sedmak, C. Cook, J. Waldman, and J. Trgovcich Antisense Transcription in the Human Cytomegalovirus Transcriptome J. Virol., October 15, 2007; 81(20): 11267 - 11281. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. E. Fish, C. C. Matouk, E. Yeboah, S. C. Bevan, M. Khan, K. Patil, M. Ohh, and P. A. Marsden Hypoxia-inducible Expression of a Natural cis-Antisense Transcript Inhibits Endothelial Nitric-oxide Synthase J. Biol. Chem., May 25, 2007; 282(21): 15652 - 15666. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Werner, G. Schmutzler, M. Carlile, C. G. Miles, and H. Peters Expression profiling of antisense transcripts on DNA arrays Physiol Genomics, February 12, 2007; 28(3): 294 - 300. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Zhang, X. S. Liu, Q.-R. Liu, and L. Wei Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species Nucleic Acids Res., July 18, 2006; 34(12): 3465 - 3475. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Sun, L. D. Hurst, G. G. Carmichael, and J. Chen Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcription and organismic complexity Genome Res., July 1, 2006; 16(7): 922 - 933. [Abstract] [Full Text] [PDF]
|
|