Evidence for a preferential targeting of 3 '-UTRs by cis-encoded natural antisense transcripts

M Sun, L D Hurst, G G Carmichael, J J Chen

Research output: Contribution to journalArticle

74 Citations (Scopus)

Abstract

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.
Original languageEnglish
Pages (from-to)5533-5543
Number of pages11
JournalNucleic Acids Research
Volume33
Issue number17
DOIs
Publication statusPublished - 2005

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3' Untranslated Regions
5' Untranslated Regions
Human Genome
Genes
Antisense RNA
Genome
Messenger RNA

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Evidence for a preferential targeting of 3 '-UTRs by cis-encoded natural antisense transcripts. / Sun, M; Hurst, L D; Carmichael, G G; Chen, J J.

In: Nucleic Acids Research, Vol. 33, No. 17, 2005, p. 5533-5543.

Research output: Contribution to journalArticle

Sun, M ; Hurst, L D ; Carmichael, G G ; Chen, J J. / Evidence for a preferential targeting of 3 '-UTRs by cis-encoded natural antisense transcripts. In: Nucleic Acids Research. 2005 ; Vol. 33, No. 17. pp. 5533-5543.
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