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. 2008 Sep;36(15):4833-44.
doi: 10.1093/nar/gkn470. Epub 2008 Jul 24.

Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation

Jiong-Tang Li  1 , Yong Zhang, Lei Kong, Qing-Rong Liu, Liping Wei
Affiliations

Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation

Jiong-Tang Li et al. Nucleic Acids Res. 2008 Sep.

Abstract

Natural antisense transcripts are at least partially complementary to their sense transcripts. Cis-Sense/Antisense pairs (cis-SAs) have been extensively characterized and known to play diverse regulatory roles, whereas trans-Sense/Antisense pairs (trans-SAs) in animals are poorly studied. We identified long trans-SAs in human and nine other animals, using ESTs to increase coverage significantly over previous studies. The percentage of transcriptional units (TUs) involved in trans-SAs among all TUs was as high as 4.13%. Particularly 2896 human TUs (or 2.89% of all human TUs) were involved in 3327 trans-SAs. Sequence complementarities over multiple segments with predicted RNA hybridization indicated that some trans-SAs might have sophisticated RNA-RNA pairing patterns. One-fourth of human trans-SAs involved noncoding TUs, suggesting that many noncoding RNAs may function by a trans-acting antisense mechanism. TUs in trans-SAs were statistically significantly enriched in nucleic acid binding, ion/protein binding and transport and signal transduction functions and pathways; a significant number of human trans-SAs showed concordant or reciprocal expression pattern; a significant number of human trans-SAs were conserved in mouse. This evidence suggests important regulatory functions of trans-SAs. In 30 cases, trans-SAs were related to cis-SAs through paralogues, suggesting a possible mechanism for the origin of trans-SAs. All trans-SAs are available at http://trans.cbi.pku.edu.cn/.

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Figures

Figure 1.
Figure 1.
Trans-SAs within a segment on human chromosome 10. Arcs linking two partners of a trans-SA pair were color-coded: red arc linked protein-coding–protein-coding pairs; blue arc linked noncoding–protein-coding pairs and green linked noncoding–noncoding pairs. In particular, a noncoding TU, AA187228, could pair with a coding TU (RP11-564C4.1) as well as a noncoding TU (DN831175).
Figure 2.
Figure 2.
Trans-SAs may have complex pairing patterns. (A) Trans-SAs are classified into four classes based on their HSP patterns. Grey blocks indicate exons. Folding lines between blocks indicate splicing junctions. Red, blue, yellow and green blocks indicate complementary regions. (B) The abundance of four classes of trans-SAs in 10 species.
Figure 3.
Figure 3.
Some trans-SAs were related to cis-SAs through paralogues. (A) NDE1 and MYH11 formed a cis-SA pair sharing the last exon of NDE1 (99 bp overlap with perfect complementarity), from UCSC genome browser. The arrow indicates MYH9's paralogous exon to the cis-pairing region of MYH11. NDE1 shares this paralogous exon and thus trans-pairs with MYH9. (B) RFPL1 and RFPL1S formed a cis-SA (293 bp overlap with perfect complementarity). RFPL3 and RFPL3S formed another cis-SA (588 bp overlap with perfect complementarity). RFPL3S and RFPL1 formed a trans-SA (591 bp overlap with an e-value of 0.0 and an identity of 95%). RFPL3 and RFPL1S formed another trans-SA (519 bp overlap with an e-value of 0.0 and an identity of 96%). Red arrows indicate the cis-pairing region of RFPL1 and RFPL1S was duplicated to the locus of RFPL3 and RFPL3S.
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References

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