title: Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation.
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/.
authors.affiliation: Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, 100871, PR China.
authors.forename: Jiong-Tang
authors.initials: JT
authors.lastname: Li
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Lei
authors.initials: L
authors.lastname: Kong
authors.forename: Qing-Rong
authors.initials: QR
authors.lastname: Liu
authors.forename: Liping
authors.initials: L
authors.lastname: Wei
mesh_terms: D000818:Animals; D020029:Base Pairing; D001483:Base Sequence; D002352:Carrier Proteins / Q000235:genetics; D002417:Cattle; D019295:Computational Biology; D017124:Conserved Sequence; D004285:Dogs; D019143:Evolution, Molecular; D020440:Gene Duplication; D005786:Gene Expression Regulation; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D016372:RNA, Antisense / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D051381:Rats; D015398:Signal Transduction / Q000235:genetics
chemical_list: D002352:Carrier Proteins; D016372:RNA, Antisense; D022661:RNA, Untranslated