title: Role of antisense RNAs in evolution of yeast regulatory complexity.
abstract: Antisense RNAs (asRNAs) are known to regulate gene expression. However, a genome-wide mechanism of asRNA regulation is unclear, and there is no good explanation why partial asRNAs are not functional. To explore its regulatory role, we investigated asRNAs using an evolutionary approach, as genome-wide experimental data are limited. We found that the percentage of genes coupling with asRNAs in Saccharomyces cerevisiae is negatively associated with regulatory complexity and evolutionary age. Nevertheless, asRNAs evolve more slowly when their sense genes are under more complex regulation. Older genes coupling with asRNAs are more likely to demonstrate inverse expression, reflecting the role of these asRNAs as repressors. Our analyses provide novel evidence, suggesting a minor contribution of asRNAs in developing regulatory complexity. Although our results support the leaky hypothesis for asRNA transcription, our evidence also suggests that partial asRNAs may have evolved as repressors. Our study deepens the understanding of asRNA regulatory evolution.
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan. Electronic address: jack2030@gmail.com.
authors.forename: Chih-Hsu
authors.initials: CH
authors.lastname: Lin
authors.affiliation: Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan; Institute of Information Science, Academia Sinica, Taipei 115, Taiwan. Electronic address: zing@iis.sinica.edu.tw.
authors.forename: Zing Tsung-Yeh
authors.initials: ZT
authors.lastname: Tsai
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan. Electronic address: dywang@gate.sinica.edu.tw.
authors.forename: Daryi
authors.initials: D
authors.lastname: Wang
mesh_terms: D019143:Evolution, Molecular; D015966:Gene Expression Regulation, Fungal; D053263:Gene Regulatory Networks; D005800:Genes, Fungal; D016681:Genome, Fungal; D016372:RNA, Antisense / Q000235:genetics / Q000502:physiology*; D012331:RNA, Fungal / Q000502:physiology*; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism*
chemical_list: D016372:RNA, Antisense; D012331:RNA, Fungal
keywords: Antisense RNA; BPKM; Gene expression regulation; IDR; Molecular evolution; ORF transcript; ORF-T; PPI; PTM; RNA interference; RNAi; SAL/SRL; TFBS; Transcriptome; bases per kilobase of gene model per million mapped bases; intrinsically disordered region; ncRNA; non-coding RNA; post-translational modification; protein–protein interactions; the ratio of sense–antisense overlapping length to sense transcript length; transcription factor binding site