title: Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes.
abstract: BACKGROUND
  There is increasing realization that regulation of genes is done partly at the RNA level by sense-antisense binding. Studies typically concentrate on the role of non-coding RNAs in regulating coding RNA. But the majority of transcripts in a cell are likely to be coding. Is it possible that coding RNA might regulate other coding RNA by short perfect sense-antisense binding? Here we compare all well-described human protein coding mRNAs against all others to identify sites 15-25 bp long that could potentially perfectly match sense-antisense.
  
  
  RESULTS
  From 24,968 protein coding mRNA RefSeq sequences, none failed to find at least one match in the transcriptome. By randomizations generating artificial transcripts matched for G+C content and length, we found that there are more such trans short sense-antisense pairs than expected. Several further features are consistent with functionality of some of the putative matches. First, transcripts with more potential partners have lower expression levels, and the pair density of tissue specific genes is significantly higher than that of housekeeping genes. Further, the single nucleotide polymorphism density is lower in short pairing regions than it is in flanking regions. We found no evidence that the sense-antisense pairing regions are associated with small RNAs derived from the protein coding genes.
  
  
  CONCLUSIONS
  Our results are consistent with the possibility of common short perfect sense-antisense pairing between transcripts of protein coding genes.
authors.affiliation: Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai Jiao Tong University School of Medicine, 225 South Chong Qing Road, Shanghai 200025, PR China. pwang01@sibs.ac.cn
authors.forename: Ping
authors.initials: P
authors.lastname: Wang
authors.forename: Shanye
authors.initials: S
authors.lastname: Yin
authors.forename: Zhenguo
authors.initials: Z
authors.lastname: Zhang
authors.forename: Dedong
authors.initials: D
authors.lastname: Xin
authors.forename: Landian
authors.initials: L
authors.lastname: Hu
authors.forename: Xiangyin
authors.initials: X
authors.lastname: Kong
authors.forename: Laurence D
authors.initials: LD
authors.lastname: Hurst
mesh_terms: D020087:Alu Elements; D020029:Base Pairing; D005786:Gene Expression Regulation; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D011506:Proteins / Q000235:genetics*; D016372:RNA, Antisense / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism*; D020506:Untranslated Regions / Q000378:metabolism
chemical_list: D011506:Proteins; D016372:RNA, Antisense; D012333:RNA, Messenger; D020506:Untranslated Regions