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Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes

Ping Wang12, Shanye Yin12, Zhenguo Zhang12, Dedong Xin1, Landian Hu1, Xiangyin Kong13* and Laurence D Hurst4*

Author Affiliations

1 Institute of Health Sciences, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS) and Shanghai Jiao Tong University School of Medicine (SJTUSM), 225 South Chong Qing Road, Shanghai 200025, PR China

2 Graduate School of the Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, PR China

3 State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiaotong University, 197 Rui Jin Road II, Shanghai 200025, PR China

4 Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK

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Genome Biology 2008, 9:R169  doi:10.1186/gb-2008-9-12-r169

Published: 2 December 2008



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.


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.


Our results are consistent with the possibility of common short perfect sense-antisense pairing between transcripts of protein coding genes.