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

@article{citeulike:3741383, 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 fails to find at least one match in the transcriptome. By randomizations generating artificial transcripts matched for G+C content and length we find 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 (SNP) density is lower in short pairing regions than it is in flanking regions. We find no evidence that the sense-antisense pairing regions are associated with small RNAs derived from the protein coding gene.CONCLUSION:Our results are consistent with the possibility of common short perfect sense-antisense pairing between transcripts of protein coding genes.}, author = {Wang, Ping and Yin, Shanye and Zhang, Zhenguo and Xin, Dedong and Hu, Landian and Kong, Xiangyin and Hurst, Laurence}, citeulike-article-id = {3741383}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/gb-2008-9-12-r169}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19055728}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19055728}, doi = {10.1186/gb-2008-9-12-r169}, issn = {1465-6906}, journal = {Genome Biology}, keywords = {alu, antisense, mrna, protein, rna, snp, transcriptome}, number = {12}, posted-at = {2008-12-03 17:11:32}, priority = {0}, title = {Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes}, url = {http://dx.doi.org/10.1186/gb-2008-9-12-r169}, volume = {9}, year = {2008} }

TY - JOUR ID - citeulike:3741383 L3 - citeulike-article-id:3741383 N2 - 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 fails to find at least one match in the transcriptome. By randomizations generating artificial transcripts matched for G+C content and length we find 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 (SNP) density is lower in short pairing regions than it is in flanking regions. We find no evidence that the sense-antisense pairing regions are associated with small RNAs derived from the protein coding gene.CONCLUSION:Our results are consistent with the possibility of common short perfect sense-antisense pairing between transcripts of protein coding genes. IS - 12 JF - Genome Biology SN - 1465-6906 TI - Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes VL - 9 KW - alu KW - antisense KW - mrna KW - protein KW - rna KW - snp KW - transcriptome AU - Wang, Ping AU - Yin, Shanye AU - Zhang, Zhenguo AU - Xin, Dedong AU - Hu, Landian AU - Kong, Xiangyin AU - Hurst, Laurence PY - 2008/// UR - http://dx.doi.org/10.1186/gb-2008-9-12-r169 ER -