title: Transcriptional interferences in cis natural antisense transcripts of humans and mice.
abstract: For a significant fraction of mRNAs, their expression is regulated by other RNAs, including cis natural antisense transcripts (cis-NATs) that are complementary mRNAs transcribed from opposite strands of DNA at the same genomic locus. The regulatory mechanism of mRNA expression by cis-NATs is unknown, although a few possible explanations have been proposed. To understand this regulatory mechanism, we conducted a large-scale analysis of the currently available data and examined how the overlapping arrangements of cis-NATs affect their expression level. Here, we show that for both human and mouse the expression level of cis-NATs decreases as the length of the overlapping region increases. In particular, the proportions of the highly expressed cis-NATs in all cis-NATs examined were approximately 36 and 47% for human and mouse, respectively, when the overlapping region was <200 bp. However, both proportions decreased to virtually zero when the overlapping regions were >2000 bp in length. Moreover, the distribution of the expression level of cis-NATs changes according to different types of the overlapping pattern of cis-NATs in the genome. These results are consistent with the transcriptional collision model for the regulatory mechanism of gene expression by cis-NATs.
authors.affiliation: Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Mishima 411-8540, Japan.
authors.forename: Naoki
authors.initials: N
authors.lastname: Osato
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Suzuki
authors.forename: Kazuho
authors.initials: K
authors.lastname: Ikeo
authors.forename: Takashi
authors.initials: T
authors.lastname: Gojobori
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D017124:Conserved Sequence; D016373:DNA, Antisense / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D005786:Gene Expression Regulation; D015894:Genome, Human; D006801:Humans; D051379:Mice; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D016373:DNA, Antisense; D018076:DNA, Complementary; D012333:RNA, Messenger