Genome-wide Scanning For Cis-Natural Antisense Transcriptsand Preliminary Functional Annotation

Objective:Cis-natural antisense transcripts (cis-NATs) are the natural antisense RNAstranscribed from the same genomic locus in the opposite strand, and formsense/antisense pair (SA pair) with the sense RNAs. The cis-NATs play an importantrole in regulating the expression of their targeted genes at the transcription andpost-transcription levels, influencing various physiological and pathologicalprocesses, such as tumor. With the appearance of microarray technology andaccumulation of sequencing data, it is possible for systematically scanning forcis-NATs in the genome-wide scale. However, the previous investigation is limited tothe coding genes of several model organisms (human, mice, arabidopsis etc). There islack of the study for the scheme of transcriptomic sequencing data analysis of thenon-coding sequences.Method:We first scanned for non-coding cis-NATs based on Ensembl gene annotationsfrom18species of primates and rodents. Since the next-generation sequencing canprovide more cells/tissues transcript information, we developed a new program(Gene2DGE) for detecting cis-NATs using RNA-seq data and verification andfunction experiments based on the candidate cis-NATs.Results:For example, we identified18,510SA pairs in human genome. There were11,493non-coding cis-NATs accounting for62.1%of all, suggesting that non-codinggene is an important source of cis-NAT. Althought non-coding data from otherspecies are significantly lower than humans, numbers of conservative non-codingcis-NATs across species suggested that this kind of cis-NATs from non human speciesstill to be further studied. Based on the ssRNA-seq (strand-specific RNA-seq) fromhuman143B cells, we identified73novel antisense TARs (transcriptional activityregion), among which43are located in the mitochondria genome. In additional, these TARs were also detected using the mRNA-seq data from eight rat tissues. Mostimportance, the experiments of cell biology suggested that the novel mitochondrialantisense TARs may play an important role in mitochondria.Conclusion:1.We screened out high coverage cis-NATs and high homology and conservativeSA genes based on Ensembl gene annotations and program(Antifinder).2.Nextgeneration sequencing provided novel cis-NATs，greatly inhance the found ofcis-NATs.3.Verification and function experiments indicated novel cis-NATs do existand may have important biological function.