Genome‐wide Expression of SINE B2‐mediated Natural Antisense Transcripts

While investigated the regulation of Tspo expression, we observed that short interspersed repetitive element B2 (SINE B2) drives the expression of long transcripts. We examined whether the transcription of SINE B2‐mediated long transcripts is a genome‐wide phenomenon. Experimental data together with bioinformatics and next‐generation sequencing of the mouse transcriptome showed that some transcripts directly target the adjacent exon(s). In silico screening of the mouse genome identified 2,494 hits potentially driving long transcripts to form natural antisense transcripts (NATs) targeting coding genes. Functional clustering analysis indicated that most of the targeted loci are involved in transcriptional regulation and signal transduction. Experimental confirmation of the SINE B2‐mediated NATs showed that 45% of the clones had extended 30–357 bp tails. High throughput sequencing data confirmed the presence of long‐transcripts driven by SINE B2. A total of 16,202 from 59,203 SINE B2‐specific sequences of >130 bp in length, representing 27.43% of the SINE B2 elements in the mouse genome, were identified. Considering that 8–12 × 10000 copies of SINE B2 exist in the genome, we propose that such a large scale of previously unrecognized transcripts may serve as a “transcriptome buffer” to exclusively regulate the function/evolution of the mouse genome.