Carlile M, Nalbant P, Preston-Fayers K, McHaffie GS, Werner A. Processing of naturally occurring sense/antisense transcripts of the vertebrate Slc34a gene into short RNAs. Physiol Genomics 34: 95-100, 2008. First published April 15, 2008 doi:10.1152/physiolgenomics.00004.2008.-Overlapping sense/antisense RNAs transcribed in opposite directions from the same genomic locus are common in vertebrates. The impact of antisense transcription on gene regulation and cell biology is largely unknown. We show that sense/antisense RNAs of an evolutionarily conserved phosphate transporter gene (Slc34a2a) are coexpressed in a short time window during embryonic development of zebrafish at 48 hours postfertilization (hpf). To address the mechanism by which coexpressed sense/ antisense transcripts are processed, we injected sense/antisense RNAs in various combinations into Xenopus oocytes. In the cytoplasm RNAs were stable in whatever combination expressed. In the nucleus coinjected sense/antisense transcripts were degraded into short RNAs of ϳ23 bases within 4 h. A homologous transcript from toad or another isoform (Slc34a2b) from zebrafish failed to trigger processing. In oocytes that were primed with nuclear sense/antisense RNA coinjections, a reporter RNA was rapidly degraded. We produced evidence that the observed processing of complementary transcripts was not restricted to Xenopus oocytes, because Slc34a-related short RNAs were detected in zebrafish embryos by Northern blotting. Signals were observed at stages that showed coexpression of sense/ antisense transcripts. Remarkably, strand-specific probes revealed that the orientation of short RNAs was developmentally regulated. In addition, RNA from zebrafish embryos 48 hpf was able to induce degradation of reporter constructs in Xenopus oocytes. Our findings may give important clues to understanding the physiological role of the widespread antisense transcription. natural antisense RNA; RNA interference-related mechanism; zebrafish; sodium-phosphate cotransporter; gene regulation IN MOUSE, up to 72% of all genomic loci show evidence of sense and antisense transcription, and comparable numbers have been suggested for other organisms (13, 37). The majority of these natural antisense transcripts (NATs) are fully processed and overlap in exonic regions. NATs are underrepresented on mouse and human X chromosomes compared with autosomes (4, 14). This bias, however, is far less pronounced if the transcripts lack exonic overlaps (i.e., the potentially overlapping sequences are removed during splicing). These findings imply that antisense transcripts included in these studies are subjected to comparable evolutionary restrictions and may be processed by related mechanisms; furthermore, they indicate that the formation of RNA-RNA hybrids seems essential for the processing of these NATs (33).The biochemical function of NATs has been assessed in various organisms, and evidence for RNA interference (2), RNA editing (38), RNA splicing (11), transcriptional interference (23), or direct R...