Data from: First insights into the nature and evolution of antisense transcription in nematodes

Background: The development of multicellular organisms is coordinated by various gene regulatory mechanisms that ensure correct spatio-temporal patterns of gene expression. Recently, the role of antisense transcription in gene regulation has moved into focus of research. To characterize genome-wide patterns of antisense transcription and to study their evolutionary conservation, we sequenced a strand-specific RNA-seq library of the nematode Pristionchus pacificus. Results: We identified 1112 antisense configurations of which the largest group represents 465 antisense transcripts (ASTs) that are fully embedded in introns of their host genes. We find that most ASTs show homology to protein-coding genes and are overrepresented in proteomic data. Together with the finding, that expression levels of ASTs and host genes are uncorrelated, this indicates that most ASTs in P. pacificus do not represent non-coding RNAs and do not exhibit regulatory functions on their host genes. We studied the evolution of antisense gene pairs across 20 nematode genomes, showing that the majority of pairs is lineage-specific and even the highly conserved vps-4, ddx-27, and sel-2 loci show abundant structural changes including duplications, deletions, intron gains and loss of antisense transcription. In contrast, host genes in general, are remarkably conserved and encode exceptionally long introns leading to unusually large blocks of conserved synteny. Conclusions: Our study has shown that in P. pacificus antisense transcription as such does not define non-coding RNAs but is rather a feature of highly conserved genes with long introns. We hypothesize that the presence of regulatory elements imposes evolutionary constraint on the intron length, but simultaneously, their large size makes them a likely target for translocation of genomic elements including protein-coding genes that eventually end up as ASTs.研究背景：多细胞生物的发育由多种基因调控机制协同调控，以确保基因表达呈现精准的时空表达模式。近年来，反义转录（antisense transcription）在基因调控中的作用逐渐成为研究热点。为刻画全基因组范围内的反义转录模式并探究其进化保守性，我们针对太平洋普奇线虫（Pristionchus pacificus）构建了链特异性RNA测序（strand-specific RNA-seq）文库并进行测序。 研究结果：本研究共鉴定出1112个反义转录构型，其中数量最多的一类包含465个反义转录本（antisense transcripts, ASTs），这类转录本完全嵌入宿主基因的内含子区域。研究发现，大多数反义转录本与蛋白质编码基因具有同源性，且在蛋白质组数据中富集。结合“反义转录本与宿主基因的表达水平无相关性”这一发现，本研究表明，太平洋普奇线虫中的大多数反义转录本并非非编码RNA，且不对宿主基因发挥调控功能。本研究对20个线虫基因组中的反义基因对进行了进化分析，结果显示绝大多数反义基因对为谱系特异性的；即便是高度保守的vps-4、ddx-27与sel-2基因座，也存在大量结构变异，包括基因复制、缺失、内含子获得以及反义转录的丢失。与之形成对比的是，宿主基因整体上具有高度的保守性，且编码的内含子长度极长，进而形成了异常庞大的保守同线性（conserved synteny）区块。 研究结论：本研究表明，在太平洋普奇线虫中，反义转录本身并非非编码RNA的判定依据，而是一类带有长内含子的高度保守基因的特征。本研究推测，调控元件的存在对内含子长度施加了进化约束；但与此同时，内含子的巨大尺寸使其成为包括蛋白质编码基因在内的基因组元件易位的潜在靶点，这些编码基因最终可演变为反义转录本。