ARS2 is a general suppressor of pervasive transcription

Termination of transcription is important for establishing gene punctuation marks. It is also critical for suppressing many of the pervasive transcription events occurring throughout eukaryotic genomes and coupling their RNA products to efficient decay. In human cells, the ARS2 protein has been implicated in such function as its depletion causes transcriptional read-through of selected gene terminators and because it physically interacts with the ribonucleolytic nuclear RNA exosome. Here, we study the role of ARS2 on transcription and RNA metabolism genome-wide. We show that ARS2 depletion negatively impacts levels of promoter-proximal RNA polymerase II (RNAPII) at protein-coding (pc) genes, Moreover, our results reveal a general role of ARS2 in transcription termination-coupled RNA turnover at short transcription units like snRNA-, replication dependent histone (RDH)-, promoter upstream transcript (PROMPT)- and enhancer RNA (eRNA)-loci. Depletion of the ARS2 interaction partner ZC3H18 mimics the ARS2 depletion, although to a milder extent, whereas depletion of the exosome core subunit RRP40 selectively impacts RNA abundance post-transcriptionally. Interestingly, ARS2 is also involved in transcription termination events within first introns of pc genes. Our work therefore establishes ARS2 as a general suppressor of pervasive transcription with the potential to regulate protein-coding gene expression. This study was performed in a human Hela cell line. It contains ChIP-seq data for RNA Pol II. All sequencing was performed in paired-end sequencing runs.转录终止对于确立基因的转录标点标记具有重要意义，同时在抑制真核基因组中广泛存在的各类通读转录事件、并将其RNA产物与高效降解过程相耦联方面发挥关键作用。在人类细胞中，ARS2蛋白（ARS2）已被证实具备此类功能：其敲除会导致选定基因终止子区域出现转录通读现象，且该蛋白可与核RNA外切体（ribonucleolytic nuclear RNA exosome）发生物理相互作用。本研究在全基因组范围内探究了ARS2蛋白在转录与RNA代谢过程中的作用，研究发现ARS2敲除会对蛋白编码（pc）基因的启动子近端RNA聚合酶II（RNAPII）水平产生负向影响。此外，本研究结果揭示了ARS2在短转录单元的转录终止偶联RNA降解过程中的普遍作用，这类短转录单元包括小核RNA（snRNA）、复制依赖性组蛋白（RDH）、启动子上游转录本（PROMPT）以及增强子RNA（eRNA）位点。敲除ARS2的相互作用蛋白ZC3H18可模拟ARS2敲除的表型，尽管影响程度相对较轻；而敲除外切体核心亚基RRP40则仅在转录后阶段对RNA丰度产生影响。有趣的是，ARS2还参与了蛋白编码基因第一内含子内的转录终止过程。综上，本研究证实ARS2是广泛转录事件的广谱抑制因子，具备调控蛋白编码基因表达的潜力。本研究使用人类HeLa细胞系开展实验，包含RNA聚合酶II的染色质免疫共沉淀测序（ChIP-seq）数据，所有测序均采用双端测序模式。