R-loop dependent promoter-proximal termination ensures genome stability [KAS-seq]

Precise regulation of transcription is essential to maintain genome integrity, yet key mechanisms coordinating transcription, genome stability and downstream cellular functions remain incomplete. Here we report the identification of SOSS-INTAC, a stable association of the genome stability regulator Sensor of Single-stranded DNA (ssDNA) (SOSS) complex and transcription regulator Integrator-PP2A (INTAC). Via SSB1-mediated ssDNA recognition at its targets, SOSS-INTAC stimulates early termination of transcription and thus attenuates paused Pol II-induced formation of R-loops to prevent its aberrant accumulation that has the risk of increasing chromatin accessibility and compromising genome stability. SOSS-INTAC-mediated attenuation of R-loops is greatly enhanced by SSB1's unique property of forming liquid-like condensates. In contrast, preventing SSB1 condensation through deletion or cancer-associated mutation within its intrinsically disordered region (IDR) leads to pervasive accumulation of R-loops at a genome-wide level. Thus, our study highlights the genomic surveillance function of SOSS-INTAC that enables timely transcriptional termination to constrain aberrant R-loop accumulation and ensure genomic stability. KAS-seq with 2 biological replicates in DLD-1 cells.

转录的精准调控对于维持基因组完整性至关重要，但协调转录、基因组稳定性与下游细胞功能的关键机制仍未完全阐明。本研究报道了SOSS-INTAC复合物的鉴定结果：它是基因组稳定性调控因子单链DNA传感器（Sensor of Single-stranded DNA, ssDNA）复合物（SOSS）与转录调控因子整合素-PP2A（Integrator-PP2A, INTAC）的稳定结合体。通过SSB1介导其靶位点处的单链DNA识别，SOSS-INTAC可促进转录早期终止，进而减弱停滞的RNA聚合酶II（RNA polymerase II, Pol II）诱导的R环（R-loops）形成，以防止异常积累的R环引发染色质可及性升高、损害基因组稳定性的风险。SSB1特有的液态样冷凝集特性可极大增强SOSS-INTAC介导的R环积累抑制作用。与之相反，通过删除SSB1固有无序区域（intrinsically disordered region, IDR）或引入其癌症相关突变破坏SSB1的冷凝集能力，会导致全基因组范围内广泛的R环积累。综上，本研究揭示了SOSS-INTAC的基因组监视功能：该复合物可通过及时的转录终止，限制异常R环的积累，从而保障基因组稳定性。本研究附带DLD-1细胞中2次生物学重复的KAS-seq数据集。