An allosteric/intrinsic mechanism supports termination of snRNA transcription.

Termination of protein-coding gene transcription by RNA polymerase II (Pol II) depends on endonucleolytic cleavage at the poly(A) site and the activity of a 5’->3’ “torpedo” exoribonuclease. Other Pol II transcripts also undergo endonucleolytic cleavage suggesting common themes for its termination. Nevertheless, many RNA polymerases employ intrinsic/allosteric termination that directly defines transcript 3’ ends. We have analysed termination of snRNA transcription in humans, which utilises the endoribonucleolytic integrator complex. Integrator is involved, but termination continues after its depletion. This implicates additional mechanisms and shows that endo- and 5’->3’ exonuclease activities are not necessarily a basis for all Pol II termination. Although the alternative process acts as a failsafe in the absence of integrator it contributes significantly to snRNA termination in the natural situation. Long-read sequencing reveals its products to have stochastic 3’ ends that are terminated before integrator cleavage, ruling out 5’->3’ exonuclease contribution(s) and supporting an allosteric/intrinsic mechanism. Termination of some snRNA transcription occurs at T-runs further indicating common principles between this mechanism and those used by other RNA polymerases.

RNA聚合酶II（Pol II）介导的编码蛋白基因转录终止，依赖于多聚腺苷酸化位点（poly(A) site）处的核糖核酸内切切割，以及5’→3’方向‘鱼雷’型核糖核酸外切酶的活性。其他Pol II转录本也会发生核糖核酸内切切割，这提示其转录终止机制存在共通特征。尽管如此，诸多RNA聚合酶采用内在/变构终止机制，可直接确定转录本的3’末端。本研究对人类小核RNA（small nuclear RNA，snRNA）的转录终止过程展开分析，该过程依赖于核糖核酸内切型整合酶复合物（Integrator complex）。尽管整合酶复合物参与其中，但在其被敲除后，转录终止过程仍可继续进行。这表明存在额外的转录终止机制，同时证明核糖核酸内切酶与5’→3’核糖核酸外切酶的活性，并非所有Pol II转录终止的必要基础。尽管这种替代机制在整合酶复合物缺失时充当备用通路，但在自然生理状态下，它对snRNA转录终止亦有显著贡献。长读长测序（long-read sequencing）结果显示，该通路的转录本产物带有随机分布的3’末端，且其终止发生于整合酶复合物切割之前，这排除了5’→3’核糖核酸外切酶的参与，并支持变构/内在终止机制的存在。部分snRNA的转录终止发生于胸腺嘧啶串（T-runs）位点，这进一步表明该终止机制与其他RNA聚合酶所采用的机制存在共通原理。