Coupling of co-transcriptional splicing and 3' end Pol II pausing during termination in Arabidopsis.
Coupling of co-transcriptional splicing and 3' end Pol II pausing during termination in Arabidopsis.
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DOI：
10.1186/s13059-023-03050-4
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发表时间：
2023-09-11
期刊：
影响因子：
12.3
通讯作者：
中科院分区：
文献类型：
--
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在拟南芥中，RNA聚合酶II（Pol II）经常在多聚腺苷酸化位点下游的几百个碱基对内暂停，这反映了有效的转录终止，但这种暂停是如何调节的仍然很难理解。在这里，我们通过综合实验与数学建模相结合来分析3'端的Pol II动力学。我们生成高分辨率丝氨酸2磷酸化（Ser 2 P）Pol II定位数据，特异性富集在3'端，并定义了3'端暂停指数（3 'PI）。3'端暂停的位置而非程度与终止窗口大小相关。在终止缺陷突变体xrn 3中，3 'PI没有降低，但甚至轻微增加，表明3'末端暂停是终止期间早期和XRN 3介导的RNA衰变释放Pol II之前的调节步骤。出乎意料的是，3 'PI与基因外显子数目和共转录剪接效率密切相关。多个外显子的基因通常比具有较少外显子的基因显示更强的3'末端停顿和更有效的染色质上剪接。剪接的化学抑制强烈降低了3 'PI并破坏了其与外显子数目的相关性，但不会全面影响3'端通读水平。这些结果进一步证实了拟合Pol II定位数据与数学模型，这使得参数的估计，定义Pol II动态。我们的工作强调了通过共转录剪接的外显子的数量是植物基因3'端Pol II暂停水平的主要决定因素。在线版本包含补充材料，可通过10.1186/s13059-023-03050-4获得。
In Arabidopsis, RNA Polymerase II (Pol II) often pauses within a few hundred base pairs downstream of the polyadenylation site, reflecting efficient transcriptional termination, but how such pausing is regulated remains largely elusive. Here, we analyze Pol II dynamics at 3’ ends by combining comprehensive experiments with mathematical modelling. We generate high-resolution serine 2 phosphorylated (Ser2P) Pol II positioning data specifically enriched at 3’ ends and define a 3’ end pause index (3’PI). The position but not the extent of the 3’ end pause correlates with the termination window size. The 3’PI is not decreased but even mildly increased in the termination deficient mutant xrn3, indicating 3’ end pause is a regulatory step early during the termination and before XRN3-mediated RNA decay that releases Pol II. Unexpectedly, 3’PI is closely associated with gene exon numbers and co-transcriptional splicing efficiency. Multiple exons genes often display stronger 3’ end pauses and more efficient on-chromatin splicing than genes with fewer exons. Chemical inhibition of splicing strongly reduces the 3’PI and disrupts its correlation with exon numbers but does not globally impact 3’ end readthrough levels. These results are further confirmed by fitting Pol II positioning data with a mathematical model, which enables the estimation of parameters that define Pol II dynamics. Our work highlights that the number of exons via co-transcriptional splicing is a major determinant of Pol II pausing levels at the 3’ end of genes in plants. The online version contains supplementary material available at 10.1186/s13059-023-03050-4.
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DOI：
10.1038/nrm.2017.63
发表时间：
2017-10
期刊：
Nature reviews. Molecular cell biology
影响因子：
--
作者：
Herzel L;Ottoz DSM;Alpert T;Neugebauer KM
通讯作者：
Neugebauer KM
3'RNA聚合酶II CTD上Ser2的前MRNA的末端形成和在人类细胞中相互耦合。
影响因子：
10.5
作者：
Davidson L;Muniz L;West S
通讯作者：
West S
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
10.5
作者：
Eaton, Joshua D.;Francis, Laura;West, Steven
通讯作者：
West, Steven
影响因子：
--
作者：
Dai, Ziwei;Lai, Luhua
通讯作者：
Lai, Luhua