Wu Weifang, Ahmad Kami, Henikoff Steven
Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
Mol Cell. 2025 May 15;85(10):1982-1998.e4. doi: 10.1016/j.molcel.2025.04.013. Epub 2025 May 1.
Most mRNA splicing occurs co-transcriptionally, but it is unclear how splicing factors accurately select exons for inclusion. Using CUT&RUN profiling in K562 cells, we demonstrate that three splicing factors-SF3B1, U2AF1, and U2AF2-bind near active promoters of intron-containing and intronless genes, implying their association with the general transcriptional machinery. RNase A treatment reduces factor binding at promoters, indicating that these proteins interact with nascent transcripts. Strikingly, the U2AF2 protein also accumulates throughout intron-containing gene bodies and requires histone H3-lysine36 trimethylation but not nascent transcripts or persistent RNA polymerase II. Chromatin-bound U2AF2 preferentially binds to exons of highly expressed, exon-dense genes, with greater occupancy at exons skipped after U2AF2 knockdown, suggesting that U2AF2 enhances exon selection accuracy. U2AF2-targeted genes include those encoding splicing factors, where it improves splicing accuracy and efficiency. Our findings provide a mechanistic basis for the homeostatic regulation of efficient co-transcriptional splicing by chromatin-bound U2AF2.
大多数mRNA剪接在转录过程中同时发生，但尚不清楚剪接因子如何准确选择要包含的外显子。通过在K562细胞中进行CUT&RUN分析，我们证明了三种剪接因子——SF3B1、U2AF1和U2AF2——结合在含内含子基因和无内含子基因的活跃启动子附近，这意味着它们与一般转录机制相关联。核糖核酸酶A处理会降低因子在启动子处的结合，表明这些蛋白质与新生转录本相互作用。引人注目的是，U2AF2蛋白也在整个含内含子的基因体内积累，并且需要组蛋白H3赖氨酸36三甲基化，但不需要新生转录本或持续的RNA聚合酶II。与染色质结合的U2AF2优先结合高表达、外显子密集基因的外显子，在U2AF2敲低后跳过的外显子上占据率更高，这表明U2AF2提高了外显子选择的准确性。U2AF2靶向的基因包括那些编码剪接因子的基因，它在这些基因中提高了剪接的准确性和效率。我们的研究结果为与染色质结合的U2AF2对高效共转录剪接的稳态调节提供了机制基础。
