Center for Cancer Research, Mouse Cancer Genetics Program, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA.
Nature. 2011 Nov 3;479(7371):74-9. doi: 10.1038/nature10442.
Alternative splicing of pre-messenger RNA is a key feature of transcriptome expansion in eukaryotic cells, yet its regulation is poorly understood. Spliceosome assembly occurs co-transcriptionally, raising the possibility that DNA structure may directly influence alternative splicing. Supporting such an association, recent reports have identified distinct histone methylation patterns, elevated nucleosome occupancy and enriched DNA methylation at exons relative to introns. Moreover, the rate of transcription elongation has been linked to alternative splicing. Here we provide the first evidence that a DNA-binding protein, CCCTC-binding factor (CTCF), can promote inclusion of weak upstream exons by mediating local RNA polymerase II pausing both in a mammalian model system for alternative splicing, CD45, and genome-wide. We further show that CTCF binding to CD45 exon 5 is inhibited by DNA methylation, leading to reciprocal effects on exon 5 inclusion. These findings provide a mechanistic basis for developmental regulation of splicing outcome through heritable epigenetic marks.
前信使 RNA 的可变剪接是真核细胞转录组扩展的一个关键特征，但它的调控机制还了解甚少。剪接体的组装是在转录过程中发生的，这就提出了一种可能性，即 DNA 结构可能直接影响可变剪接。最近的研究报告支持了这种关联，报告指出外显子相对于内含子具有独特的组蛋白甲基化模式、核小体占有率升高和 DNA 甲基化富集。此外，转录延伸的速度与可变剪接有关。在这里，我们提供了第一个证据，证明一种 DNA 结合蛋白，CCCTC 结合因子（CTCF），可以通过介导局部 RNA 聚合酶 II 暂停，促进弱上游外显子的包含，这在 CD45 的哺乳动物可变剪接模型系统和全基因组范围内都得到了证实。我们进一步表明，CTCF 与 CD45 外显子 5 的结合受到 DNA 甲基化的抑制，导致外显子 5 包含的相互作用。这些发现为通过可遗传的表观遗传标记对剪接结果进行发育调控提供了机制基础。
