Braunschweig Ulrich, Barbosa-Morais Nuno L, Pan Qun, Nachman Emil N, Alipanahi Babak, Gonatopoulos-Pournatzis Thomas, Frey Brendan, Irimia Manuel, Blencowe Benjamin J
Donnelly Centre, University of Toronto, Ontario, M5S 3E1, Canada;
Donnelly Centre, University of Toronto, Ontario, M5S 3E1, Canada; Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal;
Genome Res. 2014 Nov;24(11):1774-86. doi: 10.1101/gr.177790.114. Epub 2014 Sep 25.
Alternative splicing (AS) of precursor RNAs is responsible for greatly expanding the regulatory and functional capacity of eukaryotic genomes. Of the different classes of AS, intron retention (IR) is the least well understood. In plants and unicellular eukaryotes, IR is the most common form of AS, whereas in animals, it is thought to represent the least prevalent form. Using high-coverage poly(A)(+) RNA-seq data, we observe that IR is surprisingly frequent in mammals, affecting transcripts from as many as three-quarters of multiexonic genes. A highly correlated set of cis features comprising an "IR code" reliably discriminates retained from constitutively spliced introns. We show that IR acts widely to reduce the levels of transcripts that are less or not required for the physiology of the cell or tissue type in which they are detected. This "transcriptome tuning" function of IR acts through both nonsense-mediated mRNA decay and nuclear sequestration and turnover of IR transcripts. We further show that IR is linked to a cross-talk mechanism involving localized stalling of RNA polymerase II (Pol II) and reduced availability of spliceosomal components. Collectively, the results implicate a global checkpoint-type mechanism whereby reduced recruitment of splicing components coupled to Pol II pausing underlies widespread IR-mediated suppression of inappropriately expressed transcripts.
前体RNA的可变剪接（AS）极大地扩展了真核生物基因组的调控和功能能力。在不同类型的可变剪接中，内含子保留（IR）是了解最少的。在植物和单细胞真核生物中，内含子保留是可变剪接最常见的形式，而在动物中，它被认为是最不常见的形式。利用高覆盖度的聚腺苷酸（+）RNA测序数据，我们观察到内含子保留在哺乳动物中出人意料地频繁，影响多达四分之三的多外显子基因的转录本。一组高度相关的顺式特征组成了一个“内含子保留密码”，可可靠地区分保留型内含子和组成型剪接内含子。我们表明，内含子保留广泛作用于降低在其被检测的细胞或组织类型的生理过程中不需要或较少需要的转录本水平。内含子保留的这种“转录组微调”功能通过无义介导的mRNA降解以及内含子保留转录本的核隔离和周转来发挥作用。我们进一步表明，内含子保留与一种涉及RNA聚合酶II（Pol II）局部停滞和剪接体成分可用性降低的串扰机制有关。总体而言，这些结果暗示了一种全局检查点型机制，即剪接成分募集减少与Pol II暂停相结合是内含子保留介导的对异常表达转录本广泛抑制的基础。
