Ule Jernej, Stefani Giovanni, Mele Aldo, Ruggiu Matteo, Wang Xuning, Taneri Bahar, Gaasterland Terry, Blencowe Benjamin J, Darnell Robert B
Howard Hughes Medical Institute, New York, New York 10021, USA.
Nature. 2006 Nov 30;444(7119):580-6. doi: 10.1038/nature05304. Epub 2006 Oct 25.
Nova proteins are a neuron-specific alternative splicing factors. We have combined bioinformatics, biochemistry and genetics to derive an RNA map describing the rules by which Nova proteins regulate alternative splicing. This map revealed that the position of Nova binding sites (YCAY clusters) in a pre-messenger RNA determines the outcome of splicing. The map correctly predicted Nova's effect to inhibit or enhance exon inclusion, which led us to examine the relationship between the map and Nova's mechanism of action. Nova binding to an exonic YCAY cluster changed the protein complexes assembled on pre-mRNA, blocking U1 snRNP (small nuclear ribonucleoprotein) binding and exon inclusion, whereas Nova binding to an intronic YCAY cluster enhanced spliceosome assembly and exon inclusion. Assays of splicing intermediates of Nova-regulated transcripts in mouse brain revealed that Nova preferentially regulates removal of introns harbouring (or closest to) YCAY clusters. These results define a genome-wide map relating the position of a cis-acting element to its regulation by an RNA binding protein, namely that Nova binding to YCAY clusters results in a local and asymmetric action to regulate spliceosome assembly and alternative splicing in neurons.
Nova蛋白是神经元特异性的可变剪接因子。我们结合了生物信息学、生物化学和遗传学方法，得出了一张RNA图谱，该图谱描述了Nova蛋白调控可变剪接的规则。这张图谱显示，Nova结合位点（YCAY簇）在信使前体RNA中的位置决定了剪接的结果。该图谱正确预测了Nova抑制或增强外显子包含的作用，这促使我们研究该图谱与Nova作用机制之间的关系。Nova与外显子YCAY簇结合会改变在信使前体RNA上组装的蛋白质复合物，阻止U1小核核糖核蛋白（U1 snRNP）结合以及外显子包含，而Nova与内含子YCAY簇结合则会增强剪接体组装和外显子包含。对小鼠大脑中Nova调控转录本的剪接中间体进行的分析表明，Nova优先调控含有（或最接近）YCAY簇的内含子的去除。这些结果定义了一张全基因组图谱，该图谱将顺式作用元件的位置与其受RNA结合蛋白调控的情况联系起来，即Nova与YCAY簇结合会导致局部和不对称的作用，从而在神经元中调控剪接体组装和可变剪接。
