Silencer elements as possible inhibitors of pseudoexon splicing
Silencer elements as possible inhibitors of pseudoexon splicing
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DOI：
10.1093/nar/gkh341
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发表时间：
2004-03-01
影响因子：
14.9
通讯作者：
Pozzoli, U
中科院分区：
文献类型：
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作者：
Sironi, M;Menozzi, G;Pozzoli, U
人前mRNA含有一定数量的外显子和几个位于内含子区域内的假外显子。我们应用了一种计算方法来解决这个问题，如何假外显子被忽视，有利于外显子，并可能确定防止假外显子剪接的序列元素。一个可能的剪接沉默子进行了搜索的假外显子的选择，类似外显子的剪接位点强度和外显子剪接增强子（ESE）的代表性;三个图案检索通过六聚体组成比较。这些功能之一作为一个强大的沉默子在基于转染的剪接测定和匹配以前确定的沉默子序列与hnRNP H结合能力。其他两个基序是新的，未能诱导跳跃的组成型外显子，表明它们可能作为弱阻遏物或协同与其他未鉴定的元素。与内含子区域相比，所有三个基序都在假外显子中富集，并且与外显子相比，在无内含子基因编码序列中显示更高的频率。我们认为，一个亚群的假外显子可能依赖于负调控剪接抑制，这一假设，如果实验验证，可能会提高我们的理解外显子剪接调控序列，并提供一个新的突变靶点，为人类遗传疾病的鉴定。
Human pre-mRNAs contain a definite number of exons and several pseudoexons which are located within intronic regions. We applied a computational approach to address the question of how pseudoexons are neglected in favor of exons and to possibly identify sequence elements preventing pseudoexon splicing. A search for possible splicing silencers was carried out on a pseudoexon selection that resembled exons in terms of splice site strength and exon splicing enhancer (ESE) representation; three motifs were retrieved through hexamer composition comparisons. One of these functions as a powerful silencer in transfection-based splicing assays and matches a previously identified silencer sequence with hnRNP H binding ability. The other two motifs are novel and failed to induce skipping of a constitutive exon, indicating that they might act as weak repressors or in synergy with other unidentified elements. All three motifs are enriched in pseudoexons compared with intronic regions and display higher frequencies in intronless gene-coding sequences compared with exons. We consider that a subpopulation of pseudoexons might rely on negative regulators for splicing repression; this hypothesis, if experimentally verified, might improve our understanding of exonic splicing regulatory sequences and provide the identification of a novel mutation target for human genetic diseases.