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Exonic Splicing Enhancer Motif Recognized by Human SC35 under Splicing Conditions

机译：人SC35在剪接条件下识别的Exonic剪接增强子基序

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摘要

Exonic splicing enhancers (ESEs) are important ciselements required for exon inclusion. Using an in vitro functional selection and amplification procedure, we have identified a novel ESE motif recognized by the human SR protein SC35 under splicing conditions. The selected sequences are functional and specific: they promote splicing in nuclear extract or in S100 extract complemented by SC35 but not by SF2/ASF. They can also function in a different exonic context from the one used for the selection procedure. The selected sequences share one or two close matches to a short and highly degenerate octamer consensus, GRYYcSYR. A score matrix was generated from the selected sequences according to the nucleotide frequency at each position of their best match to the consensus motif. The SC35 score matrix, along with our previously reported SF2/ASF score matrix, was used to search the sequences of two well-characterized splicing substrates derived from the mouse immunoglobulin M (IgM) and human immunodeficiency virus tat genes. Multiple SC35 high-score motifs, but only two widely separated SF2/ASF motifs, were found in the IgM C4 exon, which can be spliced in S100 extract complemented by SC35. In contrast, multiple high-score motifs for both SF2/ASF and SC35 were found in a variant of the Tat T3 exon (lacking an SC35-specific silencer) whose splicing can be complemented by either SF2/ASF or SC35. The motif score matrix can help locate SC35-specific enhancers in natural exon sequences.
机译：外显子剪接增强子（ESE）是外显子包涵所需的重要 cis 元素。使用体外功能选择和扩增程序，我们已经确定了在剪接条件下被人SR蛋白SC35识别的新型ESE基序。所选的序列具有功能性和特异性：它们可促进核提取物或S100提取物中的剪接，并由SC35而非SF2 / ASF进行剪接。它们还可以在与选择过程所用的外显子环境不同的环境中起作用。所选序列与一个短且高度简并的八聚体共有序列GRYYcSYR共享一个或两个紧密匹配。根据它们与共有基序最匹配的每个位置处的核苷酸频率，从选择的序列中生成分数矩阵。使用SC35评分矩阵以及我们先前报道的SF2 / ASF评分矩阵，搜索源自小鼠免疫球蛋白M（IgM）和人类免疫缺陷病毒 tat 的两种特征明确的剪接底物的序列基因。在IgM C4外显子中发现了多个SC35高分基序，但仅发现两个广泛分离的SF2 / ASF基序，可以将其剪接在SC35补充的S100提取物中。相反，在Tat T3外显子的一个变体（缺少SC35特异性沉默子）中发现了SF2 / ASF和SC35的多个高分基序，其剪接可通过SF2 / ASF或SC35进行补充。基序得分矩阵可以帮助在自然外显子序列中定位SC35特异性增强子。

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