Some microsatellites may act as novel polymorphic cis-regulatory elements through transcription factor binding
Some microsatellites may act as novel polymorphic cis-regulatory elements through transcription factor binding
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DOI：
10.1016/j.gene.2004.06.035
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发表时间：
2004-10-27
期刊：
影响因子：
3.5
通讯作者：
Wadelius, C
中科院分区：
文献类型：
--
作者：
Iglesias, AR;Kindlund, E;Wadelius, C
虽然已经描述了具有功能效应的微卫星，但通常，这些重复序列与其他重复序列一样被认为是“垃圾”DNA。我们的目的是调查，如果某些微卫星可以有一个功能的作用，顺式调控元件。创建了位于人类基因组所有注释基因的转录起始位点的前10-kb 5'的2至10个碱基的所有短串联重复序列的数据库。在根据其大小和在启动子中的位置选择的114个微卫星中，发现51个是多态的。利用电泳迁移率变动分析（EMSA），我们研究了在12个多态性微卫星中发现的5个重复基序和3个显示特异性蛋白结合的基序。一个有趣的微卫星是CTC/GAG重复，作为双链（DS）DNA，结合特异性蛋白1（SP1）具有高亲和力，在体外形成三链体，并显示不同数目的重复单元的重复在SP1结合和三链体形成能力的差异。有趣的是，多聚嘧啶链的重复序列（CTC）结合其他蛋白质，如多聚嘧啶片段结合蛋白I（PTBP 1）作为单链（SS）DNA，并提出了一个模型与两个替代的DNA构象这些重复。不同数量的AAACA和AAAAT重复序列也观察到不同的蛋白质结合DS DNA。我们的研究结果表明，某些微卫星可能作为顺式调控元件，通过转录因子结合和/或二级DNA结构的形成控制基因的表达。由于其高度的多态性和丰富性，它们可能是数量遗传变异的重要来源。(C)2004 Elsevier B. V.保留所有权利。
Although microsatellites with functional effects have been described, generally, these repeats are considered as "junk" DNA in the same way as other repetitive sequences. Our aim was to investigate if certain microsatellites can have a functional role as cis-regulatory elements. A database was created of all short tandem repeats, from 2 to 10 bases, located in the first 10-kb 5' of the transcription start sites of all annotated genes of the human genome. Of 114 microsatellites selected based on their size and location in the promoter, 51 were found to be polymorphic. Using electrophoretic mobility shift assay (EMSA), we studied five repetitive motifs and three displayed specific protein binding which were found in 12 of the polymorphic microsatellites. An interesting microsatellite is the CTC/GAG repeat which, as double-stranded (DS) DNA, bound specificity protein 1 (SP1) with high affinity, formed triplexes in vitro and displayed differences in SP1 binding and triplex formation capacity for repeats with distinct numbers of repeat units. Interestingly, the polypyrimidine strand of the repeat (CTC) bound other proteins such as polypyrimidine tract-binding protein I (PTBP 1) as single-stranded (SS) DNA, and a model with two alternative DNA conformations is proposed for these repeats. Distinct protein binding to DS DNA was also observed for different numbers of AAACA and AAAAT repeats. Our results suggest that certain microsatellites may act as cis-regulatory elements, controlling gene expression through transcription factor binding and/or secondary DNA structure formation. Due to their high polymorphism and abundance, they might represent an important source of quantitative genetic variation. (C) 2004 Elsevier B.V. All rights reserved.