DNA-binding sequence specificity of DUX4.
DNA-binding sequence specificity of DUX4.
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DOI：
10.1186/s13395-016-0080-z
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发表时间：
2016
期刊：
影响因子：
4.9
通讯作者：
Kyba M
中科院分区：
文献类型：
--
作者：
Zhang Y;Lee JK;Toso EA;Lee JS;Choi SH;Slattery M;Aihara H;Kyba M
双同源结构域转录因子DUX4的错误表达导致面肩肱型肌营养不良症（FSHD）。已经发现了基于染色质IP峰的具有两个串联TAAT基序的DNA结合共识;然而，该共识具有未知相对活性的多种变化（风味）。此外，并非所有的峰都具有这种一致性，并且Pitx1启动子（第一个提出的DUX4靶序列）具有不同的富含TAAT的序列。此外，目前还不知道是否以及在何种程度上偏离共识影响DNA结合亲和力和转录激活潜力。在这里，我们采用无偏和一致序列驱动的方法来确定DUX4的DNA结合特异性及其对一致序列内每个位点错配的耐受性。我们发现，最好的结合和最大的转录激活时，观察到两个TAAT基序是由C残基分开。共有序列中的第二个TAAT基序实际上是（T/C）AAT。我们发现这里的T是优选的。DUX4在"半位点"上没有转录活性，即，只有一个TAAT基序。我们进一步发现DUX4不与Pitx1启动子中的TAATTA基序结合，Pitx1序列没有竞争性条带移动活性，并且Pitx1序列是转录失活的，这就对PITX1作为DUX4靶基因提出了质疑。最后，通过多聚化结合位点，我们发现DUX4转录激活表现出巨大的协同作用，并且在低DNA浓度下，至少需要两个基序来检测转录反应。这些研究阐明了DUX4的DNA结合序列偏好。本文的在线版本（doi：10.1186/s13395 - 016 - 0080-z）包含补充材料，可供授权用户使用。
Misexpression of the double homeodomain transcription factor DUX4 results in facioscapulohumeral muscular dystrophy (FSHD). A DNA-binding consensus with two tandem TAAT motifs based on chromatin IP peaks has been discovered; however, the consensus has multiple variations (flavors) of unknown relative activity. In addition, not all peaks have this consensus, and the Pitx1 promoter, the first DUX4 target sequence mooted, has a different TAAT-rich sequence. Furthermore, it is not known whether and to what extent deviations from the consensus affect DNA-binding affinity and transcriptional activation potential. Here, we take both unbiased and consensus sequence-driven approaches to determine the DNA-binding specificity of DUX4 and its tolerance to mismatches at each site within its consensus sequence. We discover that the best binding and the greatest transcriptional activation are observed when the two TAAT motifs are separated by a C residue. The second TAAT motif in the consensus sequence is actually (T/C)AAT. We find that a T is preferred here. DUX4 has no transcriptional activity on “half-sites”, i.e., those bearing only a single TAAT motif. We further find that DUX4 does not bind to the TAATTA motif in the Pitx1 promoter, that Pitx1 sequences have no competitive band shift activity, and that the Pitx1 sequence is transcriptionally inactive, calling into question PITX1 as a DUX4 target gene. Finally, by multimerizing binding sites, we find that DUX4 transcriptional activation demonstrates tremendous synergy and that at low DNA concentrations, at least two motifs are necessary to detect a transcriptional response. These studies illuminate the DNA-binding sequence preferences of DUX4. The online version of this article (doi:10.1186/s13395-016-0080-z) contains supplementary material, which is available to authorized users.