Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches
Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches
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DOI：
10.1101/gr.6006107
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发表时间：
2007-06-01
期刊：
影响因子：
7
通讯作者：
Farnham, Peggy J.
中科院分区：
文献类型：
--
作者：
Jin, Victor X.;O'Geen, Henriette;Farnham, Peggy J.
ChIP芯片研究已经揭示，许多体内结合位点与所分析的转录因子的共有序列具有弱匹配。这些观察结果的可能解释包括（1）体外衍生的共有位点不代表体内结合位点和/或（2）因子通过与另一种蛋白质相互作用被募集到弱结合位点。为了解决这些可能性，我们开发了一种方法（ChIPMotifs），该方法结合了自举响应方法，以统计推断从头基序发现程序从ChIP芯片数据中识别的基序的位置权重矩阵（PWM）的最佳截止阈值。使用OCT 4 ChIP芯片数据和ChIPMotifs方法，我们首先开发了一个改进的OCT 4 PWM。然后，我们使用改进的PWM和ChIPModules方法来鉴定与Ntera 2睾丸胚胎癌细胞中的OCT 4共定位的转录因子。我们发现，SRY的共识结合位点，睾丸发育的关键转录因子，共定位与OCT 4 PWM。为了进一步表征OCT 4和SRY之间的关系，我们用人启动子微阵列进行了ChIP-芯片实验，发现与1000个OCT 4靶启动子相似的前49%也被SRY结合。该分析代表了SRY靶启动子的首次鉴定。有趣的是，我们确定了与OCT 4和SRY结合的启动子，而不是那些单独与SRY结合的启动子，也与转录抑制因子KAP 1结合。我们的研究不仅验证了ChIPMotifs和ChIPModules的组合方法，而且还确定了OCT 4可能的新调控伙伴。
ChIP-chip studies have revealed that many in vivo binding sites have a weak match to the consensus sequence for the transcription factor being analyzed. Possible explanations for these observations include ( 1) the in vitro-derived consensus site does not represent the in vivo binding site and/ or ( 2) the factor is recruited to a weak binding site via interaction with another protein. To address these possibilities, we developed an approach (ChIPMotifs) that incorporates a bootstrap resampling method to statistically infer the optimal cutoff threshold for a position weight matrix (PWM) of a motif identified from ChIP- chip data by ab initio motif discovery programs. Using OCT4 ChIP- chip data and the ChIPMotifs approach, we first developed a refined OCT4 PWM. We then used the refined PWM and a ChIPModules approach to identify transcription factors colocalizing with OCT4 in Ntera2 testicular embryonal carcinoma cells. We found that the consensus binding site for SRY, a transcription factor critical for testis development, colocalizes with the OCT4 PWM. To further characterize the relationship between OCT4 and SRY, we performed ChIP- chip experiments with human promoter microarrays, and found that 49% of the top similar to 1000 OCT4 target promoters were also bound by SRY. This analysis represents the first identification of SRY target promoters. Interestingly, we determined that promoters bound by OCT4 and SRY, but not those bound by SRY alone, were also bound by the transcriptional repressor KAP1. Our studies not only validate the ChIPMotifs and ChIPModules combinatorial approach but also identify a possible new regulatory partner of OCT4.