ETS family protein GABP is a novel co-factor strongly associated with genomic YY1 binding sites in various cell lines

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• 作者：Taijun Han ; Sejong Oh ; Keunsoo Kang
• 关键词：ChIP ; seq ; Meta ; analysis ; YY1 ; GABP ; CTCF ; ETS ; Alzheimer’s disease
• 刊名：Genes & Genomics
• 出版年：2016
• 出版时间：February 2016
• 年：2016
• 卷：38
• 期：2
• 页码：119-125
• 全文大小：2,108 KB
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• 作者单位：Taijun Han (1)
  Sejong Oh (1)
  Keunsoo Kang (2)
  
  1. Department of NanoBioMedical Science, Dankook University, Cheonan, 330-714, Republic of Korea
  2. Department of Microbiology, Dankook University, Cheonan, 330-714, Republic of Korea
  
• 刊物主题：Microbial Genetics and Genomics; Plant Genetics & Genomics; Animal Genetics and Genomics; Human Genetics;
• 出版者：Springer Netherlands
• ISSN：2092-9293

文摘

The Yin Yang 1 (YY1) protein is a ubiquitously expressed transcription factor involved in gene activation, repression, and genomic imprinting. Recent studies have revealed genome-wide target loci of YY1 in different cell types using chromatin immunoprecipitation with massively parallel DNA sequencing (ChIP-seq). However, it is unclear how the same YY1 controls different sets of genes in various cell types. To unveil potential co-factors of YY1, we reanalyzed YY1 and CTCF ChIP-seq data sets generated by the ENCODE consortium for various cell lines. As reported previously, CCCTC-binding factor (CTCF) is one of the most frequently associated co-factors around genomic YY1 binding sites in all cases. When it comes to strong YY1 binding sites, however, binding motifs of the E26 transformation-specific (ETS) family proteins are significantly prevalent. Indeed, meta-analysis of the ETS transcription factor GABP ChIP-seq performed in various cell types confirmed the strong genomic association between YY1 and GABP. Particularly, genes around common YY1 binding sites that are defined as invariable strong binding across cell lines were significantly associated with GABP in almost all cell types examined. In addition, the association between YY1 and GABP is strongly conserved in primate genomes such as chimpanzee, orangutan and baboon. Gene ontology analysis revealed that the YY1-GABP co-regulated genes are significantly associated with Alzheimer’s disease in human. Overall, the meta-analysis of available YY1, CTCF, and GABP ChIP-seq data showed a novel genomic association between YY1 and GABP, suggesting that the YY1–GABP co-regulatory network is common across multiple cell types. Keywords ChIP-seq Meta-analysis YY1 GABP CTCF ETS Alzheimer’s disease