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Integrating ChIP-sequencing and digital gene expression profiling to identify BRD7 downstream genes and construct their regulating network

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Abstract

BRD7 is a single bromodomain-containing protein that functions as a subunit of the SWI/SNF chromatin-remodeling complex to regulate transcription. It also interacts with the well-known tumor suppressor protein p53 to trans-activate genes involved in cell cycle arrest. In this paper, we report an integrative analysis of genome-wide chromatin occupancy of BRD7 by chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) and digital gene expression (DGE) profiling by RNA-sequencing upon the overexpression of BRD7 in human cells. We localized 156 BRD7-binding peaks representing 184 genes by ChIP-sequencing, and most of these peaks were co-localized with histone modification sites. Four novel motifs were significantly represented in these BRD7-enriched regions. Ingenuity pathway analysis revealed that 22 of these BRD7 target genes were involved in a network regulating cell death and survival. DGE profiling identified 560 up-regulated genes and 1088 down-regulated genes regulated by BRD7. Using Gene Ontology and pathway analysis, we found significant enrichment of the cell cycle and apoptosis pathway genes. For the integrative analysis of the ChIP-seq and DEG data, we constructed a regulating network of BRD7 downstream genes, and this network suggests multiple feedback regulations of the pathways. Furthermore, we validated BIRC2, BIRC3, TXN2, and NOTCH1 genes as direct, functional BRD7 targets, which were involved in the cell cycle and apoptosis pathways. These results provide a genome-wide view of chromatin occupancy and the gene regulation network of the BRD7 signaling pathway.

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Acknowledgments

This study was supported in part by grants from the National Natural Science Foundation of China (81172189, 81272298, 81372907, 81472531, 81572787, 81528019, and 81572748) and the Natural Science Foundation of Hunan Province (14JJ1010, 2015JJ1022, and 2015JJ2148).

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Authors and Affiliations

  1. Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China

    Ke Xu, Wei Xiong, Ming Zhou, Heran Wang, Pan Chen, Qianjin Liao, Xiaoling Li, Guiyuan Li & Zhaoyang Zeng

  2. Key Laboratory of Carcinogenesis of Ministry of Health and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China

    Ke Xu, Wei Xiong, Ming Zhou, Heran Wang, Jing Yang, Xiaoling Li, Guiyuan Li & Zhaoyang Zeng

  3. Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China

    Wei Xiong, Ming Zhou, Xiayu Li, Hao Deng, Xiaoling Li, Guiyuan Li & Zhaoyang Zeng

Authors
  1. Ke Xu
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  2. Wei Xiong
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  3. Ming Zhou
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  4. Heran Wang
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  5. Jing Yang
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  6. Xiayu Li
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  7. Pan Chen
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  8. Qianjin Liao
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  9. Hao Deng
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  10. Xiaoling Li
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  11. Guiyuan Li
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  12. Zhaoyang Zeng
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Corresponding author

Correspondence to Zhaoyang Zeng.

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The authors declare that they have no conflicts of interest.

Electronic supplementary material

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Supplemental Table S1. BRD7-binding peaks identified by ChIP-seq. Supplementary material 1 (XLS 38 kb)

Supplemental Table S2. BRD7 target genes identified by ChIP-seq. Supplementary material 2 (XLS 52 kb)

Supplemental Table S3. Differentially expressed genes dysregulated by BRD7. Supplementary material 3 (XLS 976 kb)

11010_2015_2568_MOESM4_ESM.jpg

Supplemental Fig. S1. Regulatory network of BRD7 target genes and their potential downstream genes identified by ChIP-seq and DGE profiling. A total of 184 BRD7 target genes identified by ChIP-seq, as well as 1648 BRD7-regulated genes identified by DGE profiling, were entered into an interaction database, STRING, to find their functional interacting relationships, and then a regulatory network of BRD7 target genes and regulated genes was constructed and illustrated by Cytoscape. BRD7 was surrounded by its target genes, while other BRD7-regulated genes were laid in the outer cycle. Supplementary material 4 (JPEG 1915 kb)

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Xu, K., Xiong, W., Zhou, M. et al. Integrating ChIP-sequencing and digital gene expression profiling to identify BRD7 downstream genes and construct their regulating network. Mol Cell Biochem 411, 57–71 (2016). https://doi.org/10.1007/s11010-015-2568-y

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  • DOI: https://doi.org/10.1007/s11010-015-2568-y

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