染色质互作相关转录因子的挖掘及功能分析
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南京医科大学生物医学工程与信息学院,生物信息学系,南京 210029

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江苏省自然科学基金青年基金项目(BK20161026),江苏省高校自然科学研究面上项目(16KJB180022)和南京医科大学科技发展基金重点项目(2015NJMUZD003)资助.


Mining and Functional Analysis of Chromatin Interaction-related Transcription Factors
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Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 210029, China

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This work was supported by grants from the Natural Science Foundation of Jiangsu Province(BK20161026),Natural Science Foundation of the Higher Education Institutions of Jiangsu Province(16KJB180022),Science and Technology Development Foundation of Nanjing Medical University(2015NJMUZD003).

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    摘要:

    染色质互作是真核生物基因组组装的基础,并且在调控真核基因细胞特异性表达中发挥重要作用. 染色质互作的发生与特定的蛋白质有关,目前已经发现CTCF(CCCTC binding facor,转录阻抑物)和黏连蛋白与染色质互作相关,然而并不清楚是否还有其他蛋白质参与染色质互作. 我们将整合高通量染色体构象捕获(Hi-C)和染色质免疫沉淀-测序(ChIP-seq)数据,在GM12878和K562细胞系中挖掘与染色质互作相关的转录因子,并对发现的转录因子做功能分析. 我们在频繁发生互作的染色质位点中发现RUNX3、SPI1等转录因子也可能参与染色质互作. 另外,通过FP-growth的数据挖掘方法还发现多个转录因子可能协同作用参与染色质互作. 研究结果将为染色质互作相关实验的开展提供先验知识.

    Abstract:

    Chromatin interaction is the basis of eukaryotic genome assembly and plays an important role in regulating cell-specific expression of eukaryotic genes. The formation of chromatin interactions is associated with specific proteins. It has been suggested that CTCF and adhesion proteins are associated with chromatin interactions, but it is still unclear whether other proteins are involved in chromatin interactions. In this paper, we integrated Hi-C and ChIP-seq data to mine transcription factors related to chromatin interaction in both GM12878 and K562 cell lines, and performed the functional analysis of discovered transcription factors. We found that RUNX3, SPI1 and other transcription factors may also be involved in chromatin interaction in chromatin sites where interaction occurs frequently. In addition, using the data mining method of FP-growth, we found that multiple transcription factors may cooperate to participate in chromatin interaction. Our findings will provide prior knowledge for the development of chromatin interaction experiments.

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王琪,丁砚书,耿宝宝,聂玉敏.染色质互作相关转录因子的挖掘及功能分析[J].生物化学与生物物理进展,2019,46(4):406-414

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历史
  • 收稿日期:2018-11-23
  • 最后修改日期:2019-02-20
  • 接受日期:2019-02-25
  • 在线发布日期: 2019-04-19
  • 出版日期: 2019-04-20