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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    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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WANG Qi, DING Yan-Shu, GENG Bao-Bao, NIE Yu-Min. Mining and Functional Analysis of Chromatin Interaction-related Transcription Factors[J]. Progress in Biochemistry and Biophysics,2019,46(4):406-414

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History
  • Received:November 23,2018
  • Revised:February 20,2019
  • Accepted:February 25,2019
  • Online: April 19,2019
  • Published: April 20,2019