title: A possible role of Drosophila CTCF in mitotic bookmarking and maintaining chromatin domains during the cell cycle.
abstract: BACKGROUND
  The CCCTC-binding factor (CTCF) is a highly conserved insulator protein that plays various roles in many cellular processes. CTCF is one of the main architecture proteins in higher eukaryotes, and in combination with other architecture proteins and regulators, also shapes the three-dimensional organization of a genome. Experiments show CTCF partially remains associated with chromatin during mitosis. However, the role of CTCF in the maintenance and propagation of genome architectures throughout the cell cycle remains elusive.
  
  
  RESULTS
  We performed a comprehensive bioinformatics analysis on public datasets of Drosophila CTCF (dCTCF). We characterized dCTCF-binding sites according to their occupancy status during the cell cycle, and identified three classes: interphase-mitosis-common (IM), interphase-only (IO) and mitosis-only (MO) sites. Integrated function analysis showed dCTCF-binding sites of different classes might be involved in different biological processes, and IM sites were more conserved and more intensely bound. dCTCF-binding sites of the same class preferentially localized closer to each other, and were highly enriched at chromatin syntenic and topologically associating domains boundaries.
  
  
  CONCLUSIONS
  Our results revealed different functions of dCTCF during the cell cycle and suggested that dCTCF might contribute to the establishment of the three-dimensional architecture of the Drosophila genome by maintaining local chromatin compartments throughout the whole cell cycle.
authors.affiliation: Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, Fengtai District, 100071, China. shenwl1988@gmail.com.
authors.forename: Wenlong
authors.initials: W
authors.lastname: Shen
authors.affiliation: Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, Fengtai District, 100071, China. wdong.run1112@gmail.com.
authors.forename: Dong
authors.initials: D
authors.lastname: Wang
authors.affiliation: Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, Fengtai District, 100071, China. byy0804@gmail.com.|College of Life Science, Capital Normal University, 105 Xisihuanbei Road, Beijing, Haidian District, 100048, China. byy0804@gmail.com.
authors.forename: Bingyu
authors.initials: B
authors.lastname: Ye
authors.affiliation: Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, Fengtai District, 100071, China. shiml79@126.com.
authors.forename: Minglei
authors.initials: M
authors.lastname: Shi
authors.affiliation: Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, Fengtai District, 100071, China. zany1983@gmail.com.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, Fengtai District, 100071, China. zhaozh@nic.bmi.ac.cn.
authors.forename: Zhihu
authors.initials: Z
authors.lastname: Zhao
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D002453:Cell Cycle / Q000502:physiology; D002843:Chromatin / Q000502:physiology*; D042002:Chromatin Assembly and Disassembly / Q000502:physiology; D019295:Computational Biology; D017124:Conserved Sequence; D066264:Datasets as Topic; D029721:Drosophila Proteins / Q000502:physiology*; D004331:Drosophila melanogaster / Q000737:chemistry*; D049750:Genome, Insect / Q000235:genetics*; D007399:Interphase / Q000502:physiology; D008938:Mitosis / Q000502:physiology*; D058977:Molecular Sequence Annotation; D012097:Repressor Proteins / Q000502:physiology*; D026801:Synteny
chemical_list: D000076246:CCCTC-Binding Factor; D002843:Chromatin; D029721:Drosophila Proteins; D012097:Repressor Proteins