4C-seq characterization of Drosophila BEAF binding regions provides evidence for highly variable long-distance interactions between active chromatin

PLoS One. 2018 Sep 24;13(9):e0203843. doi: 10.1371/journal.pone.0203843. eCollection 2018.

Abstract

Chromatin organization is crucial for nuclear functions such as gene regulation, DNA replication and DNA repair. Insulator binding proteins, such as the Drosophila Boundary Element-Associated Factor (BEAF), are involved in chromatin organization. To further understand the role of BEAF, we detected cis- and trans-interaction partners of four BEAF binding regions (viewpoints) using 4C (circular chromosome conformation capture) and analyzed their association with different genomic features. Previous genome-wide mapping found that BEAF usually binds near transcription start sites, often of housekeeping genes, so our viewpoints were selected to reflect this. Our 4C data show the interaction partners of our viewpoints are highly variable and generally enriched for active chromatin marks. The most consistent association was with housekeeping genes, a feature in common with our viewpoints. Fluorescence in situ hybridization indicated that the long-distance interactions occur even in the absence of BEAF. These data are most consistent with a model in which BEAF is redundant with other factors found at active promoters. Our results point to principles of long-distance interactions made by active chromatin, supporting a previously proposed model in which condensed chromatin is sticky and associates into topologically associating domains (TADs) separated by active chromatin. We propose that the highly variable long-distance interactions we detect are driven by redundant factors that open chromatin to promote transcription, combined with active chromatin filling spaces between TADs while packing of TADs relative to each other varies from cell to cell.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Binding Sites
  • Chromatin / genetics
  • Chromatin / physiology
  • Chromatin Assembly and Disassembly / genetics
  • Chromosome Mapping
  • Chromosomes / metabolism
  • DNA-Binding Proteins / genetics*
  • DNA-Binding Proteins / physiology
  • Drosophila Proteins / genetics*
  • Drosophila Proteins / metabolism
  • Drosophila Proteins / physiology
  • Drosophila melanogaster / genetics
  • Drosophila melanogaster / metabolism
  • Eye Proteins / genetics*
  • Eye Proteins / physiology
  • Gene Expression Regulation / genetics
  • Genome, Insect
  • In Situ Hybridization, Fluorescence
  • Insulator Elements / genetics*
  • Promoter Regions, Genetic / genetics
  • Sequence Analysis, DNA / methods
  • Transcription Initiation Site
  • Transcriptional Activation / physiology*

Substances

  • BEAF-32 protein, Drosophila
  • Chromatin
  • DNA-Binding Proteins
  • Drosophila Proteins
  • Eye Proteins

Grants and funding

This work was supported by the National Science Foundation [1244100 to CMH; 1616827 to DHO and MD]; Louisiana Board of Regents [LEQSF-EPS(2012)-PFUND-274 to CMH]; and Rural Development Administration, Republic of Korea Next-Generation BioGreen21 Program [PJ01317301 to DHO and MD]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.