Chromatin immunoprecipitation indirect peaks highlight long-range interactions of insulator proteins and Pol II pausing

Mol Cell. 2014 Feb 20;53(4):672-81. doi: 10.1016/j.molcel.2013.12.029. Epub 2014 Jan 30.


Eukaryotic chromosomes are partitioned into topologically associating domains (TADs) that are demarcated by distinct insulator-binding proteins (IBPs) in Drosophila. Whether IBPs regulate specific long-range contacts and how this may impact gene expression remains unclear. Here we identify "indirect peaks" of multiple IBPs that represent their distant sites of interactions through long-range contacts. Indirect peaks depend on protein-protein interactions among multiple IBPs and their common cofactors, including CP190, as confirmed by high-resolution analyses of long-range contacts. Mutant IBPs unable to interact with CP190 impair long-range contacts as well as the expression of hundreds of distant genes that are specifically flanked by indirect peaks. Regulation of distant genes strongly correlates with RNAPII pausing, highlighting how this key transcriptional stage may trap insulator-based long-range interactions. Our data illustrate how indirect peaks may decipher gene regulatory networks through specific long-range interactions.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites
  • CCCTC-Binding Factor
  • Chromatin Immunoprecipitation / methods*
  • DNA-Binding Proteins / metabolism
  • Drosophila Proteins / metabolism
  • Drosophila melanogaster
  • Eye Proteins / metabolism
  • Gene Expression Regulation*
  • Gene Regulatory Networks
  • Insulator Elements / physiology*
  • Mutation
  • Promoter Regions, Genetic
  • Protein Binding
  • Protein Interaction Mapping
  • RNA Interference
  • RNA Polymerase II / metabolism*
  • Repressor Proteins / metabolism
  • Transcription Factors / metabolism


  • BEAF-32 protein, Drosophila
  • CCCTC-Binding Factor
  • CTCF protein, Drosophila
  • DNA-Binding Proteins
  • Drosophila Proteins
  • Eye Proteins
  • Repressor Proteins
  • Transcription Factors
  • Trl protein, Drosophila
  • RNA Polymerase II

Associated data

  • GEO/GSE52887