Robust 4C-seq data analysis to screen for regulatory DNA interactions

Nat Methods. 2012 Oct;9(10):969-72. doi: 10.1038/nmeth.2173. Epub 2012 Sep 9.


Regulatory DNA elements can control the expression of distant genes via physical interactions. Here we present a cost-effective methodology and computational analysis pipeline for robust characterization of the physical organization around selected promoters and other functional elements using chromosome conformation capture combined with high-throughput sequencing (4C-seq). Our approach can be multiplexed and routinely integrated with other functional genomics assays to facilitate physical characterization of gene regulation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / chemistry*
  • Gene Expression Regulation
  • High-Throughput Nucleotide Sequencing / methods*
  • Locus Control Region
  • Polymerase Chain Reaction
  • Promoter Regions, Genetic


  • DNA

Associated data

  • GEO/GSE40420