4C technology: protocols and data analysis

Methods Enzymol. 2012;513:89-112. doi: 10.1016/B978-0-12-391938-0.00004-5.

Abstract

Chromosome conformation capture (3C) technology and its genome-wide derivatives have revolutionized our knowledge on chromatin folding and nuclear organization. 4C-seq Technology combines 3C principles with high-throughput sequencing (4C-seq) to enable for unbiased genome-wide screens for DNA contacts made by single genomic sites of interest. Here, we discuss in detail the design, application, and data analysis of 4C-seq experiments. Based on many hundreds of different 4C-seq experiments, we define criteria to assess data quality and show how different restriction enzymes and cross-linking conditions affect results. We describe in detail the mapping strategy of 4C-seq reads and show advanced strategies for data analysis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin / chemistry*
  • Chromatin Assembly and Disassembly
  • Chromosome Mapping / methods*
  • Cross-Linking Reagents
  • DNA / chemistry*
  • DNA / genetics
  • DNA Restriction Enzymes / chemistry
  • Formaldehyde / chemistry
  • High-Throughput Nucleotide Sequencing / methods
  • Nucleic Acid Conformation
  • Polymerase Chain Reaction / methods
  • Sequence Analysis, DNA / methods*
  • Statistics as Topic / methods*
  • beta-Globins / chemistry
  • beta-Globins / genetics

Substances

  • Chromatin
  • Cross-Linking Reagents
  • beta-Globins
  • Formaldehyde
  • DNA
  • DNA Restriction Enzymes