1. 4C technology: protocols and data analysis.
- Author
-
van de Werken HJ, de Vree PJ, Splinter E, Holwerda SJ, Klous P, de Wit E, and de Laat W
- Subjects
- Chromatin Assembly and Disassembly, Cross-Linking Reagents, DNA genetics, DNA Restriction Enzymes chemistry, Formaldehyde chemistry, High-Throughput Nucleotide Sequencing methods, Nucleic Acid Conformation, Polymerase Chain Reaction methods, beta-Globins chemistry, beta-Globins genetics, Chromatin chemistry, Chromosome Mapping methods, DNA chemistry, Sequence Analysis, DNA methods, Statistics as Topic methods
- 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., (Copyright © 2012 Elsevier Inc. All rights reserved.)
- Published
- 2012
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