4C technology: protocols and data analysis

H.J. van de Werken, P.J. de Vree, E. Splinter, S.J. Holwerda, P. Klous, E. de Wit, W. de Laat

Research output: Contribution to journal/periodicalArticleScientificpeer-review


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.
Original languageEnglish
Pages (from-to)89-112
JournalMethods in Enzymology
Publication statusPublished - 2012

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    van de Werken, H. J., de Vree, P. J., Splinter, E., Holwerda, S. J., Klous, P., de Wit, E., & de Laat, W. (2012). 4C technology: protocols and data analysis. Methods in Enzymology, 513, 89-112. https://doi.org/10.1016/B978-0-12-391938-0.00004-5