Chromosome Conformation Capture on Chip (4C): Data Processing

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  • Benjamin Olivier Leblanc
  • Itys Comet
  • Frédéric Bantignies
  • Giacomo Cavalli

4C methods are useful to investigate dependencies between regulatory mechanisms and chromatin structures by revealing the frequency of chromatin contacts between a locus of interest and remote sequences on the chromosome. In this chapter we describe a protocol for the data analysis of microarray-based 4C experiments, presenting updated versions of the methods we used in a previous study of the large-scale chromatin interaction profile of a Polycomb response element in Drosophila. The protocol covers data preparation, normalization, microarray probe selection, and the multi-resolution detection of regions with enriched chromatin contacts. A reanalysis of two independent mouse datasets illustrates the versatility of this protocol and the importance of data processing in 4C. Methods were implemented in the R package MRA.TA (Multi-Resolution Analyses on Tiling Array data), and they can be used to analyze ChIP-on-chip data on broadly distributed chromatin components such as histone marks.

Original languageEnglish
Title of host publicationPolycomb Group Proteins : Methods and Protocols
EditorsChiara Lanzuolo, Beatrice Bodega
Number of pages19
Volume1480
PublisherSpringer
Publication date2016
Pages243-61
Chapter21
ISBN (Print)978-1-4939-6378-2
ISBN (Electronic) 978-1-4939-6380-5
DOIs
Publication statusPublished - 2016
SeriesMethods in Molecular Biology
ISSN1064-3745

    Research areas

  • Journal Article

ID: 179362694