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

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

    Publikation: Bidrag til bog/antologi/rapportBidrag til bog/antologiForskningpeer review

    Abstract

    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.

    OriginalsprogEngelsk
    TitelPolycomb Group Proteins : Methods and Protocols
    RedaktørerChiara Lanzuolo, Beatrice Bodega
    Antal sider19
    Vol/bind1480
    ForlagSpringer
    Publikationsdato2016
    Sider243-61
    Kapitel21
    ISBN (Trykt)978-1-4939-6378-2
    ISBN (Elektronisk) 978-1-4939-6380-5
    DOI
    StatusUdgivet - 2016
    NavnMethods in Molecular Biology
    ISSN1064-3745

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