| Chapter title |
Polycomb Group Proteins
|
|---|---|
| Chapter number | 21 |
| Book title |
Polycomb Group Proteins
|
| Published in |
Methods in molecular biology, January 2016
|
| DOI | 10.1007/978-1-4939-6380-5_21 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-6378-2, 978-1-4939-6380-5
|
| Authors |
Leblanc, Benjamin, Comet, Itys, Bantignies, Frédéric, Cavalli, Giacomo, Benjamin Leblanc, Itys Comet, Frédéric Bantignies, Giacomo Cavalli |
| Editors |
Chiara Lanzuolo, Beatrice Bodega |
| 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. |
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