Chromosome Conformation Capture on Chip (4C): Data Processing
Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
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 language | English |
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Title of host publication | Polycomb Group Proteins : Methods and Protocols |
Editors | Chiara Lanzuolo, Beatrice Bodega |
Number of pages | 19 |
Volume | 1480 |
Publisher | Springer |
Publication date | 2016 |
Pages | 243-61 |
Chapter | 21 |
ISBN (Print) | 978-1-4939-6378-2 |
ISBN (Electronic) | 978-1-4939-6380-5 |
DOIs | |
Publication status | Published - 2016 |
Series | Methods in Molecular Biology |
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ISSN | 1064-3745 |
- Journal Article
Research areas
ID: 179362694