Test Case Title

FAIRE-seq data analyser

Test Case Acronyme: FAIRE-seq


Test Case Class


Contact person

Bernd Mueller-Roeber, University of Potsdam



Test Case Description

FAIRE is a procedure allowing the isolation of nucleosome-depleted regions from eukaryotic chromatin. FAIRE is based on the fact that different chromosomal regions are cross-linked to formaldehyde with different efficiencies, depending on the openness of the chromatin and the proteins binding to it. It has been used by researchers to identify differences in chromatin structures in different cell types (e.g. healthy vs. sick cells); FAIRE has also been employed to discover gene regulatory elements (e.g. motifs in promoters) genome-wide. Such regions of the chromatin can be straightforwardly isolated using a simple biochemical phenol-chloroform extraction procedure after formaldehyde-mediated crosslinking of histones to chromosomal DNA and random fragmentation of the DNA by sonication. The extracted genomic DNA fragments are generally free of histones and represent regions containing regulatory elements (to which transcription factors bind). Such genome segments can be analyzed by quantitative PCR, hybridization to genome tiling arrays or deep sequencing. Based on high resolution and decreasing the costs of deep sequencing, usually FAIRE-seq is using nowadays. But analysing FAIRE-seq data and finding the FAIRE peaks among the genome (which show e.g. regulatory elements) is time consuming and need different steps and is non trivial procedure.

Background knowledge

Gene expression is regulated at different levels but one of the first and most important events includes changes in chromatin structure, which can be identified using FAIRE-seq. FAIRE-seq experiments are starting to become more and more important for the identification of (long-range) gene regulatory elements; currently no tools for facile handling of such data is awailable.



Initial state of the Test case

We established FAIRE-seq experiments on Arabidopsis thaliana as a model plant, started collaboration with Riano-Pachon´s group on data analysis.

Desired final state of the Test Case

The tool should allow an experimentalist to efficiently identify FAIRE peaks at a genome-wide scale. Also, the tool should allow to link FAIRE peaks to gene expression patterns, to discover peaks associated with transcriptional changes (stimulus-dependent, developmentally regulated, etc.)

Test Case Work Plan

Different tools can be used to align FAIRE-seq data to the genome like “bowtie” and also peak calling can be done by “MACS” or “ZINBA”.

1 Pre-processing the data. 2 Identify reads which will be aligned to the nuclear genome. 3 Identification of FAIRE peaks which will present open chromatin parts of the genome. 4 Find close genes to FAIRE peaks. 5 Doing motif analysis. 6 Identification of FAIRE peak sequences.


Simon J.M. et al. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. 2012. Nature protocol. 7, 256–267.

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