Comparative analysis of methods for genome-wide nucleosome cartography

Abstract

Nucleosomes contribute to compacting the genome into the nucleus and regulate the physical access of regulatory proteins to DNA either directly or through the epigenetic modifications of the histone tails. Precise mapping of nucleosome positioning across the genome is, therefore, essential to understanding the genome regulation. In recent years, several experimental protocols have been developed for this purpose that include the enzymatic digestion, chemical cleavage or immunoprecipitation of chromatin followed by next-generation sequencing of the resulting DNA fragments. Here, we compare the performance and resolution of these methods from the initial biochemical steps through the alignment of the millions of short-sequence reads to a reference genome to the final computational analysis to generate genome-wide maps of nucleosome occupancy. Because of the lack of a unified protocol to process data sets obtained through the different approaches, we have developed a new computational tool (NUCwave), which facilitates their analysis, comparison and assessment and will enable researchers to choose the most suitable method for any particular purpose. NUCwave is freely available at http://nucleosome.usal.es/nucwave along with a step-by-step protocol for its use.

Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome

“…S1). Alignment files were processed using the NUCwave algorithm (Quintales et al 2015b) to generate the nucleosome occupancy maps. Altogether, we generated duplicates of 23 MNase-seq maps corresponding to the mutants described in the text.…”

Long non-coding RNA repertoire and regulation by nuclear exosome, cytoplasmic exonuclease and RNAi in fission yeast

“…MNAse sequencing data was mapped using Bowtie2 (Langmead and Salzberg 2012). Nucleosome maps for visualisation were performed with nucwave (Quintales et al 2015), following the web recommendations (http://nucleosome.usal.es/nucwave/). Data were analysed using the 'computeMatrix reference-point' and 'heatmapper' functions from the deeptools package with transcription start sites as reference points (Ramírez et al 2014).…”

Nucleosome positioning: resources and tools online

“…Alternatively, one does not call nucleosome positions at all, and instead operates with the continuous nucleosome occupancy profile, defining regions of cell type/state specific differential occupancy (e.g. DANPOS/DANPOS2 [137], DiNuP [138], NUCwave [139]). We have been also applying the latter idea when analysing nucleosome positioning in mouse and human [12,26,76] using custom made scripts (Vainshtein and Teif, unpublished).…”