A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data

Abstract

CSdeconv is a novel method for determining the location of transcription factor binding from ChIP-seq data that discriminates closely-spaced sites.

Characterization of the Fur Regulon in Pseudomonas syringae pv. tomato DC3000

“…Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) has been extensively used to study nucleic acid-protein interactions in eukaryotes. However, this technology has only recently been applied to the study of DNA binding proteins in bacteria (24,27). Integration of our results with our previously published microarray and transcriptome data sets provides stronger evidence for regulation by Fur and suggests that Fur function in P. syringae involves activation as well as repression.…”

“…Peak calling. ChIP-seq data corresponding to the main DC3000 chromosome (NC_004578.1) were analyzed using CSDeconv (27) to detect regions that had been enriched by immunoprecipitation ("peaks"). The log-likelihood threshold for the initial phase of enriched region estimation was set to 200, and the penalty term for estimating multiple binding sites within an enriched region was set to 20,000, resulting in a total of 322 called binding sites within the set of 300 enriched regions.…”

Uniform, optimal signal processing of mapped deep-sequencing data

“…For example, distinct, assay-specific tools have been designed for analyzing transcription factor ChIP-seq (TF ChIP-seq), histone ChIP-seq, DNase-seq and formaldehydeassisted isolation of regulatory elements (FAIRE)-seq data 1,4-9 . Examples of specialized algorithms include blind deconvolution for TF ChIP-seq analysis 8 and nonlocal means for detecting RNA polymerase II (Pol II)-enriched genomic segments 10 . However, the specialized nature of most existing analytical methods makes it difficult to compare, integrate or uniformly analyze data from multiple sources, particularly when they differ in signal patterns and noise characteristics.…”

Mapping the regulon of Vibrio cholerae ferric uptake regulator expands its known network of gene regulation

“…8) but has yet to be used significantly to study bacterial transcriptional regulators. To our knowledge, only two investigations using ChIP-seq in bacteria have been published, reporting the mapping of the chromatin-remodeling proteins HN-S and Fis in Escherichia coli (9) and the DosR transcriptional regulator in Mycobacterium tuberculosis (10). This paucity of studies may reflect a lack of ChIPquality antibodies for bacterial proteins (11) or suboptimal expression of the regulator of interest under laboratory conditions.…”