Transcription Factor Binding Site Mapping Using ChIP-Seq.

  title={Transcription Factor Binding Site Mapping Using ChIP-Seq.},
  author={Suma Jaini and Anna Lyubetskaya and Antonio Gomes and Matthew Peterson and Sang Tae Park and Sahadevan Raman and Gary K. Schoolnik and James E. Galagan},
  journal={Microbiology spectrum},
  volume={2 2}
Transcription factors (TFs) play a central role in regulating gene expression in all bacteria. Yet until recently, studies of TF binding were limited to a small number of factors at a few genomic locations. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) provides the ability to map binding sites globally for TFs, and the scalability of the technology enables the ability to map binding sites for every DNA binding protein in a prokaryotic organism. We have developed a protocol for… 

Figures from this paper

Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications
A method based on hidden Markov models to integrate DHS and histone modifications occupancy for the detection of open chromatin regions and active binding sites is proposed and obtained a good trade-off between sensitivity versus specificity and superior area under the curve statistics than competing methods.
Dual Function of DNA Sequences: Protein-Coding Sequences Function as Transcriptional Enhancers
Most of our genome comprises noncoding sequences that include diverse transcriptional regulatory elements, such as enhancers, while only ~1.5% of the genome codes for proteins. Nevertheless, DNA
BINDER: computationally inferring a gene regulatory network for Mycobacterium abscessus
The developed BINDER framework has broad applicability, useable in settings where computational inference of a gene regulatory network requires integration of data sources derived from both the primary organism of interest and from related proxy organisms.
Elucidating the Regulon of a Fur-like Protein in Mycobacterium avium subsp. paratuberculosis (MAP)
This work provides a regulatory network of MAP Fur binding sites during iron-replete and -deplete conditions, highlighting unique properties of Fur regulon in MAP.
The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell Fusion
It is shown that ADV-1 is necessary for transducing light and/or temporal information to its immediate downstream targets, including controlling rhythms in genes critical to somatic cell fusion, and suggests that a complex regulatory network downstream of ADV- 1 functions to generate distinct temporal dynamics of target gene expression relative to the central clock mechanism.
An Interaction Proteomics Perspective on Chromatin Biology
The proteins that influence the compaction of DNA and thereby affect transcription are studied, including protein complexes involved in chromatin compaction and transcriptional regulation and a novel technique that can measure the amounts of all proteins present in a protein complex.
Path‐seq identifies an essential mycolate remodeling program for mycobacterial host adaptation
It is demonstrated that disrupting MadR program is lethal to diverse mycobacteria making this evolutionarily conserved regulator a prime antitubercular target for both early and late stages of infection.
An essential mycolate remodeling program for mycobacterial adaptation in host cells
Novel technology (Path-seq) discovers cell wall remodeling program during Mycobacterium tuberculosis infection of macrophages and demonstrates that disrupting MadR program is lethal to diverse mycobacteria making this evolutionarily conserved regulator a prime antitubercular target for both early and late stages of infection.
Mycobacterial SigA and SigB Cotranscribe Essential Housekeeping Genes during Exponential Growth
The mechanism underlying the observed hypersensitivity of ΔsigB deletion mutants of Mycobacteriumsmegmatis, M. abscessus, and M. tuberculosis to rifampin (RIF) is explored and an additional constitutive role of σB during exponential growth of mycobacteria that complements the function of the primary sigma factor, σA is uncovered.


ChIP-Seq and the complexity of bacterial transcriptional regulation.
This chapter discusses two aspects of the binding discovered by ChIP-Seq that were unexpected given the canonical model: the substantial binding outside the proximal promoter region and the large number of weak binding sites.
Genome-Wide Analysis of Transcription Factor Binding Sites Based on ChIP-Seq Data
Molecular interactions between protein complexes and DNA mediate essential gene-regulatory functions. Uncovering such interactions by chromatin immunoprecipitation coupled with massively parallel
Extensive low-affinity transcriptional interactions in the yeast genome.
This work shows that low-affinity interactions are abundant in vivo and quantifiable from current high-throughput ChIP experiments, and develops algorithms that predict DNA-binding energies from sequences and ChIP data across a wide dynamic range of affinities and use them to reveal widespread functionality of low-Affinity transcription factor binding.
Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm
Surprisingly, for five of the six factors, their recognition sites are not unambiguously more constrained evolutionarily than the immediate flanking DNA, even in more highly bound and presumably functional regions, indicating that comparative DNA sequence analysis is limited in its ability to identify functional transcription factor targets.
Analysis of Combinatorial cis-Regulation in Synthetic and Genomic Promoters
A quantitative model based on the analysis of synthetic promoter libraries in yeast, which predicts a number of Mig1-regulated genes that lack significant Mig2-binding sites in their promoters and suggests that the information encoded by combinations of cis-regulatory sites is interpreted primarily through simple protein–DNA and protein–protein interactions.
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
ChIP-seq identified 41,582 and 11,004 putative STAT1-binding regions in stimulated and unstimulated cells, respectively, and found 24 loci known to contain STAT1 interferon-responsive binding sites, including 24 that were enriched in sequences similar to known STAT1 binding motifs.
Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response
An experimental pipeline is established in Caenorhabditis elegans that permits global identification of the binding sites for transcription factors using chromatin immunoprecipitation and deep sequencing, and this strategy is applied to the transcription factor PHA-4, which plays critical roles in organ development and other cellular processes.
Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites.
It is demonstrated that, unlike eukaryotic genomes, the E. coli genome is permissive to transcription factor binding, and LexA binds comparably to ectopic target sites introduced at various positions in the genome.