ChIP-Seq Binding Dataset

We cloned 206 (of the estimated 214) DNA binding genes into an anhydrotetracycline -inducible Gateway shuttle vector to contain an N- or C-terminal FLAG epitope tag.Once transformed, we cultured MTB strains to a uniform growth stage and induced expression of the gene-of-interest for 18 hours – approximately one cell division. We then harvested chromatin samples for ChIP-seq as well as total RNA for high-density transcriptional profiling by custom tiled microarray.

ChIP samples were sequenced, and a custom algorithm performed read alignment and ChIP peak calling (Methods). To determine significance thresholds for peak inclusion we generated a ChIP-seq negative control compendium consisting of 10 different sequencing data sets. Because no single control captures all known or potential ChIP artifacts we included several control samples, including: wild-type H37Rv chromatin immunoprecipitated with and without anti-FLAG antibody, chromatin samples from uninduced expression-vector bearing cells immunopreciptated with and without anti-FLAG antibody, as well as chromatin samples from induced non-TF genes immunoprecipitated with anti-FLAG antibody. We subjected each control data set to peak calling, creating a negative control peak set that contained ~2000 scored final peaks. We then compared each experimental peak with this negative control peak set to define a collection of pass-filter DNA binding events (Methods). This approach identified both global and local binding patterns with associated significance scores for every TF assayed.

For more details see Minch et al. 2015, Nat Commun.
ChIP-seq Profiles

You can visualize ChIP-seq profiles for a given experiment in UCSC Genome Browser by clicking on the browser icon

Displaying 1 - 10 of 261
Regulator UCSC Genome Browser
Transcriptional regulator, AraC family
UCSC Browser Tracks
Beta-carotene ketolase (EC 1.14.-.-)
UCSC Browser Tracks
UCSC Browser Tracks
Cell envelope-associated transcriptional attenuator LytR-CpsA-Psr, subfamily A1 (as in PMID19099556)
UCSC Browser Tracks
ESX-1 secreted protein regulator EspR
UCSC Browser Tracks
ESX-1 secreted protein regulator EspR
UCSC Browser Tracks
POSSIBLE HISTONE-LIKE PROTEIN HNS
UCSC Browser Tracks
Transcriptional repressor EthR, TetR family
UCSC Browser Tracks
Transcriptional repressor EthR, TetR family
UCSC Browser Tracks
Transcriptional regulator WhiB-like WhiB6
UCSC Browser Tracks
Chip-Seq Binding Table

Displaying 1 - 10 of 5874

ChipSeq TF Gene Target Position/Center Distance Expression Differential Expression pvalue Operon Strand Type Browser View
Transcriptional regulator, AsnC family
Chromosomal replication initiator protein DnaA
4411177/ 4411242 65 -0.54 No 0.0700302 1 + Primary.TSS UCSC
Transcriptional regulator, ArsR family
Chromosomal replication initiator protein DnaA
4411177/ 4411097 -80 -0.56 No 0.00145696 1 + Primary.TSS UCSC
Transcriptional regulatory protein
DNA polymerase III beta subunit (EC 2.7.7.7)
1935/ 1803 -132 0.63 Induced 0.000700791 2 + Primary.TSS UCSC
Transcriptional regulator, TetR family
DNA polymerase III beta subunit (EC 2.7.7.7)
1935/ 1922 -13 0.09 No 0.861457 2 + Primary.TSS UCSC
Transcriptional regulator, ArsR family
DNA recombination and repair protein RecF
3034/ 3061 27 0.79 Induced 7.25e-14 2 + Primary.TSS UCSC
Transcriptional regulator, IclR family
DNA recombination and repair protein RecF
3034/ 3081 47 0 No 0.999076 2 + Primary.TSS UCSC
DNA-binding response regulator TrcR
Zn-ribbon-containing, possibly RNA-binding protein and truncated derivatives
4434/ 4462 28 -0.08 No 0.877564 2 + CDS UCSC
Transcriptional regulator, TetR family
DNA gyrase subunit A (EC 5.99.1.3)
7302/ 7326 24 0 No 0.997072 3 + CDS UCSC
Organic hydroperoxide resistance transcriptional regulator
DNA gyrase subunit A (EC 5.99.1.3)
7302/ 7371 69 0.23 No 0.225915 3 + CDS UCSC
Transcriptional regulator, PadR family
DNA gyrase subunit A (EC 5.99.1.3)
7302/ 7350 48 0.09 No 0.729306 3 + CDS UCSC
MTB TF binding locations from ChIP-seq experiments (Turkarslan et al., submitted)

Table summarizing TF binding locations for target genes from ChIP-seq experiments, expression levels of these genes in the corresponding TF overexpression tiling array experiments and overlap with regulatory network model (Source figshare).

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