GEO DataSets

(Submitter supplied) Most homeodomains are unique within a genome, yet many are highly conserved across vast evolutionary distances, implying strong selection on their precise DNA-binding specificities. We determined the binding preferences of the majority (168) of mouse homeodomains to all possible 8-base sequences, revealing rich and complex patterns of sequence specificity, and showing for the first time that there are at least 65 distinct homeodomain DNA-binding activities. more...

Organism:

synthetic construct; Mus musculus

Type:

Other

Platform:

GPL6796

178 Samples

Download data

(Submitter supplied) Eukaryotic transcription factors (TFs) form complexes with various partner proteins to recognize their genomic target sites. Yet, how the DNA sequence determines which TF complex forms at any given site is poorly understood. Here, we demonstrate that high-throughput in vitro DNA binding assays coupled with unbiased computational analysis provide unprecedented insight into how different DNA sequences select distinct compositions and configurations of homeodomain TF complexes. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing

Platforms:

GPL19132 GPL13304

33 Samples

Download data: BED, BW, HIC

(Submitter supplied) We utilized a bacterial selection system to isolate Engrailed variants from a randomized library that are compatible with each of the 64 possible 3’ triplet sites (i.e. TAANNN). The DNA-binding specificity of 151 representative HD variants from these populations was subsequently characterized. Many of these variants contain novel combinations of specificity determinants that are uncommon or absent in extant HDs. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL15228

249 Samples

Download data: TXT

(Submitter supplied) Binding of transcription factors to DNA is mediated by the recognition of the chemical signatures of the DNA bases and the three-dimensional shape of the DNA molecule. The direct contribution of DNA shape to DNA-binding specificity has been difficult to assess, as DNA shape is a consequence of its sequence. Here, we teased apart these two modes of recognition in the context of Hox-DNA binding. We made a series of mutations in Hox residues that, in a co-crystal structure, only recognize DNA shape, and tested the effect on DNA binding preferences using SELEX-seq. more...

Organism:

Drosophila melanogaster

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17275 GPL9061

32 Samples

Download data: TXT

(Submitter supplied) This protein binding microarray (PBM) involved binding GST-tagged proteins to custom-designed, double-stranded 44K Agilent microarrays in order to determine their sequence preferences. The method is described in Berger et al., Nature Biotechnology 2006. A key feature is that the microarrays are composed of de Bruijn sequences that contain each 10-base sequence once and only once, providing an evenly balanced sequence distribution. more...

Organism:

synthetic construct

4 Series

383 Samples

Download data

(Submitter supplied) Homeodomains (HDs) are the second largest class of DNA binding domains (DBDs) in eukaryotic sequence-specific transcription factors (TFs) and are the TF structural class with the largest number of disease mutations in the Human Gene Mutation Database (HGMD). Despite numerous structural studies and large-scale analyses of HD DNA binding specificity, HD-DNA recognition is still not fully understood. Here, we analyzed 92 human HD mutants, including disease-associated variants and variants of unknown significance (VUS), for their effects on DNA binding activity. more...

Organism:

synthetic construct; Homo sapiens

Type:

Genome binding/occupancy profiling by array

Platform:

GPL33450

122 Samples

Download data: GPR, XLS

(Submitter supplied) The homeobox transcription factor Prox1 is critical for organogenesis including brain, retina, liver and pancreas and lymphatic system. Prox1 is transiently expressed in mouse cochlear hair cells (HCs) and supporting cells (SCs), however, it remains elusive about its in vivo DNA binding site and roles during cochlear development. Here, by using fresh cochlear tissues and Prox1 antibody, we firstly mapped out the genome-wide binding sites of Prox1 via Cleavage Under Targets and Release Using Nuclease (CUT&RUN). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24247 GPL21273

6 Samples

Download data: BW