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REPOSITORIES: ENA
Similar Datasets
Project description:Impact of cytosine methylation on DNA binding specificities of human transcription factors.
| PRJNA371642 | ENA
Project description:The Compendium of DNA-Binding Specificities of Transcription Factors in a Pathogenic Bacterium
| PRJNA611637 | ENA
Project description:Accurate predictions of the DNA binding specificities of transcription factors (TFs) are necessary for understanding gene regulatory mechanisms. Traditionally, predictive models are built based on nucleotide sequence features. Here, we employed three- dimensional DNA shape information obtained on a high-throughput basis to integrate intuitive DNA structural features into the modeling of TF binding specificities using support vector regression. We performed quantitative predictions of DNA binding specificities, using the DREAM5 dataset for 65 mouse TFs and genomic-context protein binding microarray data for three human basic helix-loop-helix TFs. DNA shape-augmented models compared favorably with sequence-based models for these predictions. Although both k-mer and DNA shape features encoded the interdependencies between nucleotide positions of the binding site, using DNA shape features reduced the dimensionality of the feature space compared to k-mer use. Finally, analyzing the weights of DNA shape-augmented models uncovered TF family- specific structural readout mechanisms that were not obvious from the nucleotide sequence.
2014-11-04 | GSE59845 | GEO
Project description:The nucleosome is a fundamental unit of chromatin in eukaryotes, and generally prevents the binding of transcription factors to genomic DNA. Pioneer transcription factors overcome the nucleosome barrier, and bind their target DNA sequences in chromatin. OCT4 is a representative pioneer transcription factor that plays a role in stem cell pluripotency. In the present study, we biochemically analyzed the nucleosome binding by OCT4. Crosslinking mass spectrometry showed that OCT4 binds the nucleosome.
2020-05-13 | PXD019160 | JPOST Repository
Project description:Inherent DNA binding specificities of the HIF-1α and HIF-2α transcription factors in chromatin
| PRJNA494827 | ENA
Project description:Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae transcription factors but a comprehensive evaluation of their data has been lacking. Results: We analyzed in vitro and in vivo TF-DNA binding data reported in previous large-scale studies to generate a comprehensive, curated resource of DNA binding specificity data for all characterized S. cerevisiae transcription factors. Our collection comprises DNA binding site motifs and comprehensive in vitro DNA binding specificity data for all possible 8 bp sequences. Included in this database is DNA binding specificity data for 27 TFs independently generated by PBM analysis in this current study. Investigation of the DNA binding specificities within the basic leucine zipper (bZIP) and VHR transcription factor families revealed unexpected plasticity in TF-DNA recognition: intriguingly, the VHR transcription factors, newly characterized by protein binding microarrays in this study, recognize bZIP like DNA motifs, while the bZIP transcription factor Hac1 recognizes a motif highly similar to the canonical E-box motif of basic helix-loop-helix (bHLH) transcription factors. We identified several transcription factors with distinct primary and secondary motifs, which might be associated with different regulatory functions. Finally, integrated analysis of in vivo transcription factor binding data with protein binding microarray data lends further support for indirect DNA binding in vivo by sequence-specific transcription factors.
2011-12-10 | GSE34306 | GEO
Project description:The sequence specificity of DNA-binding proteins is the primary mechanism by which the cell recognizes genomic features. Here, we describe systematic determination of yeast transcription factor DNA-binding specificities. We obtained binding specificities for 112 DNA-binding proteins representing 19 distinct structural classes. One-third of the binding specificities have not been previously reported. Several binding sequences have striking genomic distributions relative to transcription start sites, supporting their biological relevance and suggesting a role in promoter architecture. Among these are Rsc3 binding sequences, containing the core CGCG, which are found preferentially ~100 bp upstream of transcription start sites. Mutation of RSC3 results in a dramatic increase in nucleosome occupancy in hundreds of proximal promoters containing a Rsc3 binding element, but has little impact on promoters lacking Rsc3 binding sequences, indicating that Rsc3 plays a broad role in targeting nucleosome exclusion at yeast promoters. Keywords: Protein binding microarrays, DNA, proteins
2008-12-26 | GSE12349 | GEO