Project description:Five-vertebrate ChIP-seq reveals the evolutionary dynamics of trancription factor binding. The SRF files for this experiment can be found in the European Read Archive with study accession number ERP000054. ArrayExpress Submission Date: Apr 07 2010 ArrayExpress Release Date: Apr 08 2010 Publication Author List: Dominic Schmidt; Michael D Wilson; Benoit Ballester; Petra C Schwalie; Gordon D Brown; Aileen Marshall; Claudia Kutter; Stephen Watt; Celia P Martinez-Jimenz; Sarah MacKay; Iannis Talianidis; Paul Flicek; Duncan T Odom Publication Title: Transcription factor binding evolution in five vertebrates Person Roles: submitter Person Last Name: Flicek Person First Name: Paul Person Email: flicek@ebi.ac.uk Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Person Affiliation: EBI
Project description:Zoo-ChIP: Functional analysis of experimentally determined combinatorial transcription factor binding in multiple mammalian species
Project description:Variations in noncoding regulatory sequences play a central role in evolution but interpreting such variations remains difficult even in the context of defined attributes such as transcription factor (TF) binding sites. Here, we systematically link variations in cis-regulatory sequences to TF binding by profiling the allele-specific binding of 27 TFs expressed in a yeast hybrid, which contains two related genomes within the same nucleus. TFs localize preferentially to sites containing their known binding motifs, but occupy only a small fraction of the potential motif-coding genomic sites. Differential binding of TFs to the two orthologues is well explained by sequence variations that alter the consensus core motif, while changes in chromatin accessibility were of little apparent effect. Motif variations that abolish binding when present in one allele show only moderately reduced binding when common to both alleles, suggesting evolutionary compensation. At the promoter level, we report cases of turnover, where binding in the two orthologues localized to different promoter regions, yet most interspecies differences resulted from higher number of binding sites in one of the alleles. Our results suggest that cis variations affecting TF binding occur primarily through the gain and loss of cis-regulatory motifs at accessible regions.
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.
Project description:1. evaluation of diagnostic importance of insulin like growth factor binding protein3 in patient with recently diagnosed as Colorectal cancer
2. correlation between the diagnostic efficacy of insulin like growth factor binding protein 3 with routine marker carcinoembryonic antigen.
