Protein/DNA in vitro Binding seq (PB-seq) for Drosophila HSF and genomic Drosophila DNA

ABSTRACT: DNA sequence and local chromatin landscape act jointly to determine transcription factor (TF) binding intensity profiles. To disentangle these influences, we developed an experimental approach, called protein/DNA binding and high-throughput sequencing (PB-seq), that allows the binding energy landscape to be characterized genome-wide in the absence of chromatin. We applied our methods to the Drosophila Heat Shock Factor (HSF), which inducibly binds a target DNA sequence element (HSE) following heat shock stress. PB-seq involves incubating sheared naked genomic DNA with recombinant HSF, partitioning the HSF-bound and HSF-free DNA, and then detecting HSF-bound DNA by high throughput sequencing. We compared PB-seq binding profiles with ones observed in vivo by ChIP-seq, and developed statisti

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Michael Guertin 

PROVIDER: E-GEOD-32570 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress