RT Journal Article
SR Electronic
T1 Network Dynamics of ER-α activation reveals reprogramming of GRHL2
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 266908
DO 10.1101/266908
A1 Andrew N. Holding
A1 Federico M. Giorgi
A1 Amanda Donnelly
A1 Amy E. Cullen
A1 Luke Selth
A1 Florian Markowetz
YR 2018
UL http://biorxiv.org/content/early/2018/02/16/266908.abstract
AB Background Estrogen Receptor-alpha (ER) is the main driver of ~75% of all breast cancers. Upon stimulation, ER forms a complex on the chromatin at enhancers and promoters that leads to increased transcription of nearby genes. A critical feature of ER action is a cyclical binding pattern with a period of 90 minutes. However, analysis of ER binding dynamics has so far been restricted to the promoters of individual target genes. It is unknown how cyclical ER binding occurs genome-wide and whether this phenomenon is influenced by ER cofactors.Results Here, we present a novel approach to dissect the regulation of ER activation based on network analysis of time-course genome-wide DNA binding data. We measured ER binding by ChIP-Seq at three timepoints (0, 45, 90 minutes) and developed an approach, called VULCAN, to overlay this binding information on a gene coexpression network. We benchmarked our approach in a comparison study and confirmed that it rediscovered known components of the ER signalling axis. Using VULCAN, we found that the activation ER results in the reprogramming of the transcription factor GRHL2 and independently validated this result by ChIP-seq and quantitative proteomics (qPLEX-RIME). Further, E2-responsive GRHL2 binding was found to be concurrent with an ER-responsive increase in eRNA transcription, and we show GRHL2 negatively regulates transcriptional activity at these sites.Conclusions We present a general framework to predict key regulatory proteins from differential transcription factor binding data, which uncovered that activation of the ER leads to reprogramming of GRHL2.ARAndrogen ReceptorARACNe-APAccuRate Algorithm for reConstruction of Network through Adaptive PartitioningCCLECancer Cell Line EncyclopediaChIPChromatin ImmunoPrecipitationEREstrogen Receptor-AlphaEREEstrogen-Response ElementsGSEAGene Set Enrichment AnalysisGRHL2Grainyhead Like Transcription Factor 2METABRICMolEcular TAxonomy of BReast cancer International ConsortiumPBSPhosphate Buffered SalinePIProtease InhibitorsPRProgesterone ReceptorTCGAThe Cancer Genome AtlasTFTranscription FactorVIPERVirtual Inference of Protein activity by Enriched Regulon analysisVULCANVirtUaL ChIP-Seq Analysis through Networks