Stage Master

Binding of sequence-specific transcription factors (TFs) to DNA regulates transcriptional gene expression. Combinatorial binding of TFs has been shown to be a hallmark of regulatory regions where TF binding depends on the presence of its motif and motifs of other co-expressed TFs. Clusters of TF binding sites have then been used to characterize functional regulatory elements.

During this internship, you will investigate the cooperativity of TFs in mouse and human cell types. Using regions of open chromatin and TF sequence motifs, you will infer TF binding and will set a up a resource for the visualization of TF binding sites.

Contact: Anaïs Bardet, CR CNRS
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Laboratory: Michaël Weber - Epigenetic regulation of cell identity – CNRS UMR 7242
http://irebs.cnrs.fr/spip.php?rubrique186

References
Spitz F, and Furlong EEM. Transcription factors: from enhancer binding to developmental control. Nat Rev Genet (2012) 13, 613–626.
Domcke S*, Bardet AF*, Ginno P, Hartl D, Burger L, Schübeler D. Competition between DNA methylation and transcription factors determines binding of NRF1. Nature (2015) 528(7583):575-9
Bardet AF*, Steinmann J*, Bafna S, Knoblich JA, Zeitlinger J, Stark A. Identification of transcription factor binding sites from ChIP-seq data at high-resolution. Bioinformatics (2013) 29(21):2705-13
Bardet AF, He Q, Zeitlinger J, Stark A. A computational pipeline for comparative ChIP-seq analyses. Nature Protocols (2012) 7(1):45-61
He Q*, Bardet AF*, Patton B, Purvis J, Johnston J, Paulson A, Gogol M, Stark A, Zeitlinger J. High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. Nature Genetics (2011) 43(5):414-20