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. You will set a up a resource for the visualization of TF binding sites. Finally, you will explore the cooperativity of TFs and compare the architecture of regulatory elements across species.

Throughout this work, you will integrate a large variety of sequencing datasets (e.g. ChIP-seq, DNase-seq, RNA-seq) across cell types and species and integrate them to the underlying sequence information (e.g. TF motifs, sequence composition) to identify features of TF binding.

Skills:
Bioinformatics background with experience working in a linux environment
Good level in a scripting language (e.g. bash, python, perl) and R as well as data analysis techniques and statistics
Previous experience working with NGS datasets is a plus
Good knowledge of biology and interest in genomics and gene regulation
Ability to work in a team with both experimental and computational biologists
Good level in spoken and written english

This internship can be extended to a PhD project

Contact: Anaïs Bardet, CR CNRS
Please send a cover letter, CV and grades and ranking to This email address is being protected from spambots. You need JavaScript enabled to view it.
Do not hesitate to contact us for more details

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