WP 5: Transcription factor binding site perturbation experiments and model refinements

Mouse

Objectives

The objective of this work package is to challenge integrative predictive models of transcriptional response in inflammation by modifying TFBS to alter TF-DNA interactions in vivo.

Specific aims:

  • Understanding the contribution of individual TF to the expression of model inflammatory genes;
  • Understanding the role of the binding affinity of individual TFBS in determining transcriptional regulation by introducing mutations into reporter plasmids;
  • Assessing the role of individual TFBS in the transcription of model genes by introducing mutations on endogenous genetic loci by homologous recombination in human somatic cell lines;
  • Evaluating the cell-specific or stimulus specific role of individual TFBS in the transcription of model genes by generating and analysing mice carrying mutation on TFBS in selected endogenous inflammatory genes via homologous recombination in mouse embryonic stem cells;
  • Refining models predicted from WP4 based on the results of perturbation experiments