Conservation and Evolution of Regulatory Elements in Mammalian Genomes

CREATED: 200703270931 Speaker: Guillaume Bourque

** ChIP-PET

• against ChIP on Chip which uses micro array instead of sequencing to get tags
• enrichment ~10% of fragments
• locate PET clusters to find target sites
• enrichment of motifs near binding regions
• clear signals of conserved motifs across multiple species ** conserved motifs (specific to TF) more specific than just conserved elements
• many of the binding sites are not conserved! (up to 50%) ** conserved binding sites are more meaningful
• proportion of conserved binding sites independent of distance from gene
• looking for other motifs in these conserved regions ** cofactors etc.
• binding sites in regions with repeats ** repeats are highly dynamic in recent evolution ** different TF appears in different types of repeats ** ChIP-PET is able to detect repeats but ChIP on Chip is biased away from repeats