Genome-wide Identification of Craniofacial Transcriptional Enhancers Axel Visel Genomics Division Lawrence Berkeley Nat’l Lab Motivation: To understand the genetics of craniofacial development and clefting disorders, we must understand distant-acting gene regulation Challenge 1: Non-coding GWAS hits Example: 8q24 640kb NSCL/P risk interval MYC PVT1 (Birnbaum et al. 2009) Challenge 2: Complex regulatory architecture Msx1 protein (nLacZ, Coudert et al.) Msx1 Stx18 enhancer hCF154 Distal enhancers (Visel, unpublished) -75kb -95kb -140kb -230kb Tools 1. Tissue-ChIP-seq to FIND enhancers in the genome 2. CHARACTERIZE craniofacial enhancer activities in transgenic mice 1

Genome-wide Identification of Craniofacial Transcriptional Enhancers Axel Visel Genomics Division Lawrence Berkeley Nat’l Lab Workflow Data genome-wide sets of candidate enhancers and matched expression data peak coordinates “wiggle tracks” expression profiles Progress (Year 1) ChIP-seq: E11.5 face available E13.5 palate in progress RNA-seq: first data for E12.5/E14.5 collect face/palate tissues p300 ChIP-seq + RNA-seq test candidate enhancers in transgenic mice results of transgenic mouse assays 25-30 candidate sequences/yr whole-mount photos OPT data transgenics: 30 candidates testing done (reference or mouse alleles) GWAS/resequencing follow-ups: candidate regions in progress (8q24, Twist1) OPT data test known risk variants 2