1. 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(Visel, unpublished)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

2. 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