Genome-wide Identification of
Craniofacial Transcriptional Enhancers
Axel Visel
Scientist, Genomics Division
Lawrence Berkeley National Laboratory
Outline
1 Distant-Acting Enhancers
Why are they important?
How can we find them in the genome (and determine their function)?
2 Finding Developmental Face/Palate Enhancers
Data from preliminary ChIP-seq and transgenic mouse studies
3 FaceBase – Contributions and Expectations
Data and reagents
Interactions
Enhancers are Required for Development
distant-acting enhancers
promoter
proteincoding
wild-type
limb enhancer deleted
limb enhancer
Sagai et al. 2005
1 megabase
Shh gene
mouse embryo
Lettice et al. 2003
Lettice et al. 2003
human Shh enhancer point mutations
Noncoding Sequences in Human Disease
Meta-Analysis of Genome-Wide Association Studies (GWAS):
Distant Enhancers?
60%
Linked to Exons
40%
Noncoding LD blocks
Of 1,200 disease-associated SNPs, 40% are not linked to
any coding gene
Visel/Pennacchio/Rubin 2009 (Nature 461:199)
How do we find enhancers?
Approach A: Extreme Conservation of Non-coding sequences
mouse
inject into fertilized mouse egg
fugu
PCR amplify
clone
P
LacZ
pHsp68LacZ
>500 enhancers identified to date
see http://enhancer.lbl.gov
reimplant
collect at e11.5
LacZ staining
Major limitation:
can’t find enhancers
active in a particular
process, e.g. face
development
minimum reproducibility: 3 embryos
How do we find enhancers?
Approach B: ChIP-seq with the enhancer-associated p300 protein
microdissection
midbrain
tissue
forebrain
tissue
limb
tissue
limb
p300
ChIP-Seq
forebrain
midbrain
2,400,000 reads 3,600,000 reads 3,500,000 reads
2,100 peaks 2,400 peaks
600 peaks
mouse embryo (e11.5)
Test in transgenic mouse assay
(Nature 457:854, 2009)
p300 ChIP-Seq Predicts in vivo Enhancer Activity
ChIP-seq
forebrain
midbrain
limb
transgenic mouse assay
80%-90% success rate (n>100)
11/12
5/5
8/8
Enables accurate
predictions
of genomic
locations AND activity of enhancers
11/11
(Nature 457:854, 2009)
Outline
1 Distant-Acting Enhancers
Why are they important?
How can we find them in the genome (and determine their function)?
2 Finding Developmental Face/Palate Enhancers
Data from preliminary ChIP-seq and transgenic mouse studies
3 FaceBase – Contributions and Expectations
Data and reagents
Interactions
Enhancers Play a Role in Clefting Disorders
enhancer
SNP disrupts a single AP-2a binding site
x
SNP
human chr1
IRF6 gene
human cleft lip and palate
associated with cleft lip/palate
virtual section of mouth region
enhancer activity in ectoderm of
fusing facial prominences
Rahimov et al. 2008 (Nature Genetics 40:1341)
Jeff Murray Lab, OPT data: David FitzPatrick
ChIP-seq for Craniofacial Enhancer Discovery
Example: Enhancer near known clefting gene MSX1
mx
mx
mx
Msx1 gene expression in
maxillary component of
1st branchial arch
(Mackenzie et al., Development 111:269)
Three-dimensional imaging of enhancer activity
Optical Projection Tomography
(Sharpe et al., Science 296:541)
OPT of Enhancer Browser embryos: David FitzPatrick/Harris Morrison, MRC Edinburgh
Three-dimensional imaging of enhancer activity
Optical Projection Tomography
(Sharpe et al., Science 296:541)
OPT of Enhancer Browser embryos: David FitzPatrick/Harris Morrison, MRC Edinburgh
In vivo validation of ChIP-seq predictions
OPT scans: David FitzPatrick/Harris Morrison, MRC Edinburgh
Outline
1 Distant-Acting Enhancers
Why are they important?
How can we find them in the genome (and determine their function)?
2 Finding Developmental Face/Palate Enhancers
Data from preliminary ChIP-seq and transgenic mouse studies
3 FaceBase – Contributions and Expectations
Data and reagents
Interactions
Visel Lab – FaceBase Aims
Genome-wide identification of enhancer candidates
p300 ChIP-seq: timepoints (e11.5 – e15.5), better spatial resolution
large-scale sequencebased data
RNA-seq data
Transgenic validation and characterization
test 30 candidate sequences/year in transgenic mice
whole-mount photos and OPT data (collaboration with FitzPatrick lab)
provide validated vectors as reagents to other FaceBase investigators
image/video/3D data
Follow-up of human genetic studies
test risk alleles of clefting-associated craniofacial enhancers in mice
integration of enhancer data with
human genetic data
Visel Lab – FaceBase Expectations
Developmental biology and expression imaging groups
Intersect with gene expression data
Please approach us with regions of interest!
Human genetics groups
Please approach us with non-coding cleft-associated regions!
Use ChIP-seq and transgenics to search for enhancers
Transgenic testing of cleft-associated risk variants
Acknowledgments
Lawrence Berkeley National Lab
and DOE Joint Genome Institute
Len Pennacchio
Eddy Rubin
Matt Blow
Shyam Prabhakar
Mouse Transgenics
Malak Shoukry
Jennifer Akiyama
Veena Afzal
Amy Holt
Ingrid Plaijzer-Frick
Roya Hosseini
Collaborators/Contributors:
Terri Beaty, Robert Cornell, Michael
Dixon, David FitzPatrick, Rulang Jiang,
Michael Lovett, Mary Marazita, Jeff
Murray, Stephen Murray, Leif Oxburgh,
Bing Ren, John Rubenstein, Brian
Schutte, Alan Scott, Douglas Spicer
http://enhancer.lbl.gov
Next-Gen Sequencing
NIDCR (FaceBase)
Tao Zhang
Feng Chen
Crystal Wright
Enhancer Browser
Inna Dubchak
Simon Minovitsky
DOE, NHGRI