Can we correlate RNA expression
and DNase hypersensitivity sites in
DNA domains?
David John Haan
Stuart’s Lab
Nov 20, 2014
UCSC
Topological Associated Domains (TAD)
• Megabase-sized local chromatin interaction
domains
• Determined thru HiC Assay
GTEX Portal RNAseq Data
2,921 samples
“Wrangle” the Data!
• HiC Assay Domain data:
chr14_24960000_26280000
CMA1
CTSG
chr14_26560000_28200000
MIR4307
NOVA1
chr14_29080000_30080000
FOXG1
C14orf23
chr14_30160000_30920000
MIR548AI
PRKD1
GZMH
GZMB
MIR548AI
PRKD1
STXBP6
• GTEX RNAseq Data in RPKMs:
Gene
CMA1
CTSG
GZMH
GZMB
STXBP6
Pancreas1 Pancreas2
61.305
44.22
100.5
21.105
4.02
86.43
64.32
85.425
14.07
97.485
Heart1
17.085
53.265
89.445
39.195
8.04
• Take the mean of each domain and each tissue type
6
4
Breast
AdiposeTissue
Nerve
Thyroid
Prostate
Bladder
Lung
Uterus
FallopianTube
Ovary
BloodVessel
SmallIntestine
Colon
Stomach
Vagina
CervixUteri
Esophagus
Skin
SalivaryGland
Muscle
Heart
Kidney
AdrenalGland
Testis
Pituitary
Brain
Spleen
Blood
Pancreas
Liver
Tissue Type
High Expression
12
Low Expression
2
DNA Domains
GTEX RNAseq expression in 150 most
variable domains
10
8
DNase Hypersensitivity Sites
Histogram of DNA hypersensitivity coverage among HiC Domains
200
DNase HS assay is an
adequate assay to
determine if a domain is
open for transcription
100
These 5 tissue samples are
from the Human Epigenome
Atlas
0
# of Domains
300
400
Pancreas1
Pancreas2
Heart
Ovary
Small Intestine
0.0
0.1
0.2
0.3
0.4
Fraction of hypersensitive sites within domain
0.5
2
4
6
8
Points in red are
significantly (p<.05) more
expressed in Pancreas than
other tissues determined
by a right sided t-test.
0
log2(mean RNA level+1)
10
12
Pancreas DNase coverage Vs RNA level
0.0
0.1
0.2
0.3
DNase coverage
0.4
0.5
0.10
0.05
0.00
Hypersensitivity Difference (Pancreas − Mean)
0.15
How does pancreas HS coverage in DNA
domains differ from other tissue types?
0
500
1000
1500
Domains
2000
2500
0.10
RNAseq p<10^−2 N=150
RNAseq p<10^−12 N=64
0.05
SOX9 – progenitor gene
REG Family
0.00
Hypersensitivity Difference (Pancreas − Mean)
0.15
Pancreas HS differential in
significantly expressed Domains
0
500
1000
1500
Domains
2000
2500
0.00
0.05
0.10
0.15
RNAseq p<10^−2 N=673
RNAseq p<10^−12 N=89
−0.05
−0.05
0.00
0.05
0.10
Hypersensitivity Difference (Ovary − Mean)
0.15
0.20
RNAseq p<10^−2 N=318
RNAseq p<10^−12 N=220
−0.10
Hypersensitivity Difference (Heart − Mean)
0.20
More tests: Heart and Ovary
0
500
1000
1500
Domains
2000
2500
0
500
1000
1500
Domains
2000
2500
Future direction
• Use more DNase hypersensitivity data
• Gene-specific analysis
• Analyze tissue specific “closed” domains
• Compare domains among tissue types including
cancer
• Integrating domains into pathway models
Thank you
• Josh’s lab specifically Josh Stuart, Dan Carlin,
Kiley Graim, and Evan Paull
• Charles Markello for helping create the t-test
• Evan for helping determine what I need (or
don’t need) on my bike to get up the hill faster
Pancreas HS differential VS
significantly expressed Breast domains
In black is the Dnase
HS coverage
differential plot
In red/blue is a
density plot of
significant
expression levels
*No Correlation!!!