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Assessing functional consequences
of epigenetic modifications
An Data Analysis Activity
for Students
This teacher slide set was created by Dana Haine, MS, of the
UNC Superfund Research Program, which is funded by the
National Institute of Environmental Health Sciences
Assessing functional consequences
of epigenetic modifications
Is there is a relationship between prenatal
exposure to arsenic and functional
epigenetic changes to newborn DNA ?
Does exposure + epigenetic changes =
changes to gene expression?
Dr. Rebecca Fry
Studies the link
between prenatal
exposure to arsenic
and cadmium and
newborn health.
Link to Video
describing her
Research Questions in the Fry Lab
• What is the relationship between prenatal arsenic
exposure and changes to gene expression?
• Are any of the genes that are altered in association
with arsenic controlled by the epigenetic mechanism
DNA methylation?
How were these questions
38 newborns
– Prenatal arsenic exposure
– DNA Methylation Profiles
– RNA (Gene expression)
Microarray analysis was
used to determine which
genes exhibited
differential expression
• The microarray works by first
extracting DNA or RNA and
hybridizing different pieces
representing different genes to a
• It allows us to measure how
many copies of each gene is
• This can tell us whether there is
no, some or a lot of RNA
transcript present
334 U-tAs-associated transcripts
A heatmap is a way to visualize
data trends from microarray
N=38 subjects with range of arsenic exposure, cord blood (vein) isolated
Conclusions from Heat Map
• There are 334 genes that show a change in transcript
profiles in association with arsenic exposure in the 38
• Some gene expression profiles increase with
increasing arsenic exposure and some gene expression
profiles decrease with decreased arsenic exposure
• These changes suggest that prenatal arsenic exposure
does affect a baby’s gene expression profile
Are any of the genes whose
expression is altered in
association with arsenic
controlled by DNA
The traditional view of DNA
What would you expect to find?
Level of
Methylation Level
What would you expect to find?
What did we see when looking at
individual genes?
RNA Transcript
Gene Expression
DNA Methylation
Gene Methylation
• 2,919 genes exhibited differential methylation in
response to arsenic exposure
• 334 gene exhibited corresponding changes in gene
expression (mRNA transcripts)
• Only 16 genes exhibited a significant linear
relationship between methylation and gene
• Seven of these genes were related to important birth
outcomes including gestational age and head
For most genes, researchers found
no correlation between gene
expression and methylation
This pattern is present across the
entire genome!