The Magical World of Chromatin in the

Mushroom, Coprinopsis cinerea

Roanoke College October 1
st
, 2012 Ginnie Hench, PhD
Magical mushrooms are from the genus
Psilocybe
psilocybin psilocin
The Magical World of Chromatin.
Image courtesy of Brian Strahl, UNC
. in the Mushroom, Coprinopsis cinerea
Talk Outline
1. Background on epigenetics and chromatin
2. Chromatin in C. cinerea: DNA Methylation
3. Chromatin in C. cinerea: Mapping open
chromatin
a. FAIRE technique and data
b. Meiosis


Street signs in the talk
indicate breaks between
sections
January 11, 2010
August, 2011
Some scientists respond
to the hype!
Why are so many people talking about
epigenetics and chromatin these days?
Epigenetics

Heritable changes in gene expression that
are not due to any alteration in the DNA
sequence

Epigenetics in Health and Disease
Epigenetics and Obesity
A link between maternal diet,
epigenetics and asthma
Gene Coding vs. Control of Gene Expression
Central Dogma
One Epigenetic
Mechanism
Gene expression
Gene inhibition
Maxwell, A, (2009) Lab Medicine, 40, 171-178.
Cytosine Methylation and CpGs
Zaidi S K et al. Mol. Cell. Biol. 2010;30:4758-4766
DNA Methylation in the context of
chromatin
Chromatin in C.
cinerea: DNA
Methylation
Methylation at a single gene locus
S. Frazier-Bowers and Pukkila, unpublished
25/25 CpG sites
0/106 non-CpG sites
Stajich et al. 2010
DNA methylation in C. cinerea

Two methyltransferase genes:
DNMT1a and DNMT1b

4.2% cytosines methylated

12.2% CpGs methylated

Zemach et al. 2010
Zemach et al., Science 238: 916-919, 2010
Methylation on different scales of
resolution
Thanks to ChunHang (Tommy) Au for display of DNA methylation
Repeat element
Gene
Methylation at single
base pair resolution
Figure from Stajich et al, 2010 and unpublished from Pukkila and Au
Gene expression does not usually
occur in methylated domains
Genes
Repeat elements
Methylated domains
RNA Seq Gene
expression
54 Kb Window
Summary for DNA Methylation
Like most other organisms, DNA
methylation is associated with repression
of gene expression in C. cinerea
C. cinerea is unique compared to other
model organisms because
It has methylated DNA and methyltransferase
genes
it has member of just one family of DNA
methyltransferase genes
Chromatin in C.
cinerea: Mapping
open chromatin
with the FAIRE
technique
Zaidi S K et al. Mol. Cell. Biol. 2010;30:4758-4766
Chromatin is comprised of DNA wrapped
around histones
FAIRE (Formaldehyde Assisted Isolation of
Regulatory Elements) enriches for open chromatin
Giresi & Lieb, 2009
DNA Gel Showing FAIRE Samples
http://galaxy.psu.edu/
Rashid N, et al. Genome Biology 2011
Viewing Genome Data!

Entire Genome
Input
FAIRE
FAIRE peaks
Genes
Repeat elements
Methylated dom.
RNA Seq
expression
Seeing FAIRE Peaks
Input
FAIRE
FAIRE peaks
Giresi & Lieb, 2009
The tallest FAIRE Peak in C. cinerea is
upstream of an expressed gene
FAIRE data alignment
FAIRE peaks
Gene expression
Genes
FAIRE peaks are absent from
methylated domains/repeat elements
Input
FAIRE
FAIRE peaks
Genes
Repeat elements
Methylated domains
Highlights from FAIRE analysis
6% of genome enriched by FAIRE
~7000 peaks
Peak width ranges from 100-1000 bps;
median 322 bps
Chromatin in C.
cinerea: Mapping
open chromatin
to understand
meiosis
C. cinerea Lifecycle
Sexual
Reproductive
Phase
Asexual
Reproductive
Phase
Meiotic Recombination Results in Crossovers
Handel and Schimenti, Nature Reviews Genetics, 2010
Sister chromatids
Meiotic recombination rates vary
across the genome
Recombination rates
Red = High Grey = Average Blue = Low
Recombination Map for Chromosome 2
Stajich, et al., 2010
DO CHANGES IN
CHROMATIN OPENNESS
CORRELATE WITH MEIOTIC
RECOMBINATION RATES?
Genes that have a fundamental role in meiosis are not expressed
in oidia & lack adjacent, upstream FAIRE peaks
dmc1
Chromosome I (5.9 kb window)
Genes
FAIRE peaks
Gene expression
by RNA Seq
Meiotic-specific genes
spo11
Chromosome III (21 kb/window)
Genes
FAIRE peaks
Meiotic-specific
genes
Gene expression
by RNA Seq
Take Away Points for Tonights Talk
Chromatin dynamics have
direct consequences for
health and disease

DNA methylation is associated
with repression of gene
expression across many
species

The FAIRE technique enriches
for open chromatin

Acknowledgements
Dr. Patricia Pukkila
Dr. Jason Stajich
Dr. Claire Burns
Tommy Au

The entire Coprinus
community

Dr. Jason Lieb
Jeremy Simon
Other Lieb lab
members
All of the
computational
biologists who have
made my work possible

Tree of Life image 2007 Tree of Life Web Project. Image of rose
1999 Nick Kurzenko. Image of annelid worm 2001 Greg W. Rouse.
Questions?