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The Magical World of Chromatin in the Mushroom, Coprinopsis cinerea
Roanoke College October 1st, 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 Outline1. Background on epigenetics and chromatin 2. Chromatin in C. cinerea: DNA Methylation 3. Chromatin in C. cinerea: Mapping open
chromatin a. FAIRE technique and datab. Meiosis
Street signs in the talk indicate breaks between sections
January 11, 2010August, 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 ObesityA link between maternal diet,
epigenetics and asthma
Gene Coding vs. Control of Gene Expression
Central DogmaOne Epigenetic
Mechanism
Gene expression
Gene inhibition
Maxwell, A, (2009) Lab Medicine, 40, 171-178.
Cytosine Methylation and CpG’s
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S. Frazier-Bowers and Pukkila, unpublished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Figure from Stajich et al, 2010 and unpublished from Pukkila and Au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
GenesRepeat elementsMethylated 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 Seqexpression
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 Tonight’s 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?