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S. Frazier-Bowers and Pukkila, unpublished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Figure from Stajich et al, 2010 and unpublished from Pukkila and Au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?