Download Epigenetics 12

Lecture outline
1. Class organization
2. Introduction to Epigenetics
Lecture outline
1. Class organization
a. Target audience
b. Organization: lecture, research lecture, student
presentations
Lecture outline
1. Class organization
a. Target audience
b. Organization: lecture, research lecture, student
presentations
c. What is expected:
• attendance, participation, questions for the student papers
• 2 exams (recitations before them)
• student presentations
• (grad and CAMB enrolled: final proposal)
Student presentations
1. TWO volunteers for next week (September 13th): chromatin assembly
2. For all other slots: everyone needs to present, choose a date or topic
and e-mail me as soon as possible
IMPORTANT: if you decide to drop the class and have chosen a
presentation date already please let me know
3. If >19 students then we double up on papers
one students presents the background of the field plus the first half
of the paper the second student does the second half of the paper
and future directions
Lecture outline
1. Class organization
2. Introduction to Epigenetics
what are epigenetic phenomena
where does epigenetic regulation occur
Epigenetic phenomena: heritable
alternative states of gene activity
that do not result from altered
nucleotide sequence
Examples of Epigenetic Phenomena
Monozygotic:
Genomes are identical
Examples of Epigenetic Phenomena
Monozygotic:
Genomes are identical
Arturas Petronis
2006
Monozygotic (identical) twins and disease etiology
Examples of Epigenetic Phenomena
Monozygotic:
Genomes are identical
Rainbow and Copycat
Cloned cat: Genome is identical
Yet looks different from mother
Rainbow and Copycat
Calico cat coat color cannot be cloned!!!
Not based on genetics
Based on Epigenetics:
Color gene is X-linked
Random X-inactivation of cells in blastula
all daughter cells will inherit that pattern
Genetics vs. Epigenetics
+germline
invariable
* transient (not heritable)
* mitotically heritable
* meiotically heritable
Plants: many examples of meiotically heritable
or transgenerational epigenetic phenomena
http://learn.genetics.utah.edu/content/epigenetics/inheritance/
Animals: fewer examples known
http://learn.genetics.utah.edu/content/epigenetics/inheritance/
Animals: fewer examples known
Kaati, G., Bygren, L.O., Pembrey, M., and Sjostrom, J. (2007). Transgenerational response to nutrition,
early life circumstances and longevity. European Journal of Human Genetics 15: 784-790.
http://learn.genetics.utah.edu/content/epigenetics/inheritance/
Human transgenerational epigenetic phenomena?
Time magazine 2010
Utah Epigenetics website
View NOVA special “A ghost in your genes”
http://en.sevenload.com/videos/tX02lnf-Nova-The-Ghost-In-Your-Genes-1-6
The material for Epigenetics
Nucleus;
chromatin
Starting at the beginning
The conundrum
Human DNA: 2 m
Human nucleus r = 10 µm
10,000 x compaction
The solution
DNA is compacted via interaction with proteins
THIS IS THE TEMPLATE FOR EPIGENTIC PHENOMENA
Chromatin organizes and
compacts DNA
Nucleosome
ac
DNA
methylation
from Horn and Peterson Science, 2002
ac ac
ac
ac
Chromatin structures
Woodcock and Dimitrov, COGD, 2001
Caterino and Hayes, Nature Structural and Molecular Biology, 2007
Primary structure
the NUCLEOSOMAL DNA
Beads on a string
Twenty-Five Years of the Nucleosome,
Fundamental Particle of the Eukaryote Chromosome
Roger D. Kornberg and Yahli Lorch; Cell, 1999.
Nucleosome:
147 bp of DNA
Histone octamer
= 1.7 turns
The nucleosome: histones plus DNA
HISTONES
Two classes of histones (canonical)
Core Histones
H2A
conserved
H2B
conserved
H3 highly conserved
H4 very highly conserved
Linker Histones
H1 not conserved
Small proteins, ca. 10 kD, very basic
Three domains
A. Histone fold
B. Histone fold extension
C. Extended N (and C)-termini
Histone fold: 3 conserved alpha helices
Histone fold extension and N-termini
Linker histone
Tails are K (lysine) and R (argenine) rich
C-termini
HISTONE/ DNA INTERACTIONS
1. Charge neutralization: basic residues lysine,
argenine
2. Hydrophobic side chains; threonine, proline, valine,
isoleucine with deoxyribose
3. Main chain amide with phosphate oxygen
Canonical histones and histone variants
Secondary structure
linker histone
30 nm fiber
Chromatin organizes and
compacts DNA
Nucleosome
ac
DNA
methylation
from Horn and Peterson Science, 2002
ac ac
ac
ac
Chromatin restricts
accessibility of the genome
Nucleosome
ac
DNA
methylation
from Horn and Peterson Science, 2002
ac ac
ac
ac
Types of Chromatin
Euchromatin
Transcriptionally active, less compacted
Heterochromatin
Less transcriptionally active, very compacted
a) constitutive heterochromatin
centromeres, telomeres
b) facultative heterochromatin
rDNA, transposons, inactive X chromosome
www.nenno.it/publications/mnphdthesis/diss08.jpg
Heterochromatin (stained)
http://www.biology.wustl.edu/faculty/elgin/hp2chrom.jpg
Barr Body Region
* Immunofluorescent straining of the human interphase nucleus.
* The white box indicates the Barr body region where the inactive X chromosome
resides during interphase.
Chadwick and Willard (2004) PNAS
Nucleosomes are obstacles to transcription
Hodges et al. Science 2009
Transcription happens outside of condensed
chromatin
2003
Transcription happens outside of condensed
chromatin
2003
DNA that contacts histones is not readily
accessible
Nucleosome:
147 bp of DNA
Histone octamer
= 1.7 turns
Nucleosome position and spacing matters
Linker size is variable: 10-50 bp
Regular linker size: common in inactive chromatin
Irregular linker size: common in active chromatin
Histone tails are modified, this influences
accessibility of the genomic DNA
Luger et al. Nature, 1995
Histone modifications matter
Latham and Dent
Nat Struct Mol Biol 2007
DNA methylation status
is important
Nature News, May 2006
All levels of chromatin condensation have been
implicated in controlling accessibility of
the genomic DNA
effect on:
replication, recombination, repair, and transcription
Chromatin restricts
accessibility of the genome
Nucleosome
ac
DNA
methylation
from Horn and Peterson Science, 2002
ac ac
ac
ac
Chromatin regulators
alter accessibility of the genome
Nucleosome
ac
DNA
methylation
from Horn and Peterson Science, 2002
ac ac
ac
ac
Mechanism exist to “open up” chromatin
Chromatin remodeling complexes
alter primary structure of chromatin
Histone modifying enzymes
alter histone tail modifications
Leschziner lab, Harvard
Mechanism exist to “condense” chromatin
Histone modifying enzymes
alter histone tail modifications
DNA methylases,
Recruitment of chromatin binding proteins
Polycomb proteins
Heterochromatin Protein
Francis Science 2005
Mechanism exist to “open up” chromatin
Chromatin remodeling, histone modifications
Mechanism exist to “condense” chromatin
Histone modifications, DNA methylation, chromatin binding proteins
Can alter gene activity
without change in DNA
Is it the existing chromatin
state heritable?
Regulatory roles of chromatin
if yes: EPIGENETIC REGULATION
if no: CHROMATIN REGULATION
Epigenetic/chromatin phenomena
Chromatin-based restriction of genome accessibility during
differentiation
Selective activation of genome after perception of stimulus
(influence of environment/stress)
Mitotic maintenance of cell identity (or loss thereof in cancer)
Dosage compensation in the male versus female genome
(X inactivation in mammals)
Memory, Behavior, Aging
HDAC Inhibitor treated
Pelag et al., Science 2010
Chemotherapy plus
HDAC inhibitor?
Sharma et al. Cell 2010
Change in histone modification
alters lifespan
Greer et al., Nature 2010
Lecture outline
1. Class organization
check blackboard site
2. Introduction to Epigenetics
next chromatin assembly
chromatin remodeling
histone modifications
histone variants
Glossary
Chromatin: nucleosomal arrays
Nucleosome: DNA plus histone octamer
DNA wound around the histone octamer: core DNA
DNA between nucleosomes: linker DNA
Differences in the epigenome of monozygotic
twins
Fraga et al. PNAS, 2005