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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 organizationa. 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 (identical) twins and disease etiology
Arturas Petronis
2006
Monozygotic:Genomes are identical
Examples of Epigenetic Phenomena
Monozygotic:Genomes are identical
Cloned cat: Genome is identicalYet looks different from mother
Rainbow and Copycat
Calico cat coat color cannot be cloned!!!Not based on geneticsBased on Epigenetics: Color gene is X-linkedRandom X-inactivation of cells in blastula
all daughter cells will inherit that pattern
Rainbow and Copycat
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/
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/
Animals: fewer examples known
Human transgenerational epigenetic phenomena?
Time magazine 2010Utah Epigenetics website
View NOVA special “A ghost in your genes” http://en.sevenload.com/videos/tX02lnf-Nova-The-Ghost-In-Your-Genes-1-6
Nucleus; chromatin
The material for Epigenetics
The conundrum
Human DNA: 2 m
Human nucleus r = 10 µm
10,000 x compaction
Starting at the beginningStarting at the beginning
The solution
DNA is compacted via interaction with proteins
THIS IS THE TEMPLATE FOR EPIGENTIC PHENOMENA
Nucleosome
Chromatin organizes andcompacts DNA
from Horn and Peterson Science, 2002
acacac
ac
acDNA
methylation
Woodcock and Dimitrov, COGD, 2001Caterino and Hayes, Nature Structural and Molecular Biology, 2007
Chromatin structures
Primary structure
the NUCLEOSOMAL DNA
Beads on a string
Twenty-Five Years of the Nucleosome, Fundamental Particle of the Eukaryote ChromosomeRoger D. Kornberg and Yahli Lorch; Cell, 1999.
Nucleosome:147 bp of DNAHistone octamer= 1.7 turns
The nucleosome: histones plus DNA
HISTONES
Two classes of histones (canonical)Core HistonesH2A conservedH2B conservedH3 highly conservedH4 very highly conservedLinker HistonesH1 not conserved
Small proteins, ca. 10 kD, very basic
Three domainsA. Histone foldB. Histone fold extensionC. Extended N (and C)-
termini
Tails are K (lysine) and R (argenine) rich
Histone fold: 3 conserved alpha helices
Histone fold extension and N-termini C-termini
Linker histone
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
30 nm fiber
linker histone
Nucleosome
Chromatin organizes andcompacts DNA
from Horn and Peterson Science, 2002
acacac
ac
acDNA
methylation
Nucleosome
Chromatin restricts accessibility of the genome
from Horn and Peterson Science, 2002
acacac
ac
acDNA
methylation
Types of Chromatin
EuchromatinTranscriptionally active, less compacted
HeterochromatinLess transcriptionally active, very compacted
a) constitutive heterochromatincentromeres, telomeres
b) facultative heterochromatinrDNA, transposons, inactive X chromosome
Heterochromatin (stained)http://www.biology.wustl.edu/faculty/elgin/hp2chrom.jpg
www.nenno.it/publications/mnphdthesis/diss08.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
2003
Transcription happens outside of condensed chromatin
DNA that contacts histones is not readilyaccessible
Nucleosome:147 bp of DNAHistone octamer= 1.7 turns
Regular linker size: common in inactive chromatin
Irregular linker size: common in active chromatin
Linker size is variable: 10-50 bp
Nucleosome position and spacing matters
Luger et al. Nature, 1995
Histone tails are modified, this influencesaccessibility of the genomic DNA
Latham and DentNat Struct Mol Biol 2007
Histone modifications matter
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
Nucleosome
Chromatin restricts accessibility of the genome
from Horn and Peterson Science, 2002
acacac
ac
acDNA
methylation
Nucleosome
Chromatin regulators alter accessibility of the genome
from Horn and Peterson Science, 2002
acacac
ac
acDNA
methylation
Mechanism exist to “open up” chromatin
Chromatin remodeling complexesalter primary structure of chromatin
Histone modifying enzymesalter histone tail modifications
Leschziner lab, Harvard
Mechanism exist to “condense” chromatin
Histone modifying enzymesalter histone tail modifications
DNA methylases,
Recruitment of chromatin binding proteinsPolycomb proteinsHeterochromatin 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 activitywithout change in DNACan alter gene activitywithout change in DNA
Regulatory roles of chromatin
if yes: EPIGENETIC REGULATION
if no: CHROMATIN REGULATION
Is it the existing chromatinstate heritable?Is it the existing chromatinstate heritable?
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
Epigenetic/chromatin phenomena
HDAC Inhibitor treated
Pelag et al., Science 2010
Chemotherapy plus HDAC inhibitor?
Sharma et al. Cell 2010
Change in histone modificationalters lifespan
Greer et al., Nature 2010
Lecture outline
1. Class organizationcheck blackboard site
2. Introduction to Epigeneticsnext chromatin assembly
chromatin remodelinghistone modificationshistone variants
Nucleosome: DNA plus histone octamer
DNA wound around the histone octamer: core DNA
DNA between nucleosomes: linker DNA
Glossary
Chromatin: nucleosomal arrays
Differences in the epigenome of monozygotictwins
Fraga et al. PNAS, 2005