lecture outline

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