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 13 th ): chromatin assembly 2. For all other slots: everyone needs to present, choose a date or topic and 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 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 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
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: Animals: fewer examples known
Human transgenerational epigenetic phenomena? Time magazine 2010 Utah Epigenetics website View NOVA special “A ghost in your genes”
Nucleus; chromatin The material for Epigenetics
The conundrum Human DNA: 2 m Human nucleus r = 10 µm 10,000 x compaction Starting at the beginning
The solution DNA is compacted via interaction with proteins THIS IS THE TEMPLATE FOR EPIGENTIC PHENOMENA
Nucleosome Chromatin organizes and compacts DNA from Horn and Peterson Science, 2002 ac DNA methylation
Woodcock and Dimitrov, COGD, 2001 Caterino 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 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 H2Aconserved H2Bconserved H3highly conserved H4very 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
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 and compacts DNA from Horn and Peterson Science, 2002 ac DNA methylation
Nucleosome Chromatin restricts accessibility of the genome from Horn and Peterson Science, 2002 ac DNA methylation
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
Heterochromatin (stained)
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
DNA that contacts histones is not readily accessible
Nucleosome: 147 bp of DNA Histone octamer = 1.7 turns
Regular linker size: common in inactive chromatin Irregular linker size: common in active chromatin Linker size is variable: bp Nucleosome position and spacing matters
Luger et al. Nature, 1995 Histone tails are modified, this influences accessibility of the genomic DNA
Latham and Dent Nat 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 ac DNA methylation
Nucleosome Chromatin regulators alter accessibility of the genome from Horn and Peterson Science, 2002 ac DNA methylation
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 Can alter gene activity without change in DNA
Regulatory roles of chromatin if yes: EPIGENETIC REGULATION if no: CHROMATIN REGULATION Is it the existing chromatin state heritable? Is it the existing chromatin state 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 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
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 monozygotic twins Fraga et al. PNAS, 2005