Chromatin Structure & Gene Expression The Histone Code

Structural Features of DNA

The Genome is Organized into Chromosomes

A. Chromatin fibers exploding from lysed nucleus B. Metaphase Chromosome (folded fibers). DNA-Protein Fibers Make up Chromatin

Chromosomes Are made of Thick Chromatin Fibers

Thick Fibers Can Unravel to Reveal Thin Fibers

The Fundamental Chromatin Fiber is the 10 nm Fiber (DNA Associated With Nucleosomes) 30 nm fibers 10 nm fibers :“beads on a string” nucleosome DNA

Levels of DNA Packing Based on the Fundamental Fiber

Probing the 10 nm Fiber With Nuclease

Nucleosomes Are Composed of DNA and an Ocatamer of Four Histone Pairs + DNA

Nucleosome Structure DNA H2B H4 H3 H2A

H2A Fold H2A/H2B Dimer

Histones Assemble into Core Ocatamer

Final Ocatamer Assembly

Conformations for the 30 nm Fiber

Some Chromatin Allows Access to DNA By Specific Binding Proteins (TF & Pol)

Covalent Modification of the Histone Tails Can Alter DNA- Histone Interaction or “Mark” Nucleosomes Acetylation (lys) Methylation (Lys) Phosphorylation (ser) Ubiquination (Lys)

Chromatin is Dynamic- Remodeling Complexes Alter Structure or Positioning on DNA

A model for Dynamic Regulation of Chromatin & Access to DNA

Chromatin Remodeling Complexes Like Sir Can Recognize Acetylated Histone Tails

Heterochromatin Inactivates Specific Regions of Chromosomes With Defined Borders (Epigenetic Modification)

Variegated Position Effects Occur When Normally Active Genes Become Heterochromatin ~30-40 Loci modify PEV. Su(var) Genes suppress variagation. HDACs E(var) Genes enhance variagation Bromo & Chromodomain proteins Bromo domains bind Ac Chromo domains bind Me

Histone Modification May Mark Nucleosomes as Heterochromatin

Is There A Histone Modification Code?

David Allis’ Model For The Histone Code

Active Chromatin Can Become Extended in Looped Domains Locus Control Region (LCR)

Activation of Promoters By Acetylation & Phosporylation –The Standard Model A = Activator bound to upstream reg. seq. HAT = Histone Acetyl Transferase P = Phosphate Ac = Acetate Ki = Kinase Swi/SNF = Chromatin Remodeling Complex T = TATA Box M = Mediator

ChIP Assay

The Histone Code: What do we know for sure? The information required for proper gene transcription is not just the promotors enhancers and transcription factors Chromatin structure regulates gene expression Chromatin structure is regulated at different levels  Heterochromatin vs. Euchromatin  Nucleosome structure at promoters and other regulatory sequences Histone modification plays a role in the regulation of chromatin structure Modification of transcription factors also plays a role We can’t read the code yet!