Nucleosome Positioning

Histones and DNA Bending

DNA packaging

• 3 X 109 base pairs in human genome• ~1 m if unraveled• Compacted into nucleus

– 100 m in diamter

Histones

Histones

PDBID = 1KX3

Nucleosome Arrays

Dorigo B, et al. Science. 2004 306(5701):1571-3.

Current Opinion in Structural Biology 2006, 16:336–343

http://www2.kenyon.edu/Depts/BioEllipse/courses/biol114/Chap01/chrom1.gif

Histones vs. DNA

• Histones fold DNA• DNA sequence determines histone

binding– Does histone bind sequence?

• Absence of direct sequence specific recognition

– Bending flexibility of DNA determines affinity for complementary protein surface

DNA as a Rod

Twist

Bend

Flexibility

• Torsional Flexibility– Angle between base pairs

• Bending Flexibility– Properties of individual base steps

• Flexibility of DNA is a Sequence-dependent property

Flexibility determinants

• Hydrogen bonds• Electronic configuration of base pairs• Base Pair Stacking energy• Exocyclic groups in major and minor

grooves

Base Pairing

http://en.wikipedia.org/wiki/Base_pair

Base Pairing

Base Stacking

http://researchnews.osu.edu/archive/dna_base_stacking.jpg

Base Stacking

Richmond & Davey 2003

Electrostatics

Philos. Transact. A Math Phys. Eng. Sci. 2004 Jul 15;362(1820):1423-38.

Sequence-directed positioning

Widlund et al. 1997• Mouse Genome• Micrococcal nuclease• 146 bp DNA fragments• DNA seq added to end• Amplify using PCR• 10 rounds cycles

– competitive nucleosome assembly

Chromatin: Structure and Function Alan P. Wolffe

Intrinsically curved DNA sequences

• Oligo(dA).oligo(dT) tracts (4-6bp)– Phased with a periodicity similar to that

of DNA helix

• TATA boxes repeated every 10 bp• CA and CTG di/tri-nucleotide repeats

Energy Landscape

Matrix Method

• Nucleotide phasing of 10bp repeats influences bending of DNA

Periodic occurrence of A/T & GC

• A/T & G/C out of phase

• A/T narrow minor groove

• G/C wide minor groove

Satchwell et al. J. Mol. Biol. 1986 191:659-75

Minor Groove bending facilitated by Arg side chain into minor groove when it faces histone octamer

Major groove narrows to ~9Å

Minor groove narrows to ~3Å

Structure of DNA in Nucleosome

• Discontinuous curvature

Richmond & Davey 2003

Summary

Ong, Richmond & Davey 2007

• Major Gray• Minor White

Unusual DNA conformation parameters induced by histone

binding• Implicates sequence-dependent

– protein recognition– nucleosome positioning– nucleosome mobility

• Can we predict DNA:Nucleosome binding based on sequence?