DNA and Chromosome Organization

• DNA and Chromosome Organization are explored

Prokaryote Chromosome

• The DNA length is approximately 1,100 μm
• The size of the chromosome is 4 x 10^6 kb
• DNA length is 1000x the length of cell
• DNA is highly folded and supercoiled
• DNA associates with basic (+) proteins HU and H
• It has 100 independent domains
• Each domain measures 40 kb = 13 μm and is negatively supercoiled

Eukaryote

• A human diploid nucleus contains 5.5 x 10^9 bp of DNA
• If stretched end to end, DNA would measure approximately 6ft (~200cm)
• DNA combines with nucleosomes
• Chromatin fiber undergoes higher-order folding

Chromatin Packing

• Chromatin is packed with histones, forming nucleosomes

Nucleosome Core

• Nucleosome core consists of an octamer
• The octamer is constructed of:
• Two H2A proteins
• Two H2B proteins
• Two H3 proteins
• Two H4 proteins
• DNA is wound around this core
• Linker DNA connects nucleosomes
• Histone H1 is also present

Nucleosome Structure

• DNA in the core consists of 147 bp, wrapped around the protein core one and two-thirds times
• Histone core/octamer consists of H32-H42 tetramer associated w/ two H2A-H2B dimers
• Each histone is extensively interdigitated with its partner
• N-terminal tails extend out of the nucleosome
• Linker DNA measures 8-114 bp
• Its length varies among species and even between the different cells within an organism
• Histone H1 associates with linker DNA
• It is required for 30 nm fiber formation

Histone Tails

• They feature a flexible N-terminus, extending from the nucleosome's globular structure
• Histone tails range from 19 to 39 residues
• H2A and H2B have flexible C-terminus tails
• They enable chromatin to condense from the "beads-on-a-string" form into the 30-nm fiber
• These tails are subject to post-translational modifications

Post-translational Modifications of Histone Tails

• Acetylation, methylation, ubiquitination, sumoylation and phosphorylation are included

Acetylation

• Acetylation involves adding an acetyl group to a lysine residue, such as H4 lys 16
• Chromatin is converted to the less condensed "beads-on-a-string" form
• This is conducive to transcription and replication
• Acetylation at other H4 sites and in other histones correlates with increased chromatin DNA sensitivity to nuclease digestion
• Histone acetyltransferases (HATs) add acetyl groups (Ac) onto histone tails
• Results in a nucleosome opening, allowing transcription factors to access DNA and start gene transcription
• Histone deacetylases (HDACs) remove Ac from the histone tails, causing a closed chromatin structure

Methylation

• Methylation can occur once, twice, or thrice at lysine ε-amino groups of H3 and H4
• Arginine residues also undergo methylation
• Methylation prevents acetylation, thus maintaining positive charge
• The responsible enzyme is histone methyltransferase

Phosphorylation

• Serine and threonine side chains can be reversibly phosphorylated, introducing a negative charge
• It is involved in multiple cellular processes
• Phosphorylation and other post-translational modifications cross-talk extensively
• Various biological processes, including DNA repair and cell cycle progression, are regulated

Phosphorylation of Histones

• Histone H3, H2AX, and H2B phosphorylation regulates transcription and mitotic chromatin condensation
• Additional processes regulated are DNA damage response and apoptosis

Ubiquitination

• Ubiquitin can be reversibly added to a lysine in the C-terminal of H2A and H2B tails
• It usually occurs as monoubiquitination
• It alters chromatin structure, allowing transcriptions proteins access
• Functions as a binding site for proteins that either activate or inhibit transcription
• Induces further post-translational modifications of proteins
• Ubiquitin ligases and deubiquitinating enzymes control monoubiquitination of histones H2A & H2B
• Important post-translational modifications on histone H3 and H4 tails are highlighted

Sumoylation

• Sumoylation is the addition of ubiquitin-like proteins such as SUMO or sentrin
• Only a single residue is added
• Used for protein localization or protection against ubiquitination
• Gene silencing is mediated through recruitment of histone deacetylase
• Proteases can reverse process by cleaving the conjugate from the target protein

Non-Histone Proteins

• Non-histone proteins include scaffold proteins
• In DNA, they are found in scaffold-associated regions (SARs) or matrix-attachment regions (MARs)
• Located at the base of DNA loops observed in histone-depleted metaphase chromosomes
• SARs/MARs are generally found between transcription units
• Genes are located primarily within the chromosome loops

Chromosome structure

• Chromosome structure requires a complete chromatin complex
• The complex contains DNA, histone octamers, and nonhistone chromatin-associated proteins