#chromatin structure

Basics of Cell Biology

Which of the following is a characteristic of euchromatin?

Chromatin packaging varies dynamically to regulate transcription, replication timing, and repair accessibility. Euchromatin corresponds to decondensed 11 nanometer beads-on-string fiber loosely arranged, staining lightly in interphase nuclei under electron microscopy, preferentially located in interior away from nuclear lamina, enriched in active housekeeping and developmentally regulated genes, characterized by post-translational modifications including histone H3 lysine 4 trimethylation at transcription start sites deposited by SET1/MLL methyltransferase complexes, H3K27 acetylation marking active enhancers by p300/CBP acetyltransferases, incorporation of histone variant H3.3 and high overall acetylation recognized by bromodomain reader proteins and chromatin remodelers SWI/SNF that mobilize nucleosomes to allow access of RNA polymerase II and transcription factors. It is DNase I hypersensitive and ATAC-seq positive indicating open accessibility, early replicating in S phase, less condensed than mitotic chromosomes, interspersed with non-coding regions. In contrast heterochromatin is highly condensed, late replicating, H3K9me3 and HP1 bound, transcriptionally silent, often repeat-rich at centromeres and telomeres, illustrating active compartment distinction maintained by dynamic modifications.

Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 4: Euchromatin Structure and Transcription.

View Details

Regulation of chromatin structure

What happens if two DNA-binding proteins bind closer than 147 bp?

Nucleosome formation requires approximately 147 base pairs of DNA wrapping 1.65 turns around histone octamer plus accessible linker. When sequence-specific DNA binding proteins occupy sites less than this distance apart, steric hindrance prevents octamer deposition because binding proteins block wrapping path and compete for major groove contacts. In vitro reconstitution shows that tight clustering of transcription factors, insulators or polymerases creates nucleosome-depleted regions, while cooperative positioning can generate phased arrays adjacent to barriers. This principle underlies promoter architecture where regulatory factor clusters maintain open chromatin for transcriptional initiation.

Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 4: Nucleosome Positioning and Barrier Models

View Details

Regulation of chromatin structure

Which histone modification loosens DNA-histone interaction?

Lysine acetylation directly weakens histone-DNA electrostatic attraction. Transfer of acetyl from acetyl-CoA to ε-amino group removes positive charge, reducing net basic character of tail and diminishing binding to phosphate backbone. Structural studies reveal increased tail disorder, enhanced nucleosome breathing and greater accessibility for transcription factors. Bromodomain proteins further recognize acetyl-lysine, recruiting remodelers that slide or eject nucleosomes. Functionally, hyperacetylation at promoters and enhancers correlates with euchromatin formation, while deacetylation restores compaction. This biophysical effect distinguishes acetylation from methylation that preserves charge.

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 8: Acetylation Loosens DNA-Histone Interaction, Chromatin Opening

View Details

Regulation of chromatin structure

Which protein domain interacts with unmodified histone tails?

Reader domains distinguish modification state of histone tails to translate histone code into functional outcomes. SANT domains, named after Swi3, Ada2, N-Cor, TFIIIB, are structurally related to Myb DNA-binding motifs and found in co-repressor and remodeling subunits including SMRT, Ada2 and ISWI. Biochemical studies show SANT2 of SMRT and SANT of Ada2 preferentially bind unacetylated H3 and H4 tails, increasing affinity of associated deacetylase and acetyltransferase complexes for hypoacetylated substrates. Tetracetylation of H4 disrupts this interaction, illustrating sensitivity to modification status without direct recognition of methyl or acetyl marks.

Ref: Guo et al., Nature Scientific Reports, EZH2 SANT1 Domain Reads Unmodified H4 Tail, Structural Basis

View Details

Regulation of chromatin structure

Which DNA feature favors nucleosome positioning?

Genome-wide nucleosome positioning maps reveal sequence features influencing octamer affinity. Experimental SELEX and computational models show DNA sequences where AT-rich minor grooves face inward compress more easily, alternating AT/GC every five base pairs, approximately half helical turn, aligns flexible pyrimidine-purine steps with curvature required around histone, reducing elastic energy cost of wrapping stiff DNA. Poly-A tracts rigid and intrinsically curved disfavor nucleosomes acting as excluding signals, random sequence intermediate, pure GC stretches less bendable. Periodic AT/GC pattern predicts nucleosome occupancy, positioning at promoters and transcription start site depletion, guiding transcriptional regulation across eukaryotic genomes.

Ref: Satchwell et al., J Mol Biol 1986; Segal et al., Nature 2006: DNA Feature Favoring Nucleosome Positioning AT/GC Periodicity

View Details

Regulation of chromatin structure

Which histone variant replaces H3 at the centromere?

Centromere identity epigenetically marked by incorporation of histone H3 variant CENP-A instead of canonical H3, producing specialized nucleosomes that survive throughout cell cycle and are replenished after replication. CENP-A contains centromere targeting domain CATD within histone fold, divergent N-terminus replaced, deposited specifically by HJURP chaperone complex at centromeres during early G1. H3.3 variant replaces H3 at actively transcribed genes and regulatory elements, H2A.Z at promoter flanks, H2A.X marks DNA double strand break sites. CENP-A depletion causes centromere inactivation, chromosome loss and aneuploidy. Therefore CENP-A represents H3 variant defining centromere.

Ref: Palmer et al., 1991 and Black et al., 2007; Lodish et al., Chapter 8: CENP-A Variant Replaces H3 at Centromere

View Details

Regulation of chromatin structure

Which histone tail modification is mainly associated with chromatin opening?

Chromatin accessibility regulated by chemical state of histone tails altering net charge. Among modifications, lysine acetylation catalyzed by HAT families GCN5, p300, Myst neutralizes epsilon-amino positive charge, weakening histone-DNA electrostatic contacts and disrupting internucleosomal H4 tail-acidic patch interaction essential for 30 nanometer fiber condensation, thereby promoting open euchromatic state. Methylation retains positive charge and can recruit repressors or activators depending context, phosphorylation adds negative charge mainly signaling mitosis or damage rather than general opening, ubiquitination adds bulky 76 amino acid protein altering stability. Therefore acetylation most directly linked to chromatin opening.

Ref: Allfrey et al., 1964; Lodish et al., Molecular Cell Biology, 9th ed., Histone Tail Modification Mainly Acetylation Opening

View Details

Nucleosome Packing

Main driving force for DNA bending around histones is:

Bending rigid DNA duplex around small histone octamer radius about 4.2 nanometers overcomes electrostatic repulsion and mechanical stiffness. Strong driving force arises from extensive attractive interactions between positively charged lysine and arginine side chains lining histone octamer superhelical ramp and negatively charged phosphate groups, plus multitude hydrogen bonds between histone main chain amides and DNA backbone phosphates and numerous water-mediated contacts. Charge neutralization lowers energetic barrier permitting sharp curvature. Hydrophobic interactions stabilize octamer core internal assembly, but DNA-histone attraction via electrostatics and hydrogen bonding governs bending energetics, not covalent bonds or dispersive forces alone.

Ref: Luger et al., Nature 1997 Structure; Lodish et al., Chapter 8: Driving Force DNA Bending Charge Neutralization

View Details

Nucleosome Packing

The nucleosome core particle contains how many histone proteins?

Biochemical reconstitution and high resolution crystal structures confirm nucleosome core particle comprises exactly eight histone proteins forming disc. Two copies each of canonical H2A, H2B, H3, H4 assemble as octamer shaping 11 nanometer particle. Central kernel forms H3-H4 tetramer via four-helix bundle through H3-H3 interface, while two H2A-H2B dimers dock on sides contacting outer DNA wraps. Six histones would destabilize wrapping, ten or twelve exceed structural capacity supported by stoichiometry measurements. Micrococcal nuclease protection and ultracentrifugation correspond to octamer alone, fundamental compaction unit conserved throughout eukaryotes.

Ref: Luger K. et al., Nature 1997 2.8 Å Structure; Alberts et al., Chapter 4: Nucleosome Eight Histones Octamer

View Details

Eukaryotic chromatin and chromosome

DNA methylation usually causes:

DNA methylation at 5-methylcytosine within CpG context catalyzed by DNMT1 maintenance during replication and DNMT3A/3B de novo enzymes generally correlates with stable gene silencing. Methyl-CpG recruits methyl-binding domain proteins MeCP2, MBD1, MBD2 which recruit histone deacetylase complexes and H3K9 methyltransferases, generating compact repressive chromatin impeding transcription factor access. Promoter methylation blocks initiation and maintains X inactivation and genomic imprinting. Removal via TET-mediated hydroxymethylation restores activity, confirming methylation predominantly represses transcription rather than activating replication or recombination alone in differentiated tissues.

Ref: Bird and Wolffe 1999 Methylation Mechanisms; Lodish et al., Chapter 8: DNA Methylation Usually Causes Repression

View Details

Eukaryotic chromatin and chromosome

Chromatosome includes:

Limited nuclease digestion in presence of H1 yields larger protected fragment than core alone. Chromatosome comprises nucleosome core particle of 147 base pairs wrapped around octamer plus additional twenty base pairs of linker DNA, ten on each side of entry exit, sealed by globular winged-helix domain of histone H1 contacts. Total DNA content becomes about 167 base pairs, determined by sequencing H1-containing fragments. Structurally H1 locks DNA crossover angle, directing trajectory of adjacent linkers for higher-order folding and reducing entry-exit breathing. Chromatosome represents complete structural unit of condensed chromatin before 30 nanometer fiber assembly.

Ref: Simpson RT 1978 J Biol Chem; Alberts et al., Molecular Biology of the Cell, Chapter 4: Chromatosome Core plus H1 167 bp

View Details

Eukaryotic chromatin and chromosome

Nucleosome repeat length in humans is ~:

Nucleosome repeat length encompasses DNA protected in core plus intervening linker. Micrococcal nuclease partial digestion of human chromatin followed by agarose gel electrophoresis shows regular ladder with approximately 200 base pair increment. Core particle contributes 147 base pairs wrapped around octamer, linker adds 20 to 60 base pairs varying by cell type, average about 53 base pairs in humans, giving total near 200 base pairs. This spacing dictates H1 binding stoichiometry and ability to fold into 30 nanometer fiber. Shorter repeats occur in yeast about 165 base pairs, longer in cortical neurons.

Ref: van Holde, Chromatin 1989 Structure; Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 4: Repeat Length Humans 200 bp

View Details