13 public questions tagged with this topic.
A nucleosome helps package DNA into a compact structure by wrapping it around histone proteins.
Ref: NCERT Class 12 Biology Chapter 5: Molecular Basis of Inheritance DNA Structure Double Helix and Packaging - Nucleosome
A nucleosome consists of DNA wrapped around histone proteins with linker DNA in between, but RNA polymerase is not part of it.
Ref: NCERT Class 12 Biology Chapter 5: Molecular Basis of Inheritance DNA Structure Double Helix and Packaging - Nucleosome
During semi-conservative DNA replication parental histone octamer distribution must conserve epigenetic information. Pulse-chase labeling combined with density gradient shows H3-H4 tetramer (H3-H4)2 remains intact as unit, does not split into dimers, segregating randomly to one of two daughter duplexes behind fork. This allows recycling of parental marks like H3K9 methylation to reestablish heterochromatin on both daughters via reader-writer mechanisms. In contrast H2A-H2B dimers exchange rapidly, mixing old and new, H1 readily dissociates. Therefore H3-H4 tetramer conservation underlies epige
Ref: Jackson V 1990 Biochemistry; Alberts et al., Molecular Biology of the Cell, Chapter 5: H3-H4 Tetramer Conservation During Replication
Linking number change measured by topoisomerase I relaxation assay using closed circular plasmids indicates each nucleosome reduces linking number approximately minus 1.2 to minus 1.26. Core particle alone contributes minus 1.0, but additional crossing of linker DNA constrained by H1 adds extra writhe bringing total to minus 1.2. This value originates from Simpson and colleagues SV40 minichromosome studies. Positive 1 would indicate overwinding opposite to nucleosome direction, 0.5 or minus 0.5 would underestimate DNA turns observed by crystallography. Topological storage underlies compaction
Ref: Simpson et al., Cell 1985; Alberts et al., Molecular Biology of the Cell, Chapter 5: Linking Number Change per Nucleosome
Topological analysis demonstrates wrapping DNA in left-handed superhelix around histone octamer introduces negative supercoiling, equivalent to underwinding helix and decreasing linking number. When plasmid DNA assembles into nucleosomes in extracts depleted of topoisomerases, agarose gel electrophoresis with intercalators shows more negative writhe, allowing eukaryotes to store negative supercoils without bacterial gyrase. Right-handed wrapping would create positive supercoiling contrary to observations. H1 binding stabilizes fiber but does not generate writhe, methylation adds epigenetic mar
Ref: Germond et al., PNAS 1975; Lewin, Genes XII, Negative Supercoiling due to Left-handed Wrap
High resolution nucleosome structure at 2.8 angstrom shows histone tails exit core not through gaps at sides but threading between DNA gyres through channels formed where minor grooves face octamer. At specific superhelical locations DNA grooves widen permitting basic tails to protrude without disrupting tight histone-DNA wrapping mediated by arginine anchors. Tail emergence through minor groove allows enzymes like GCN5 acetyltransferase and kinases access for modification while maintaining core stability. Major groove exit would clash with phosphate backbone, linker DNA path distinct from tai
Ref: Luger and Richmond 1998 Crystal; Alberts et al., Molecular Biology of the Cell, Chapter 4: Histone Tail Emergence Minor Groove
Histone N-terminal tails protrude beyond DNA gyres mediating essential internucleosomal interactions crucial for folding beyond beads-on-string. Unmodified tails, particularly H4 residues 16 to 24 highly basic, bind acidic patch formed by H2A glutamates 56,61,64 and H2B helices on adjacent nucleosome, drawing nucleosomes together during 30 nanometer fiber formation as shown by Dorigo tetranucleosome arrays. Acetylation at H4 K16 abolishes affinity, decompacting fiber. Tail removal prevents fiber condensation in vitro. Roles include recruiting modifying and remodeling enzymes, but major structu
Ref: Dorigo et al., Science 2004; Lodish et al., Chapter 8: Histone Tails Function in Chromatin Compaction
Electron microscopy of chromatin isolated in low ionic strength buffer reveals necklace-like organization: 11 nanometer particles spaced by thin linker DNA resembling beads on string. This configuration corresponds to extended primary chromatin fiber without H1-mediated coiling, exposing nucleosomes individually. Solenoid model describes 30 nanometer helix with six nucleosomes per turn, zig-zag describes two-start helix of 30 nanometer fiber, loop fiber denotes scaffold-anchored 300 nanometer domain. Beads-on-string visualization requires low salt to prevent folding, providing classic illustra
Ref: Olins and Olins 1974 J Cell Biol; Alberts et al., Chapter 4: 11 nm Fiber Called Beads-on-String
Quantitation of DNA trajectory around histone octamer shows slightly more than one and half circles. High resolution structures measure 1.65 to 1.67 superhelical turns protecting 147 base pairs, about 83 base pairs per full superhelical turn, creating fourteen histone-DNA contact points via arginine side chains inserted into minor grooves. One turn would protect only 80 base pairs, two full turns would need 166 base pairs which exceeds core length. Value 1.65 explains why linker DNA emerges close together, why H1 can bridge entry exit and sealing two turns, enabling higher order folding into 3
Ref: Luger et al., Nature 1997; Lodish et al., Molecular Cell Biology, 9th ed., 1.65 Turns of DNA
DNA path around histone octamer dictates DNA topology. Around octamer DNA follows left-handed superhelical ramp of approximately 1.65 turns, compensating positive supercoiling generated ahead of replication fork. Upon nucleosome assembly on closed circular plasmid, agarose electrophoresis shows plasmid acquires more negative writhe, measured as linking number decrease, directly proving left-handed wrapping. Right-handed wrap would produce positive supercoiling opposite to experimental observation. Random binding would produce no systematic change, zig-zag describes fiber arrangement not wrappi
Ref: Richmond Structure; Alberts et al., Molecular Biology of the Cell, Chapter 5: DNA Wraps Left-handed Around Octamer
Chromatosome differs from nucleosome core particle by retention of linker histone H1 and extra protected DNA length. Core particle with octamer protects 147 base pairs, but complete chromatosome containing H1 protects additional twenty base pairs, ten on each side beyond core entry, totaling 167 base pairs. Measurement obtained by micrococcal nuclease digestion followed by DNA sequencing of protected fragments when H1 retained; extensive digestion removes H1 reducing fragment to 147 base pairs core. Universally reported value 167 base pairs defines functional unit before 30 nanometer fiber for
Ref: Simpson RT 1978 J Biol Chem 273; NCBI Bookshelf, Chapter 4: Chromatosome 167 bp Total Length
Linker DNA connecting adjacent nucleosomes constitutes binding site for fifth histone family distinct from core. H1 binds at dyad axis where DNA enters and exits octamer, globular winged-helix domain contacts both linkers while lysine-rich C-terminal tail neutralizes linker DNA charge. Interaction seals nucleosome, determines exit angle and promotes 30 nanometer fiber folding into solenoid or zigzag conformations. Core histones H2A, H2B, H3 remain buried inside octamer forming handshake motifs, not contacting linker extensively. Therefore H1 classifies as linker histone easily extracted at mod
Ref: Allan et al., J Mol Biol 1980; Alberts et al., Molecular Biology of the Cell, Chapter 4: Linker Histone H1 Chromatosome
