Histones and packaging

Histones and packaging

1. Chromatin

   • The nucleosome
     • Made of
       • Histones
         • = most common nuclear proteins
         • Account for almost half of the proteins in DNA
         • Core histones
           • H2A
             • x2 = 28Kda
             • H2A variants
               • H2A.Z
                 • Found in nearly all eukaryotes
                   • Alters interaction stability between H2A and H2B
                     • Alters interaction between H2A:H2B tetramer
                       • Alters canonical nucleosome
                         • Makes chromatin transcriptionally active
               • H2A.X
                 • Phosphorylated at double strand breaks
               • H2A.Bbd
                 • Vertebrate specific
                   • Depleted on Xi
               • macroH2A
                 • Vertebrate specific
                   • Enriched Xi
           • H2B
             • x2 = 28Kda
           • H3
             • x2 = 30Kda
             • H3 variants
               • H3.1
               • H3.2
               • H3.3
               • H3.1t
               • Cenp
           • H4
             • x2 = 22kDa
           • Variants of H3 and H2A alter chromatin
             • Activate genes
               • Form heterochromatin
         • Linker histone
           • H1
             • x1 = 24Kda
         • All contain an N-terminal tail
           • Undergo covalent modification
       • 146bp of DNA
         • Left handed superhelix
           • 200bp DNA
             • = 130 Kda
     • Structure
       • Octameric Histone core
         • Histone fold
           • H3+H4 tetramer binds to H2A + H2B dimer --> histone core
             • H2A + H2B dimers
               • Histone handshake
                 • Increase stability
             • H3 + H4 dimer --> tetramer (H3:H4)2
               • H3 + H4 dimers
                 • Histone handshake
       • DNA double helix
         • Any DNA sequence can be wound
           • 1/5 of amino acids = basic
             • Positively charged
               • Neutralises negative phosphate backbone of DNA
                 • Therefore any DNA can bind to histone core
         • Has kinks
           • Some DNA sequences bind more titily to the octamer than others
     • The 10nm fibre
       • Looks like beads on a string
       • The most open chromatin can be
       • 20-30 bp between nucleosomes
         • These bp = linker DNA
       • 30nm Solenoid
         • 300nm Solenoid
           • Coiled 30nm solenoid
             • Coiled using protein scaffolds
               • Non-histone protein scaffolds
           • Transcriptionally silent
           • Long histone proteins keep them sufficiently open
             • To enable unravelling when necessary
               • To enable transcription
           • Coiled coil - 700nM fibre
             • Loop of chromatin coils again
               • Highly condensed
                 • No transcription or replication
             • Additional nonhistone scaffold components
             • Entire mitotic chromosome
               • Heterochromatin
                 • Highly condensed chromatin
                   • Facultative
                     • Can become transcriptionally active
                   • Constituitive
                     • Genes in consitituitive heterochromatin regions --> poorly expressed
                     • Consistent within the cell of all species
                 • Centromeres, telomeres and restricted regions of chromosome are heterochromatin
                 • Highly compact in interphase
                 • Few genes present
                 • Replicated late in S phase
               • Euchromatin
                 • Open chromatin structure
                 • Replicated early in S phase
                 • Contians both transcriptionally active and inactive genes
               • Transcriptionally silent
                 • Necessary as you are about to replicate DNA
               • 10,000 fold shorter than its original length
         • 10nm fibre further coils
           • H1 histone is essential for this packaging
             • H1 sits in the centre of each turn