Table 1.

Properties of nucleosomes and transcription sites

Transcription site
Property Nucleosome Immunogold Correlative Unpermeabilised
Diameter (nm)
   Uncorrected 11 96±31 103±22 109±26
   Corrected* 11 87 94 102
P:N ratio 1.0±0.1 0.38±0.12 0.26±0.07 0.38±0.07
Number of atoms
   P 292 4800 6500 8700
   N 2605 198,000 204,000 208,000
Equivalents§
   Nucleosome (P) 1 17 22 30
   Nucleosome (N) 1 75 115 113
   Polymerase II (N) 0.4 28 28 27
Mass (MDa)§
   Nucleic acid 0.10 1.7 2.1 3.0
   Protein 0.11 8.3 12.7 12.4
   Total 0.21 10 15 15.4
Density§
   P atoms/nm3 0.42 0.14 0.15 0.16
   N atoms/nm3 3.8 0.57 0.47 0.38
   Da/nm3 300 29 34 28
Property Chromatin GC IGC
P:N ratio 1.0±0.1 0.8±0.1 0.5±0.07
Density§
   P atoms/nm3 0.03 0.025 0.029
   N atoms/nm3 0.17 0.27 0.24
Da/nm3 17 20 20
  • Values are means (±s.d.) obtained for ⩾330 nucleosomes, and 55, 10 and 14 sites detected by immunogold labelling (e.g. Fig. 4), correlative microscopy (e.g. Fig. 5A-E) or in unpermeabilised cells (e.g. Fig. 5F-H), respectively. See Materials and Methods for procedures and assumptions

  • * Corrected for `Holmes' effect

  • Ratio of intensity (arbitrary units/pixel) after subtracting background in resin. Politz et al. (Politz et al., 2005) used ESI and nucleosomes as references to obtain P:N ratios in atoms of 0.13 (chromatin) and 0.08 (GC); these compare with our values (not shown) of 0.14 (chromatin), 0.09 (GC), and 0.12 (IGC)

  • Values for sites calculated from the area and average P or N intensity/pixel compared with nucleosome, corrected for the loss of polar caps that occurs when an 87 nm sphere is placed centrally in a 70 nm section

  • § From relative number of atoms