Extended Data Fig. 8: Loop size and occurrence of condensin at the stem of DNA loops.
From: The condensin holocomplex cycles dynamically between open and collapsed states
a, DNA loop size distribution for data obtained with ATP, with ATPγS, without ATP, and without Ycg1 (N = 94, 22, 20, and 11 loops from 5, 6, 8, and 5 independent experiments, respectively). The importance of these data lies in the larger loop size observed with ATP as compared to the data in the other three controls. The actual value of the median loop size (0.54 μm in top panel) is in fact rather dependent on experimental conditions (for example incubation time) and limited by our finite imaging area (10 μm × 10 μm) and DNA overlap, which hampers clean identification of large loops in our experiments. Hence, we measured relative small loop sizes (< 1 μm) compared to earlier fluorescence microscopy experiments14. In the data presented here, we measured the size of loops where condensin localized at the stem. b, Loop size comparision in various conditions from a (median ± s.e.m.). c, Schematic to illustrate our estimate of the localization probability of condensin at the stem of the loop versus elsewhere on the DNA. Green circles denote the loop-stem area with a size Dp. Condensin occurring there (red circle) are counted ‘at the loop stem’, whereas all other DNA-bound condensin are counted ‘not at the loop stem’ (blue circle). d, Experimentally measured fractions of DNA-bound condensins that are observed at a loop stem (red), and not at a loop stem (blue) (N = 5 independent experiments). e, Fraction of DNA-bound condensins that are observed at a DNA loop stem (red), and the estimated accidental localization of condensin at a stem of DNA loops (green; N = 5 independent experiments) – see Material and Methods. Errors are s.e.m., and ** indicates P<0.01, assessed using two-tailed Student’s t-test.
