Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques

Kerstin Bystricky; Patrick Heun; Lutz Gehlen; Jörg Langowski; Susan M. Gasser

doi:10.1073/pnas.0402766101

New Research In

Edited by Nicholas R. Cozzarelli, University of California, Berkeley, CA, and approved October 7, 2004 (received for review April 19, 2004)

Abstract

Little is known about how chromatin folds in its native state. Using optimized in situ hybridization and live imaging techniques have determined compaction ratios and fiber flexibility for interphase chromatin in budding yeast. Unlike previous studies, ours examines nonrepetitive chromatin at intervals short enough to be meaningful for yeast chromosomes and functional domains in higher eukaryotes. We reconcile high-resolution fluorescence in situ hybridization data from intervals of 14–100 kb along single chromatids with measurements of whole chromosome arms (122–623 kb in length), monitored in intact cells through the targeted binding of bacterial repressors fused to GFP derivatives. The results are interpreted with a flexible polymer model and suggest that interphase chromatin exists in a compact higher-order conformation with a persistence length of 170–220 nm and a mass density of ≈110–150 bp/nm. These values are equivalent to 7–10 nucleosomes per 11-nm turn within a 30-nm-like fiber structure. Comparison of long and short chromatid arm measurements demonstrates that chromatin fiber extension is also influenced by nuclear geometry. The observation of this surprisingly compact chromatin structure for transcriptionally competent chromatin in living yeast cells suggests that the passage of RNA polymerase II requires a very transient unfolding of higher-order chromatin structure.

Footnotes

↵ ¶ To whom correspondence should be sent at the present address: Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland. E-mail: susan.gasser{at}fmi.ch.
↵ † Present address: Laboratoire de Biologie Moléculaire Eucaryote, IFR109, Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse, France.
↵ ‡ Present address: Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720.
Author contributions: K.B., P.H., and S.M.G. designed research; K.B., P.H., and L.G. performed research; K.B., L.G., J.L., and S.M.G. analyzed data; K.B., P.H., and S.M.G. contributed new reagents/analytic tools; and K.B., J.L., and S.M.G. wrote the paper.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations: FISH, fluorescence in situ hybridization; Lp, persistence length; IF, immunofluorescence; YFP, yellow fluorescent protein; CFP, cyan fluorescent protein; SPB, spindle pole body; Chr, chromosome; NCP, nucleosome core particle.
Copyright © 2004, The National Academy of Sciences