Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

Internucleosome Interactions in Chromatin Higher-order Fibers

The architecture of the chromatin fiber, which determines DNA accessibility for transcription and other template-directed biological processes, remains unknown. We examined the internal organization of the 30 nm chromatin fiber with a new EM-assisted nucleosome interaction capture (EMANIC). This experimental technique uses formaldehyde crosslinking to fix a limited number of internucleosome contacts in the condensed state, after which the chromatin is decondensed at low salt, and transmission EM is used to provide a quantitative assessment of nucleosome-to-nucleosome contacts. We constructed biochemically defined nucleosome arrays with either uniform or variable nucleosome positioning and examined these arrays as well as native chromatin using EMANIC. For chromatin condensed at physiological salt concentration of monovalent cation (Na+), our experiments revealed a nucleosome interaction pattern consistent with predominantly straight linkers and a two-start helical arrangement of nucleosome cores and showed that nucleosomal arrays containing irregularly positioned nucleosomes are compacted as tightly as regular chromatin. However, the nucleosome fibers also contained a detectable amount of nucleosome interactions resulting from bent DNA linkers and the number of such interactions was significantly increased when chromatin condensation was promoted by a physiological divalent cation (Mg2+). 3D chromatin fiber modeling suggests that linker DNA crossed in the middle of the fiber hinders its longitudinal compaction. Remarkably, bending of one linker per 5-6 nucleosomes promotes a significant longitudinal compaction of the chromatin fiber and allows the nucleosomes to form tighter interactions between adjacent nucleosomes. Our data are in an excellent agreement with results of Monte Carlo simulations of a coarse-grained "mesoscale" chromatin fiber model by G.Arya and T.Schlick. Taken together, our results reconcile the two-start zigzag topology with the type of linker DNA bending that defines solenoid models in a single polymorphic chromatin fiber structure. We discuss our findings in relation to the mechanism(s) that regulate chromatin fiber packing towards either dynamic folding in proliferating cells or global self-association that underlie the condensed heterochromatin of terminally differentiated and senescent cells.

Sergei A. Grigoryev1
Sarah Correll1
Christopher L. Woodcock2

1Penn State University
Dept Biochemistry & Molecular Biology
Hershey, PA 17033
2Biology Department
University of Massachusetts
Amherst, MA 01003

Tel: 717-531-8588
email: sag17@psu.edu