Archaeal chromatin ‘slinkies’ are inherently dynamic complexes with deflected DNA wrapping pathways
Open Access
- 2 March 2021
- journal article
- research article
- Published by eLife Sciences Publications, Ltd in eLife
Abstract
Eukaryotes and many archaea package their DNA with histones. While the four eukaryotic histones wrap ~147 DNA base pairs into nucleosomes, archaeal histones form ‘nucleosome-like’ complexes that continuously wind between 60 and 500 base pairs of DNA (‘archaeasomes’), suggested by crystal contacts and analysis of cellular chromatin. Solution structures of large archaeasomes (>90 DNA base pairs) have never been directly observed. Here, we utilize molecular dynamics simulations, analytical ultracentrifugation, and cryoEM to structurally characterize the solution state of archaeasomes on longer DNA. Simulations reveal dynamics of increased accessibility without disruption of DNA-binding or tetramerization interfaces. Mg2+ concentration influences compaction, and cryoEM densities illustrate that DNA is wrapped in consecutive substates arranged 90o out-of-plane with one another. Without ATP-dependent remodelers, archaea may leverage these inherent dynamics to balance chromatin packing and accessibility.Keywords
Funding Information
- National Science Foundation (1552743)
- National Institute of General Medical Sciences (R35GM119647)
- Howard Hughes Medical Institute
- National Institute of General Medical Sciences (F32GM137496)
This publication has 55 references indexed in Scilit:
- Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifsBMC Genomics, 2013
- An Archaeal Histone Is Required for Transformation of Thermococcus kodakarensisJournal of Bacteriology, 2012
- Perceiving the epigenetic landscape through histone readersNature Structural & Molecular Biology, 2012
- Histone H2A variants in nucleosomes and chromatin: more or less stable?Nucleic Acids Research, 2012
- The implementation of SOMO (SOlution MOdeller) in the UltraScan analytical ultracentrifugation data analysis suite: enhanced capabilities allow the reliable hydrodynamic modeling of virtually any kind of biomacromoleculeEuropean Biophysics Journal, 2009
- Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular SimulationsThe Journal of Physical Chemistry B, 2008
- Archaeal histones and the origin of the histone foldCurrent Opinion in Microbiology, 2006
- New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioningJournal of Molecular Biology, 1998
- VMD: Visual molecular dynamicsJournal of Molecular Graphics, 1996
- Comparison of simple potential functions for simulating liquid waterThe Journal of Chemical Physics, 1983