Single-molecule compaction of megabase-long chromatin molecules by multivalent cations

Abstract

To gain insight into the conformational properties and compaction of megabase-long chromatin molecules, we reconstituted chromatin from T4 phage DNA (165 kb) and recombinant human histone octamers (HO). The unimolecular compaction, induced by divalent Mg2+ or tetravalent spermine4+ cations, studied by single-molecule fluorescence microscopy (FM) and dynamic light scattering (DLS) techniques, resulted in the formation of 250–400 nm chromatin condensates. The compaction on this scale of DNA size is comparable to that of chromatin topologically associated domains (TAD) in vivo. Variation of HO loading revealed a number of unique features related to the efficiency of chromatin compaction by multivalent cations, the mechanism of compaction, and the character of partly compact chromatin structures. The observations may be relevant for how DNA accessibility in chromatin is maintained. Compaction of saturated chromatin, in turn, is accompanied by an intra-chain segregation at the level of single chromatin molecules, suggesting an intriguing scenario of selective activation/deactivation of DNA as a result of chromatin fiber heterogeneity due to the nucleosome positioning. We suggest that this chromatin, reconstituted on megabase-long DNA because of its large size, is a useful model of eukaryotic chromatin.

Chromatin state switching in a polymer model with mark-conformation coupling

“…polymer with R ∼ N 1/3 [24], upon changing the overall twobody interaction (in the present case, v − i, j J i j x i x j ) from repulsive to attractive. Such coil-globule transitions have been observed in experiments using DNA [31] and chromatin [32]. The coil-globule transition in this case is continuous in the limit of N → ∞ [24], even beyond the mean-field approximation [25,26].…”

Marked Difference in the Conformational Transition of DNA Caused by Propanol Isomer

“…The high-order structural transition of DNA between elongated coil and compact globule states, the so-called coil–globule transition, is one of the central problems in the fields of biochemistry, biophysics, and soft matter physics. Many studies have examined this problem from both theoretical and experimental approaches [ 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 ]. Over the past couple of decades, it has been established that large DNA above the size of several tens of kilo base pairs (kbp) exhibits unique conformational characteristics, including the occurrence of discrete, or on/off, transition between the elongated coil and compact globule states on individual DNA molecular chain, as demonstrated by single-molecule observation in bulk solutions using fluorescence microscopy [ 28 , 32 , 35 , 39 ].…”

A nucleosome-free region locally abrogates histone H1–dependent restriction of linker DNA accessibility in chromatin

“…Such condensation requires internucleosome interactions mediated through the core histone tail domains (4 -8). Importantly, reconstituted arrays containing only core histones and defined DNA templates recapitulate the behavior of native chromatin with regard to salt-dependent folding and compaction (1,3,9). Oligonucleosome arrays lack-ing H1 exist as extended "beads on a string" structures (defined as primary chromatin structure (10)) in low ionic strength buffers in vitro but equilibrate between moderately compacted and fully folded secondary structures such as the chromatin fiber in 0.5-2 mM MgCl 2 .…”