The effect of linker DNA on the structure and interaction of nucleosome core particles

Abstract

In eukaryotes, the compaction of chromatin fibers composed of nucleosome core particles (NCPs) connected by a linker DNA into chromosomes is highly efficient; however, the underlying folding mechanisms remain elusive. We used small angle X-ray scattering (SAXS) to investigate the influence of linker DNA length on the local structure and the interparticle interactions of the NCPs. In the presence of the linker DNA of 30 bp or less in length, the results suggest partial unwrapping of nucleosomal DNA on the NCP irrespective of the linker DNA length. Moreover, the presence of 15 bp linker DNA alleviated the electrostatic repulsion between the NCPs and prevented the formation of an ordered columnar hexagonal phase, demonstrating that the linker DNA plays an active role in chromatin folding.

Linker histone defines structure and self-association behaviour of the 177 bp human chromatosome

“…The lower intensity in that area may be caused by more flexible linker DNA arms in solution compared to the crystal and Cryo-EM structures, which results in the transient unwrapping of DNA. DNA unwrapping from the HO was demonstrated to produce a comparable effect on the SAXS spectrum 40 and observed in solutions of NCPs with tailless H3 and H4 39 . The increased values of R g and D max from the SAXS study suggest dynamic differences in the structure of the chromatosome compared to the nucleosome, and the result indicates an influence of the linker histone as a structural factor in linker DNA compaction of the nucleosome.…”

“…R g values calculated from the distance distribution function P(r), from SAXS data for the 147 bp NCP, were previously reported to be around 42 Å in low salt conditions 36,40,41 . The R g values of the 177 bp nucleosome (47.6 Å) and the chromatosome (49.4 Å) found in this work (Table S1) are more significant due to the presence of linker DNA, and linker histone, respectively.…”

“…It was previously shown that NCPs form a columnar hexagonal phase made of domains (microcrystallites) with 20-30 columns, each consisting of 40-50 NCPs with a domain size of a few hundred nm 61 . It may also be noted that the hexagonal columnar phase can be detected either by direct SAXS experiments on the turbid solution or on the pellet obtained after centrifugation, resulting in identical ordered phase 40,61 . The resulting SAXS spectra are shown in Fig.…”

The human telomeric nucleosome displays distinct structural and dynamic properties

“…This conclusion was also supported by dynamic light scattering investigations, which displayed a larger hydrodynamic diameter for Telo-NCP in comparison with 601-NCP (data not shown). Earlier works have shown that the depth of the dip in the NCP SAXS spectrum at 0.14 Å -1 is sensitive to DNA unwrapping (71)(72)(73)(74). The NCP at low concentration (1-2.5 mg/mL) in low salt buffer (10 mM KCl) exhibit minimal inter-particle interactions, thereby facilitating the study of the form factor of the NCP SAXS spectrum (52).…”

Influence of Linker DNA on Nucleosome Structure according to Single-Particle Fluorescence Microscopy Data

“…В настоящее время значительная часть таких исследований выполняется на корнуклеосомах, не имеющих линкерных участков ДНК (линкеров) [1,6,7]. В других случаях изучаемые нуклеосомы имеют линкеры (один или два), а их длина изменяется в широких пределах [1,2,4,5,8]. При столь широкой вариабельности используемых мононуклеосом возникают вопросы о возможной зависимости результатов изучения молекулярных взаимодействий от наличия, числа и длины линкеров, а также о правомерности прямого сравнения данных, полученных в различных исследованиях.…”