Journal Article

Angle between DNA linker and nucleosome core particle regulates array compaction revealed by individual-particle cryo-electron tomography

Bustamante, Carlos, Liu, Jianfang, Tao, Jinhui, Zhang, Meng, Ren, Gang, Díaz-Celis, César, Ashby, Paul D.

2024

Overview

The conformational dynamics of nucleosome arrays generate a diverse spectrum of microscopic states, posing challenges to their structural determination. Leveraging cryogenic electron tomography (cryo-ET), we determine the three-dimensional (3D) structures of individual mononucleosomes and arrays comprising di-, tri-, and tetranucleosomes. By slowing the rate of condensation through a reduction in ionic strength, we probe the intra-array structural transitions that precede inter-array interactions and liquid droplet formation. Under these conditions, the arrays exhibite irregular zig-zag conformations with loose packing. Increasing the ionic strength promoted intra-array compaction, yet we do not observe the previously reported regular 30-nanometer fibers. Interestingly, the presence of H1 do not induce array compaction; instead, one-third of the arrays display nucleosomes invaded by foreign DNA, suggesting an alternative role for H1 in chromatin network construction. We also find that the crucial parameter determining the structure adopted by chromatin arrays is the angle between the entry and exit of the DNA and the corresponding tangents to the nucleosomal disc. Our results provide insights into the initial stages of intra-array compaction, a critical precursor to condensation in the regulation of chromatin organization. Here, using cryo-ET, the 3D structures of individual nucleosome particles were characterized to observe changes under varying ionic strengths and in the presence of protein H1, revealing key regulatory roles in chromatin organization dynamics.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 101/28 / 101/47 / 631/1647/245/2160 / 631/337/572/2102 / 631/45/147 / 631/45/535/1258/1260 / 631/57/2265 / 82/79 / Animals / Arrays / BASIC BIOLOGICAL SCIENCES / Chromatin / Chromatin - chemistry / Chromatin - metabolism / Chromatin - ultrastructure / Compaction / Core particles / cryo-electron tomography / Cryoelectron Microscopy - methods / Deoxyribonucleic acid / DNA / DNA - chemistry / DNA - metabolism / Electron Microscope Tomography - methods / fluctuation and dynamics / Histones - chemistry / Histones - metabolism / Humanities and Social Sciences / individual-particle electron tomography / Ionic strength / linker histone H1 / molecular imaging / multidisciplinary / Nucleic Acid Conformation / Nucleosome / Nucleosomes / Nucleosomes - chemistry / Nucleosomes - metabolism / Nucleosomes - ultrastructure / Osmolar Concentration / Science / Science (multidisciplinary) / single-molecule 3D structure / single-molecule biophysics / Tangents / Tomography / transcriptional regulatory elements