Structural basis for linker histone H5-nucleosome binding and chromatin fiber compaction

Area of Science:

• Structural Biology
• Epigenetics
• Molecular Biology

Background:

• Chromatin fiber hierarchical packaging is crucial for gene regulation.
• The 30-nm chromatin fiber acts as the initial level of transcriptionally silent chromatin.
• Chromatin fiber dynamics significantly impact DNA-related biological processes.

Purpose of the Study:

• To determine the high-resolution structure of the H5-bound dodecanucleosome, representing the 30-nm chromatin fiber.
• To elucidate the molecular interactions and structural features of linker histone H5 within the chromatin fiber.
• To understand the folding mechanism of nucleosomal arrays into higher-order chromatin structures.

Main Methods:

• Cryo-electron microscopy (cryo-EM) at 3.6 angstrom resolution.
• Atomic structural modeling of the H5-bound chromatin fiber and chromatosome.
• In vitro biophysical experiments and in vivo genetic/genomic studies in Saccharomyces cerevisiae.

Main Results:

• A two-start left-handed double helical structure of the H5-bound chromatin fiber was resolved, organized by tetranucleosomal units.
• Detailed structural information of full-length linker histone H5, including its domains, and its off-dyad binding to the nucleosome via a three-contact mode was obtained.
• Intra- and inter-tetranucleosomal interactions were elucidated at a molecular level.
• Histone tail asymmetries were shown to impart polarity to the chromatin fiber.

Conclusions:

• The study provides a detailed atomic model of the 30-nm chromatin fiber, revealing the role of linker histone H5 in its formation.
• The findings offer molecular insights into the folding of nucleosomal arrays into higher-order chromatin structures with defined polarity.
• This work enhances understanding of chromatin dynamics and gene regulation mechanisms in vitro and in vivo.