Cryo-EM reveals fine structural details of human chromatin remodeler in action

Chromatin remodeling plays a vital role in gene regulation, affecting how DNA is accessed. Disruptions in this process can also lead to cancer and other diseases. To better understand how chromatin remodeling works, scientists at St. Jude Children's Research Hospital used cryo-electron microscopy (cryo-EM) to obtain fine structural details of a human chromatin remodeler in action. The researchers captured 13 structures that together offer a comprehensive view of how the remodeling enzyme SNF2H works, offering insights that are likely shared across other such enzymes. The work was published today in Cell Research.

Chromatin comprises sections of DNA wrapped around proteins called histones to form nucleosomes collectively. One chromatin remodeling mechanism called "nucleosome sliding" allows a nucleosome to be "moved" to control gene access, but how this works has been incompletely understood. To address this gap, Mario Halic, PhD, St. Jude Department of Structural Biology, used cryo-EM to capture the chromatin remodeling enzyme SNF2H in action.

Previous work typically captured snapshots of the remodeler 'frozen' in some state. Here we were able to visualize the continuous motion of a chromatin remodeling enzyme while moving DNA on the nucleosome."

Mario Halic, PhD, St. Jude Department of Structural Biology

Teasing out the finer details of remodeling

SNF2H is a key enzyme in nucleosome remodeling, disruption of which has been associated with developmental disorders. Like other chromatin remodelers, SNF2H uses the energy from ATP hydrolysis to slide nucleosomes. Extensive studies have contributed to understanding the process by providing snapshots of SNF2H trapped in different states. In contrast, Halic and his team looked at SNF2H interacting with nucleosomes in the presence of ATP, thus capturing the enzyme in action.

Methodical data analysis led the researchers to obtain 13 distinct structures of the SNF2H-nucleosome complex at various intermediate points along the nucleosome sliding process. Arranging these into five groups allowed the researchers to trace the enzyme's steps and reveal the full dynamic picture of nucleosome sliding. 

The researchers gauged the functional importance of various interactions within the structure by introducing specific mutations and crosslinks - artificial restraints that lock a protein in a shape to test the significance of particular movements to the protein's function. This work allowed them to tease out previously conflicting observations to compile a comprehensive account of how nucleosome sliding works and its impact on gene regulation.

"Nucleosomes carry all the genetic information inside the nucleus of the eukaryotic cell. Chromatin remodelers help the cell access and propagate that information," said co-first author Deepshikha Malik, PhD. "Dissecting the mechanics of remodelers' action on nucleosomes is important to understand how our genome is expressed."

Authors and funding

The study's other co-first author is Ashish Deshmukh, St. Jude. The study's other author is Silvija Bilokapic, St. Jude.

The study was supported by grants from the National Institutes of Health (1R01GM135599 and 1R01GM141694) and the American Lebanese Syrian Associated Charities (ALSAC), the fundraising and awareness organization of St. Jude.