Actin-related proteins rule in nucleosome remodeling

From Dr. Sandipan Brahma, in the Henikoff lab, Basic Sciences Division

In eukaryotes, DNA is tightly wound into a complex structure called chromatin. The basic packaging unit of DNA is the nucleosome core, consisting of 147 bp of DNA tightly wrapped around a histone octamer. A linker DNA, with length varying from 20 bp to 90 bp, depending on the organism and cell type, separates nucleosomal cores.

For gene expression to occur, nucleosomal DNA has to be made accessible for the binding of sequence specific regulators. One of the processes involves molecules called chromatin remodelers that displace the histone octamers from DNA or translocate them onto neighboring DNA segments, thereby exposing underlying DNA sequences to sequence specific regulatory factors. Chromatin remodeling complexes are multi-protein assemblies containing an ATPase subunit capable of mobilizing the nucleosomes using the energy of ATP hydrolysis to alter chromatin structure. Additionally, they harbor 2 to 20 non-catalytic subunits required for targeting and regulating distinct nucleosome positioning activities of remodeling complexes. Therefore, ATP-dependent chromatin remodelers are largely responsible for establishing and maintaining promoter chromatin architecture, thereby regulating gene expression. They are an area of interest for Dr. Sandipan Brahma, currently a postdoc in the Henikoff lab in the Basic Sciences division, who has been working in this field since he was a graduate student.

Dr. Brahma explains his interest in the chromatin remodeling complex he worked on in graduate school with Blaine Bartholomew at MD Anderson Cancer Center: “INO80 is the only remodeler in budding yeast that can, without any additional protein factors, accurately reposition nucleosomes at the large majority of gene promoters to their in vivo canonical locations, and the actin-related Arp8 subunit is indispensable for this activity. Interestingly, although actin in eukaryotic nuclei was found as early as in 1963, the presence and functions of nuclear actin and actin-like proteins were debated until even the last decade.” Dr. Brahma’s work as a graduate student, published in Nature Communications, highlights the specific roles of actin-related proteins in chromatin organization in yeast.


Schematic figure of how actin-related proteins can act as a DNA sensor to effect allosteric changes in chromatin remodelers necessary for the efficient remodeling of nucleosomes. Figure from Dr. Brahma

Using DNA crosslinking and peptide mapping techniques, the authors show the molecular basis for the nucleosome-spacing function of actin-related proteins (Arps), and describe a part of the Arp8 protein that plays the role of a molecular ruler to sense the length of free-DNA immediately adjacent to a nucleosome. Specifically, Arp8 and Arp4 associate with linker DNA 37-51 bp from the edge of nucleosomes in order to accurately orient INO80 on the nucleosomes in order for precise chromatin remodeling to occur. These interactions facilitate proper docking of the ATPase domain of INO80 inside of nucleosomes, as well as stable binding of Arp5 to specific histones. Arp8 acts as a DNA sensor to effect allosteric changes in INO80 necessary for the efficient remodeling of nucleosomes.

Since INO80 plays a major role in establishing nucleosome free or depleted zones at promoters, sensing linker DNA length is a critical property; this work provides a mechanistic explanation for how INO80 carries out its role through actin-related proteins.

Currently a postdoc in the Henikoff lab, Dr. Brahma continues to investigate chromatin remodeling complexes in both yeast and mammalian cells using genomic profiling approaches.  He hints that there is more to come when it comes to revealing the inner workings of chromatin remodelers: “Detailed understanding of the mechanisms by which remodelers alter the nucleosome structure is key to understanding their physiological functions. I am currently exploring how the mammalian BAF (a SWI/SNF family remodeling complex) regulates dynamic chromatin organization at regulatory regions of the genome. Subunits of SWI/SNF complexes are some of the most commonly mutated genes in a variety of cancers, and interestingly, SWI/SNF complexes also contain nuclear actin and actin-related protein subunits.”

Brahma S, Ngubo M, Paul S, Udugama M, Bartholomew B. 2018. The Arp8 and Arp4 module acts as a DNA sensor controlling INO80 chromatin remodeling. Nat Commun, 9(1), 3309

This work was supported by the National Institutes of Health.