Researchers Reveal Key Role for RSF1 Protein in Silencing Genes

A fertilized human egg develops into multiple tissues, organs and about 200 distinct cell types. Each cell type has the same genes, but they are expressed differently during development and in mature cells.

Understanding the mechanisms that turn sets of genes on or off is a fundamental quest in biology, and one that has clinical importance in diseases like cancer, where gene control goes awry.

Researchers at the University of Alabama (UAB) at Birmingham report the discovery of an important role for the RSF1, or remodeling and spacing factor 1, protein in silencing genes. They also demonstrated that disrupting RSF1 expression in the embryos of African clawed frogs caused severe developmental defects in the tadpoles. This took place via a dysregulation of mesodermal cell fate specification.

The team published its paper (“Role of Remodeling and Spacing Factor 1 in Histone H2A Ubiquitination-Mediated Gene Silencing”) in Proceedings of the National Academy of Sciences. Understanding how genes get turned on or off is critical for developing better therapies for diseases like cancer.

“Histone H2AK119 ubiquitination (H2Aub), as mediated by Polycomb repressive complex 1 (PRC1), is a prevalent modification which has been linked to gene silencing. We report that remodeling and spacing factor 1 (RSF1), a subunit of the RSF complex, is a H2Aub-binding protein. It reads H2Aub through a previously uncharacterized ubiquitinated H2A binding (UAB) domain,” write the investigators. “We show that RSF1 is required both for H2Aub-target gene silencing and for maintaining stable nucleosome patterns at promoter regions.”

According to Hengbin Wang, Ph.D., and colleagues, RSF1 acts on chromatin, which is not static but changes in its structure to control different physiological processes. One contributor to chromatin fluidity involves modifications of the histone proteins made by adding or removing chemical groups to the histone tails, says Dr. Wang, who notes that histones can be modified by acetylation, phosphorylation, methylation, ubiquitination, or adenosine diphosphate (ADP) ribosylation.

In the current study, Dr. Wang, an associate professor of biochemistry and molecular genetics in the UAB School of Medicine, looked at the addition of ubiquitin to the histone subunit H2A. This modification is linked to gene silencing, while removing ubiquitin from H2A leads to gene activation. Dr. Wang and colleagues discovered that RSF1 mediates the gene-silencing function of ubiquitinated H2A.

They found that RSF1 is a ubiquitinated H2A binding protein that reads ubiquitinated H2A through a previously uncharacterized and obligatory ubiquitinated H2A binding domain.

Carrying out research on human and mouse cells, the team found that the genes regulated by RSF1 overlapped greatly with those controlled by part of a complex that ubiquitinates H2A. Knocking out RSF1 in cells derepressed the genes regulated by RSF1, and this was accompanied by changes in ubiquitinated H2A chromatin organization and release of linker histone H1.

In the PNAS paper, Dr. Wang and his group suggested a model for the action of RSF1 in gene silencing.

“RSF1 binds to ubiquitinated H2A nucleosomes to establish and maintain the stable ubiquitinated H2A nucleosome pattern at promoter regions,” they write. “The stable nucleosome array leads to a chromatin architecture that is refractory to further remodeling required for ubiquitinated H2A target gene activation. When RSF1 is knocked out, ubiquitinated H2A nucleosome patterns are disturbed and nucleosomes become less stable, despite the presence of ubiquitinated H2A. These ubiquitinated H2A nucleosomes are subjected to chromatin remodeling for gene activation.”

Dr. Wang believes that learning more about the ubiquitinated H2A binding site may help in the discovery of other ubiquitinated histone-binding proteins.