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RSF1 a key factor 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 genes get expressed differently during development and later in mature cells.
Understanding the mechanisms that turn sets of genes on or off is a fundamental quest to biologists, and one that has clinical importance in diseases like cancer where gene control goes destructively off target.
Hengbin Wang PhD of the University of Alabama at Birmingham, along with his colleagues, has identified the steps in one of these mechanisms. In a paper published this week in Proceedings of the National Academy of Sciences or PNAS, the team describes a key role for the gene called Remodeling and spacing factor 1, which generates the RSF1 protein (in humans) that silences or "turns off" gene function. Besides the details of the molecular biology involved, the researchers also saw how disruption of RSF1 in embryos of African clawed frogs caused severe developmental defects in tadpoles by dysregulating their mesoderm cells.
RSF1 affects chromatin, the complex macro-molecular enclosure surrounding each 6-foot-long DNA chromosome chain. Chromosomes must be highly condensed and tightly wrapped around histone protein spools in order to fit inside a cell.
It changes fluidly as numerous modifications can be made to histone protein 'tails.' Adding or removing chemical groups located on a histone 'tail' can positively charge it and, in most cases, enhance transcription. Whereas deacetylation of the histone 'tail' represses transcription. Each of the four standard histones can be simultaneously modified at multiple different sites.
In his current work, Wang, an associate professor of biochemistry and molecular genetics in the UAB School of Medicine, focused on the addition of ubiquitin to the histone subunit H2A. This frequent modification is linked to gene silencing. However, removing ubiquitin from H2A activates the gene to function and produce proteins.
Wang and colleagues discovered that RSF1 mediates the gene-silencing function of ubiquitinated-H2A.
In human and mouse cells, genes regulated by RSF1 overlapped significantly with those controlled by part of a complex that ubiquitinates H2A. Knockout of RSF1 in cells derepressed the genes it regulates, accompanied by changes in ubiquitinated-H2A chromatin organization and release of linker histone H1.
In their paper, Wang and colleagues propose a model for the action of RSF1 in gene silencing which they hope may help in the discovery of other ubiquitinated histone-binding proteins.
protein. It reads H2Aub through a previously uncharacterized ubiquitinated H2A binding (UAB) domain. We show that RSF1 is required both for H2Aub-target gene silencing and for maintaining stable nucleosome patterns at promoter regions. The role of RSF1 in H2Aub function is further supported by the observation that RSF1 and Ring1, a Xenopus PRC1 subunit mediating H2Aub, regulate in concert mesodermal cell specification and gastrulation during Xenopus embryogenesis. This study reveals that RSF1 mediates the gene-silencing function of H2Aub.
Posttranslational histone modifications play important roles in regulating chromatin-based nuclear processes. Histone H2AK119 ubiquitination (H2Aub) is a prevalent modification and has been primarily linked to gene silencing. However, the underlying mechanism remains largely obscure. Here we report the identification of RSF1 (remodeling and spacing factor 1), a subunit of the RSF complex, as a H2Aub binding protein, which mediates the gene-silencing function of this histone modification. RSF1 associates specifically with H2Aub, but not H2Bub nucleosomes, through a previously uncharacterized and obligatory region designated as ubiquitinated H2A binding domain. In human and mouse cells, genes regulated by RSF1 overlap significantly with those controlled by RNF2/Ring1B, the subunit of Polycomb repressive complex 1 (PRC1) which catalyzes the ubiquitination of H2AK119. About 82% of H2Aub-enriched genes, including the classic PRC1 target Hox genes, are bound by RSF1 around their transcription start sites. Depletion of H2Aub levels by Ring1B knockout results in a significant reduction of RSF1 binding. In contrast, RSF1 knockout does not affect RNF2/Ring1B or H2Aub levels but leads to derepression of H2Aub target genes, accompanied by changes in H2Aub chromatin organization and release of linker histone H1. The action of RSF1 in H2Aub-mediated gene silencing is further demonstrated by chromatin-based in vitro transcription. Finally, RSF1 and Ring1 act cooperatively to regulate mesodermal cell specification and gastrulation during Xenopus early embryonic development. Taken together, these data identify RSF1 as a H2Aub reader that contributes to H2Aub-mediated gene silencing by maintaining a stable nucleosome pattern at promoter regions.
All authors of the PNAS paper, "Role of remodeling and spacing factor 1 in histone H2A ubiquitination-mediated gene silencing," are Wang; Chenbei Chang, UAB Department of Cell, Developmental, and Integrative Biology; Jianjun Luo, Institute of Biophysics, Chinese Academy of Sciences, Beijing; and Louise T. Chow, UAB Department of Biochemistry and Molecular Genetics. At UAB, Chow holds the Anderson Family Chair in Medical Education, Research and Patient Care in the School of Medicine. Co-authors are Zhuo Zhang, Amanda E. Jones, Matthew B. Renfrow, Marina N. Vassylyeva, Dmitry G. Vassylyev, Keith E. Giles and Yue Gu, UAB Department of Biochemistry and Molecular Genetics; Wei Wu and Yue Kang, Institute of Biophysics, Chinese Academy of Sciences, Beijing; Jinman Kim and Woojin An, University of Southern California Department of Biochemistry and Molecular Biology; Xiaobao Bi and Chuan-Fa Liu, Nanyang Technological University, Singapore; Ivan K. Popov, UAB Department of Cell, Developmental and Integrative Biology; Dongquan Chen, UAB Division of Preventive Medicine and the UAB Comprehensive Cancer Center; Ashwath Kumar and Yuhong Fan, School of Biological Sciences, Georgia Institute of Technology; and Yufeng Tong, University of Toronto, Toronto, Canada.
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Embryonic histone H1 (RED) in Drosophila; dBigH1 regulates zygote genome activation. Image credit: Salvador Pérez-Montero; Bellvitge Biomedical Research Institute, Barcelona, Spain