Waddington's epigenetic landscape, from C.H. Waddington The strategy of genes: a discussion of some aspects of theoretical biology (Allen & Unwin, 1957)
Genomes contains the information necessary to form all the different types of cells present in the adult form. During embryonic development, the rapidly dividing cells in early embryo have a future of immense possibilities ahead. As exciting as this might sound, at some point they have to decide what kind of cells they will be in the future. Should they be neurons, muscle or skin cells? Or any one of the cell types present in adult body? The punch line in this decision is not only to know what one should become. The versatility of the genome necessitates the awareness of what one should NOT be also. The cell should lock in to the target destination by closing down the doors that might lead to erroneous fates and focusing only what it should become.
Repression of cell-type-specific fates is mediated by the activity of a group of genes called by polycomb repressor complexes (PRC1 and 2). It was known that ubiquitination of histone H2A (H2A-ubi) is implicated in polycomb-mediated transcriptional silencing. But how exactly it might be doing this was not clear. In a work lead by Luciano Di Croce in CRG in collaboration with a number of researchers in UPF (us :D), Nagasaki Univesity School of Medicine and University of Freiburg, it was shown that the phosphoprotein ZRF1 (zuotin-related factor 1) recognizes and interacts with H2A-ubi by means of a novel ubiquitin-interacting domain. Moreover, through this interaction ZRF1 displaces PRC1 from chromatin to facilitate transcriptional activation. Hence, when ZRF1 is active the genes that opens the way to differentiation are released from the repressive control of PRC1 and the cell can continue with specialization. In order to show the implication of ZRF1 in determining cell fate, we identified the genes whose activation ZRF1 affects by binding to the ubiquitinated H2A. We helped in the design and analysis of high-throughput experiments namely ChIP-on-chip and mRNA transcriptional profiling assays. ChIP-on-chip data gives a genome-wide view of where exactly ZRF1 binds on the DNA. The genome-wide transcriptional profiling for the condition when ZRF1 is down-regulated showed that a statistically significant number of the genes bound by ZRF1 are also transcriptionally down-regulated when ZRF1 is not active. This implied that ZRF1 not only binds to the genomic regions these genes are located but also leads to their transcriptional activation. To elucidate how ZRF1 might be exerting this transcriptional effect, we also analyzed ChIP-on-chip occupancy data for both H2A-ubi and RING1B, the protein that binds to H2A-ubi. Comparison of the target genes occupied by all three proteins (ZRF1, H2A-ubi and RING1B) and subsequent confirmatory experiments showed that ZRF1 in effect displaces RING1B at H2A-ubi, which further helps the dislocation of PRC1. Overall this work suggest a possible mechanism of the activation of genes repressed by polycomb-mediated signaling and how ZRF1 play a key role in the determination of cell fate.
For more information go to:
Nature paper, CRG News, UPF News (in catalan).