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Transcriptional activation of polycomb-repressed genes by ZRF1

Abstract

Covalent modification of histones is fundamental in orchestrating chromatin dynamics and transcription1,2,3. One example of such an epigenetic mark is the mono-ubiquitination of histones, which mainly occurs at histone H2A and H2B4,5,6. Ubiquitination of histone H2A has been implicated in polycomb-mediated transcriptional silencing7,8,9. However, the precise role of the ubiquitin mark during silencing is still elusive. Here we show in human cell lines that ZRF1 (zuotin-related factor 1) is specifically recruited to histone H2A when it is ubiquitinated at Lys 119 by means of a novel ubiquitin-interacting domain that is located in the evolutionarily conserved zuotin domain. At the onset of differentiation, ZRF1 specifically displaces polycomb-repressive complex 1 (PRC1) from chromatin and facilitates transcriptional activation. A genome-wide mapping of ZRF1, RING1B and H2A-ubiquitin targets revealed its involvement in the regulation of a large set of polycomb target genes, emphasizing the key role ZRF1 has in cell fate decisions. We provide here a model of the molecular mechanism of switching polycomb-repressed genes to an active state.

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Figure 1: ZRF1 interacts with H2Aub.
Figure 2: ZRF1 and PRC1 compete for binding of H2Aub.
Figure 3: Genome-wide mapping of ZRF1 target genes in NT2 cells.
Figure 4: ZRF1 functions in activating polycomb-repressed genes.

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Acknowledgements

We are indebted to S. Jentsch, S. Berger, K. Helin, J. Hasskarl, R. Shiekattar, T. Zimmermann and V. Raker for antibodies and plasmids and for discussions; and to the CRG Microarray facility and Light Microscopy Facility. This work was supported by the Spanish “Ministerio de Educación y Ciencia” (BFU2007-63059), the Association for International Cancer Research (10-0177), by the AGAUR and Consolider to L.D.C., and by FOR967 to S.R.; H.R. was supported by a FEBS fellowship; J.R. by a fellowship from Fundação para a Ciência e Tecnologia; L.R.-V. by a Juan de la Cierva Fellowship; S.D. by a PFIS fellowship.

Author information

Authors and Affiliations

Authors

Contributions

H.R. cloned, purified proteins and performed biochemical studies. H.R., L.R.-V., J.D.R. and S.D. performed ChIP analysis. G.G. and N.L.-B. performed genome-wide analysis. T.N. and T.I. performed in vitro transcription and deubiquitination experiments. S.R. provided essential tools. H.R. and L.D.C. designed the experiments, supervised the project and wrote the manuscript. All authors commented on the manuscript.

Corresponding author

Correspondence to Luciano Di Croce.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains a Supplementary Discussion, additional references and Supplementary Figures 1-12 with legends. (PDF 3601 kb)

Supplementary Table 1

This file contains a list of proteins identified by affinity-chromatography and subsequent MALDI spectrometry. (PDF 37 kb)

Supplementary Table 2

This file contains a list of ZRF1 Chip-chip targets and ZRF1/Suz12 Co-targets. (XLS 1498 kb)

Supplementary Table 3

This file contains a selection of ZRF1 target genes after induction with RA (1h), which are clustered with respect to their function in developmental pathways. (PDF 75 kb)

Supplementary Table 4

This file contains a list of Ring1b Chip-chip targets, Ring1b-ZRF1, Ring1b-Suz12 and Ring1b-H3K27me3 Co-targets. (XLS 3784 kb)

Supplementary Table 5

This file contains a list of H2Aub Chip-chip targets, H2Aub-ZRF1, H2Aub-Ring1b, H2Aub-Suz12 and H2Aub-H3K27me3 Co-targets. (XLS 2720 kb)

Supplementary Table 6

This file contains a list of genes downregulated in ZRF1 knockdown cells in comparison to control cells after stimulation with RA. (XLS 231 kb)

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Richly, H., Rocha-Viegas, L., Ribeiro, J. et al. Transcriptional activation of polycomb-repressed genes by ZRF1. Nature 468, 1124–1128 (2010). https://doi.org/10.1038/nature09574

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