BAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genome.

Nadezda A Fursova,Emma L Findlater,Paula Dobrinić,Neil P Blackledge,Miles K Huseyin,Anna Lastuvkova,Anne H Turberfield,Robert J Klose

doi:10.1101/gad.347005.120

Nadezda A Fursova, Emma L Findlater + Show 6 more

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https://doi.org/10.1101/gad.347005.120

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Journal: Genes & development	Publication Date: Apr 22, 2021
Citations: 40	License type: cc-by

Affiliation: University of Oxford

Abstract

Histone-modifying systems play fundamental roles in gene regulation and the development of multicellular organisms. Histone modifications that are enriched at gene regulatory elements have been heavily studied, but the function of modifications found more broadly throughout the genome remains poorly understood. This is exemplified by histone H2A monoubiquitylation (H2AK119ub1), which is enriched at Polycomb-repressed gene promoters but also covers the genome at lower levels. Here, using inducible genetic perturbations and quantitative genomics, we found that the BAP1 deubiquitylase plays an essential role in constraining H2AK119ub1 throughout the genome. Removal of BAP1 leads to pervasive genome-wide accumulation of H2AK119ub1, which causes widespread reductions in gene expression. We show that elevated H2AK119ub1 preferentially counteracts Ser5 phosphorylation on the C-terminal domain of RNA polymerase II at gene regulatory elements and causes reductions in transcription and transcription-associated histone modifications. Furthermore, failure to constrain pervasive H2AK119ub1 compromises Polycomb complex occupancy at a subset of Polycomb target genes, which leads to their derepression, providing a potential molecular rationale for why the BAP1 ortholog in Drosophila has been characterized as a Polycomb group gene. Together, these observations reveal that the transcriptional potential of the genome can be modulated by regulating the levels of a pervasive histone modification.

Highlights

In eukaryotes, DNA is wrapped around histones to form nucleosomes and chromatin, which packages the genome inside the nucleus
Given our recent discovery that H2AK119ub1 is deposited more broadly throughout the genome than previously appreciated (Fursova et al 2019), we set out to determine where in the genome BAP1 functions to control the levels of H2AK119ub1 and how this influences gene expression
To address these important questions, we developed a BAP1 conditional knockout mouse embryonic stem cell (ESC) line (Bap1fl/fl) in which addition of tamoxifen (OHT) enables inducible removal of BAP1, allowing us to capture the primary effects that BAP1 loss has on H2AK119ub1 and gene expression

Summary

Introduction

DNA is wrapped around histones to form nucleosomes and chromatin, which packages the genome inside the nucleus. A second Polycomb repressive complex, PRC2, is recruited to the same sites (Boyer et al 2006; Bracken 2006; Li et al 2017a; Perino et al 2018), where it deposits histone H3 lysine 27 methylation (H3K27me3) (Cao et al 2002; Czermin et al 2002; Kuzmichev 2002; Müller et al 2002), leading to the formation of transcriptionally repressive Polycomb chromatin domains that have high levels of PRC1, PRC2, and their respective histone modifications (Mikkelsen et al 2007; Ku et al 2008) In addition to this punctate high-level enrichment of H2AK119ub at Polycomb target gene promoters, we and others have recently demonstrated that H2AK119ub is found broadly throughout the genome, albeit at much lower levels (Lee et al 2015; Kahn et al 2016; Fursova et al 2019). These observations demonstrate how the levels of a pervasive histone modification must be appropriately controlled to enable the transcriptional potential of the genome

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