KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity

Wellcome Trust [102349/Z/13/Z to A.H.T., 099677/Z/12/Z to H.W.K., 098024/Z/11/Z, 209400/Z/17/Z to R.J.K.]; Lister Institute of Preventive Medicine; European Research Council [681440]; Japan Agency for Medical Research and Development, AMEDCREST Programme. Funding for open access charge: Wellcome Trus

KDM2A and KDM2B mediate widespread transcription repression in mouse embryonic stem cells

DNA methylation is widespread in vertebrate genomes, occurring on cytosine residues in the context of CpG dinucleotides. An important exception to this pervasive methylation are CpG islands (CGIs), short regions of CpG rich, non-methylated DNA that are associated with the majority of transcription start sites. CGIs are bound by proteins containing a zinc finger-CXXC (ZF-CXXC) domain, which specifically recognises nonmethylated CpG dinucleotides. These proteins are found in a variety of chromatin modifying complexes, leading to the generation of a distinctive chromatin environment at CGI gene promoters. KDM2A and KDM2B (KDM2A/B) are recruited to CGI throughout the genome via their ZF-CXXC domain, and act as histone H3 lysine 36 (H3K36) demethylases. H3K36 methylation can inhibit transcription initiation, leading to the proposal that KDM2A and KDM2B may contribute to the generation of a transcriptionally permissive chromatin state at CGI-associated gene promoters through local removal of this repressive mark. However, KDM2A/B have been implicated in transcription repression in other contexts. Furthermore, both KDM2A and KDM2B also appear to possess demethylase-independent modes of transcription regulation, including via the short isoforms of these proteins which lack demethylase activity. Therefore, the genome-wide role played by KDM2A/B in regulating gene expression remains unclear. Here I dissect the contribution of KDM2A/B to transcription regulation. I discover that the histone demethylase activity of KDM2A/B contributes little to the regulation of gene expression in mouse embryonic stem cells. In contrast, I find that loss of KDM2A/B from chromatin leads to a widespread increase in transcription, and show that KDM2B plays the predominant role in transcription repression. I demonstrate that the transcription upregulation following loss of KDM2A/B is not accompanied by changes in the accessibility of CGI gene promoters. Instead, I identify candidate substrates of the putative E3 ubiquitin ligase activity of KDM2A/B. Altered activity or stability of these substrates might result in transcription deregulation. Together, these observations reveal an unexpected and widespread role for KDM2B in transcriptional repression.</p

Histone demethylases in chromatin biology and beyond

Histone methylation plays fundamental roles in regulating chromatin‐based processes. With the discovery of histone demethylases over a decade ago, it is now clear that histone methylation is dynamically regulated to shape the epigenome and regulate important nuclear processes including transcription, cell cycle control and DNA repair. In addition, recent observations suggest that these enzymes could also have functions beyond their originally proposed role as histone demethylases. In this review, we focus on recent advances in our understanding of the molecular mechanisms that underpin the role of histone demethylases in a wide variety of normal cellular processes

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

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

An autonomous molecular assembler for programmable chemical synthesis

Molecular machines that assemble polymers in a programmed sequence are fundamental to life. They are also an achievable goal of nanotechnology. Here, we report synthetic molecular machinery made from DNA which controls and records the formation of covalent bonds. We show that an autonomous cascade of DNA hybridization reactions can create oligomers, from building blocks linked by olefin or peptide bonds, with a sequence defined by a reconfigurable molecular program. The system can also be programmed to achieve combinatorial assembly. The sequence of assembly reactions, and thus the structure, of each oligomer synthesized is recorded in a DNA molecule which enables this information to be recovered by PCR amplification followed by DNA sequencing