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Hickman, A.

Publications and source records attributed to Hickman, A..

3 recordsLinked to original sources

Cancer-associated DNA Hypermethylation of Polycomb Targets Requires DNMT3A Dual Recognition of Histone H2AK119 Ubiquitination and the Nucleosome Acidic Patch

During tumor development, promoter CpG islands (CGIs) that are normally silenced by Polycomb repressive complexes (PRCs) become DNA hypermethylated. The molecular mechanism by which de novo DNA methyltransferase(s) catalyze CpG methylation at PRC-regulated regions remains unclear. Here we report a cryo-EM structure of the DNMT3A long isoform (DNMT3A1) N-terminal region in complex with a nucleosome carrying PRC1-mediated histone H2A lysine 119 monoubiquitination (H2AK119Ub). We identify regions within the DNMT3A1 N-terminus that bind H2AK119Ub and the nucleosome acidic patch. This bidentate interaction is required for effective DNMT3A1 engagement with H2AK119Ub-modified chromatin in cells. Furthermore, aberrant redistribution of DNMT3A1 to Polycomb target genes inhibits their transcriptional activation during cell differentiation and recapitulates the cancer-associated DNA hypermethylation signature. This effect is rescued by disruption of the DNMT3A1-acidic patch interaction. Together, our analyses reveal a binding interface critical for countering promoter CGI DNA hypermethylation, a major molecular hallmark of cancer.

cancer biology↗

Assessing the potential of backscattering as a proxy for phytoplankton carbon biomass

Despite phytoplankton contributing roughly half of the photosynthesis on earth and fueling marine food-webs, field measurements of phytoplankton biomass remain scarce. The particulate backscattering coefficient (bbp) has often been used as an optical proxy to estimate phytoplankton carbon biomass (Cphyto). However, total observed bbp is impacted by phytoplankton size, cell composition, and non-algal particles. The lack of phytoplankton field data has prevented the quantification of uncertainties driven by these factors. Here, we first review and discuss existing bbp algorithms by applying them to bbp data from the BGC-Argo array in surface waters (<10m). We find a bbp threshold where estimated Cphyto differs by more than an order of magnitude. Next, we use a global ocean circulation model (the MITgcm Biogeochemical and Optical model) that simulates plankton dynamics and associated inherent optical properties to quantify and understand uncertainties from bbp-based algorithms in surface waters. We do so by developing and calibrating an algorithm to the model. Simulated error-estimations show that bbp-based algorithms overestimate/underestimate Cphyto between 5% and 100% in surface waters, depending on the location and time. This is achieved in the ideal scenario where Cphyto and bbp are known precisely. This is not the case for algorithms derived from observations, where the largest source of uncertainty is the scarcity of phytoplankton biomass data and related methodological inconsistencies. If these other uncertainties are reduced, the model shows that bbp could be a relatively good proxy for phytoplankton carbon biomass, with errors close to 20% in most regions. Plain Language SummaryPhytoplankton contribute roughly half of the photosynthesis on earth and fuel fisheries around the globe. Yet, few direct measurements of phytoplankton concentration are available. Frequently, concentrations of phytoplankton are instead estimated using the optical properties of water. Backscattering is one of these optical properties, representing the light being scattered backwards. Previous studies have suggested that backscattering could be a good method to estimate phytoplankton concentration. However, other particles that are present in the ocean also contribute to backscattering. In this paper we examine how well backscattering can be used to estimate phytoplankton. To address this question, we use data from drifting instruments that are spread across the ocean and a computer model that simulates phytoplankton and backscattering over the global oceans. We find that by using backscattering, phytoplankton can be overestimated/underestimated on average by [~]20%. This error differs between regions, and can be larger than 100% at high latitudes. Computer simulations allowed us to quantify spatial and temporal variability in backscattering signal composition, and thereby understand potential errors in inferring phytoplankton with backscattering, which could not have been done before due to the lack of phytoplankton data. Key PointsO_LIPhytoplankton carbon bbp-based algorithms can differ up to an order of magnitude at low bbp values. C_LIO_LIAn algorithm fitted to a global model output shows biases ranging between 15% and 40% in most regions. C_LIO_LIMost uncertainties are due to the relative contribution of phytoplankton to total bbp. C_LI

ecology↗

Transposase N-terminal phosphorylation and asymmetric transposon ends inhibit piggyBac transposition in mammalian cells

Mechanistic regulation of DNA transposon systems in mammalian cells remains poorly understood. Using modeling, biochemical, and cell-based assays, we sought to extend the recent cryoEM structural insight into the piggyBac transpososome to evaluate the previously unexplained role of the transposase N-terminus, the need for asymmetric transposon ends, and the complexity of transposase tetramer formation for transposition in mammalian cells. We found that N-terminal phosphorylation by casein kinase II inhibits transposase-DNA interaction and designed deletion of this phosphorylated domain releases inhibition thereby enhancing activity. We also found that the N-terminal domain promotes transposase dimerization in the absence of transposon DNA. N-terminal deletion enables transposition of symmetric transposon ends that was previously not achievable with piggyBac. The complex transposase tetramer needed for transposition of asymmetric transposon ends can be overcome via appending a second transposase C-terminal domain in combination with symmetric transposon ends overcoming the negative regulation by asymmetric ends. Our results demonstrate that N-terminal transposase phosphorylation and the requirement for asymmetric transposon ends both negatively regulate piggyBac transposons in mammalian cells. These novel insights into mechanism and structure of the piggyBac transposase expand its potential use for genomic applications.

molecular biology↗