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.

Nucleosome conformation dictates the histone code.

Histone post-translational modifications (PTMs) play a critical role in chromatin regulation. It has been proposed that these PTMs form localized 'codes' that are read by specialized regions (reader domains) in chromatin-associated proteins (CAPs) to regulate downstream function. Substantial effort has been made to define [CAP: histone PTM] specificities, and thus decipher the histone code and guide epigenetic therapies. However, this has largely been done using the reductive approach of isolated reader domains and histone peptides, which cannot account for any higher-order factors. Here, we show that the [BPTF PHD finger and bromodomain: histone PTM] interaction is dependent on nucleosome context. The tandem reader selectively associates with nucleosomal H3K4me3 and H3K14ac or H3K18ac, a combinatorial engagement that despite being in cis is not predicted by peptides. This in vitro specificity of the BPTF tandem reader for PTM-defined nucleosomes is recapitulated in a cellular context. We propose that regulatable histone tail accessibility and its impact on the binding potential of reader domains necessitates we refine the 'histone code' concept and interrogate it at the nucleosome level.

Structural basis of histone H2A lysine 119 deubiquitination by Polycomb repressive deubiquitinase BAP1/ASXL1.

Histone H2A lysine 119 (H2AK119Ub) is monoubiquitinated by Polycomb repressive complex 1 and deubiquitinated by Polycomb repressive deubiquitinase complex (PR-DUB). PR-DUB cleaves H2AK119Ub to restrict focal H2AK119Ub at Polycomb target sites and to protect active genes from aberrant silencing. The PR-DUB subunits (BAP1 and ASXL1) are among the most frequently mutated epigenetic factors in human cancers. How PR-DUB establishes specificity for H2AK119Ub over other nucleosomal ubiquitination sites and how disease-associated mutations of the enzyme affect activity are unclear. Here, we determine a cryo-EM structure of human BAP1 and the ASXL1 DEUBAD in complex with a H2AK119Ub nucleosome. Our structural, biochemical, and cellular data reveal the molecular interactions of BAP1 and ASXL1 with histones and DNA that are critical for restructuring the nucleosome and thus establishing specificity for H2AK119Ub. These results further provide a molecular explanation for how >50 mutations in BAP1 and ASXL1 found in cancer can dysregulate H2AK119Ub deubiquitination, providing insight into understanding cancer etiology.

Challenges and opportunities in rapid disaster research: lessons from the field in New Mexico and Vanuatu.

Rapid research is essential to assess impacts in communities affected by disasters, particularly those communities made "hard-to-reach" due to their active marginalization across history and in contemporary practices. In this article, we describe two rapid research projects developed to assess needs for and experiences of communities hard-hit by disasters. The first is a project on the COVID-19 pandemic in southern New Mexico (USA) that was developed to provide information to local agencies that are deploying programs to rebuild and revitalize marginalized communities. The second is a project on population displacement due to a volcanic eruption in Vanuatu, a lower-middle income country in the South Pacific, with mental and physical health outcomes data shared with the Vanuatu Ministry of Health. We describe the similar and unique challenges that arose doing rapid research in these two different contexts, the potential broader impacts of the research, and a synthesis of lessons learned. We discuss the challenges of rapidly changing rules and regulations, lack of baseline data, lack of survey instruments validated for specific populations and in local languages, limited availability of community partners, finding funding for rapid deployment of projects, rapidly training and working with research assistants, health and safety concerns of researchers and participants, and communicating with local and international partners. We also specifically discuss how we addressed our own personal challenges while also conducting time-intensive rapid research. In both studies, researchers shared results with governmental and non-governmental partners who may use the data to inform the design of their own relief programs. While different in context, type of disaster, and research strategy, our discussion of these projects provides insights into common lessons learned for working with communities at elevated risk for the worst outcomes during disasters, such as the need for flexibility, compromise, and good working relationships with community partners.

An acetylation-mediated chromatin switch governs H3K4 methylation read-write capability.

In nucleosomes, histone N-terminal tails exist in dynamic equilibrium between free/accessible and collapsed/DNA-bound states. The latter state is expected to impact histone N-termini availability to the epigenetic machinery. Notably, H3 tail acetylation (e.g. K9ac, K14ac, K18ac) is linked to increased H3K4me3 engagement by the BPTF PHD finger, but it is unknown if this mechanism has a broader extension. Here, we show that H3 tail acetylation promotes nucleosomal accessibility to other H3K4 methyl readers, and importantly, extends to H3K4 writers, notably methyltransferase MLL1. This regulation is not observed on peptide substrates yet occurs on the cis H3 tail, as determined with fully-defined heterotypic nucleosomes. In vivo, H3 tail acetylation is directly and dynamically coupled with cis H3K4 methylation levels. Together, these observations reveal an acetylation 'chromatin switch' on the H3 tail that modulates read-write accessibility in nucleosomes and resolves the long-standing question of why H3K4me3 levels are coupled with H3 acetylation.

Structural basis of histone H2A lysine 119 deubiquitination by Polycomb Repressive Deubiquitinase BAP1/ASXL1.

The maintenance of gene expression patterns during metazoan development is achieved by the actions of Polycomb group (PcG) complexes. An essential modification marking silenced genes is monoubiquitination of histone H2A lysine 119 (H2AK119Ub) deposited by the E3 ubiquitin ligase activity of the non-canonical Polycomb Repressive Complex 1. The Polycomb Repressive Deubiquitinase (PR-DUB) complex cleaves monoubiquitin from histone H2A lysine 119 (H2AK119Ub) to restrict focal H2AK119Ub at Polycomb target sites and to protect active genes from aberrant silencing. BAP1 and ASXL1, subunits that form active PR-DUB, are among the most frequently mutated epigenetic factors in human cancers, underscoring their biological importance. How PR-DUB achieves specificity for H2AK119Ub to regulate Polycomb silencing is unknown, and the mechanisms of most of the mutations in BAP1 and ASXL1 found in cancer have not been established. Here we determine a cryo-EM structure of human BAP1 bound to the ASXL1 DEUBAD domain in complex with a H2AK119Ub nucleosome. Our structural, biochemical, and cellular data reveal the molecular interactions of BAP1 and ASXL1 with histones and DNA that are critical for remodeling the nucleosome and thus establishing specificity for H2AK119Ub. These results further provide a molecular explanation for how >50 mutations in BAP1 and ASXL1 found in cancer can dysregulate H2AK119Ub deubiquitination, providing new insight into understanding cancer etiology. One Sentence Summary: We reveal the molecular mechanism of nucleosomal H2AK119Ub deubiquitination by human BAP1/ASXL1.

Single- and Cross-Commodity Delay Discounting of Cannabis.

OBJECTIVE: Despite extensive literature that has identified high rates of delay discounting as a behavioral correlate of substance misuse, associations of cannabis use measures and delay discounting are less consistent. Furthermore, there is very limited research examining cannabis use using cross-commodity delay discounting tasks, where the immediate and delayed outcomes are different commodities. METHOD: Using conventional single-commodity delay discounting tasks for money and cannabis outcomes as well as cross-commodity delay discounting tasks (i.e., cannabis now vs. money later, money now vs. cannabis later), we examined associations of delay discounting rates with cannabis use frequency, cannabis use disorder symptom count, cannabis-related problems, and craving among young adult cannabis users (N = 115; M age = 20.7, SD = 2.6; M cannabis use days per month = 15.5, SD = 10.0). RESULTS: Although associations between cannabis use measures and rates of delay discounting in single-commodity conditions were modest, significant associations were observed with delay discounting rates in cross-commodity conditions. Of note, regression and model comparison analyses generally showed positive associations of cannabis measures with immediate cannabis versus delayed money delay discounting rates, and negative associations of cannabis measures with immediate money versus delayed cannabis delay discounting rates. CONCLUSIONS: The results suggest that problematic cannabis use may not be strictly associated with the inability to wait for delayed outcomes, as suggested by previous research implementing single-commodity delay discounting tasks, but also with a willingness to wait for delayed access to cannabis.

Valuation of future alcohol in cross-commodity delay discounting is associated with alcohol misuse/consequences.

OBJECTIVE: Delay discounting (DD) refers to the reduction in reward value as a function of its delay, and individuals who misuse alcohol typically exhibit high rates of DD, which may reflect a general preference for immediate outcomes. This interpretation is based on studies utilizing single-commodity DD tasks where the same commodity is available immediately and following a delay. Cross-commodity DD tasks require individuals to choose between different commodities at varying delays and may provide the potential to further illuminate intertemporal preference associated with alcohol misuse. The present study examined associations between single-commodity and cross-commodity DD rates with alcohol use metrics among young adults. METHOD: DD by young adults (N = 70, aged 19-24, 71% male, 80% White) who engage in hazardous drinking was examined using a fully parametric combination of immediate and delayed alcohol and money outcomes. We hypothesized that past 30-day alcohol use and alcohol-related negative consequences would be associated with preference for alcohol outcomes independent of whether alcohol was immediate or delayed. RESULTS: Results support the hypothesis, as past 30-day consumption and AUDIT scores were positively associated with rate of DD in the immediate alcohol versus delayed money task and negatively associated with rate of DD in the immediate money versus delayed alcohol task. Moreover, we found the immediate money versus delayed alcohol task provided unique explanatory power for individual alcohol use. CONCLUSIONS: The observed associations indicate that willingness to invest in future access to alcohol may be associated with elevated alcohol use and related consequences. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Mapping the Morphological Landscape of Oligomeric Di-block Peptide-Polymer Amphiphiles.

Peptide-polymer amphiphiles (PPAs) are tunable hybrid materials that achieve complex assembly landscapes by combining the sequence-dependent properties of peptides with the structural diversity of polymers. Despite their promise as biomimetic materials, determining how polymer and peptide properties simultaneously affect PPA self-assembly remains challenging. We herein present a systematic study of PPA structure-assembly relationships. PPAs containing oligo(ethyl acrylate) and random-coil peptides were used to determine the role of oligomer molecular weight, dispersity, peptide length, and charge density on self-assembly. We observed that PPAs predominantly formed spheres rather than anisotropic particles. Oligomer molecular weight and peptide hydrophilicity dictated morphology, while dispersity and peptide charge affected particle size. These key benchmarks will facilitate the rational design of PPAs that expand the scope of biomimetic functionality within assembled soft materials.

Methods to Optimize Recruitment, Participation, and Retention Among Vulnerable Individuals Participating in a Longitudinal Clinical Trial.

Low-income and ethnic/racial minority adults do not often participate in research or may face unique barriers when participating in research, which delays and impedes medical advances for this vulnerable population. This article describes in detail the evidenced-based methods used to enhance recruitment, participation, and retention in a clinical trial at a center serving ethnic/racial minorities and low-income individuals. The article details the partnership with a community outreach center and describes the duties and impact of a community liaison to enhance recruitment, participation, and retention in a randomized controlled trial with a 6-month follow-up. Of the 246 individuals initially recruited for screening, 80 did not meet inclusion criteria with the most common reason for disqualification being meeting criteria for substance use disorder (n = 44). One hundred sixty-six participants qualified for participation. The majority of participants identified as African American (n = 127, 77.1%) and reported an annual individual income under $10,000 (n = 121 (74.2%). Forty-five percent of the sample completed the requested number of sessions (i.e., 12). Sixty-three percent of participants completed post intervention assessments and 42% completed 6-month follow-up data collection. The participation and retention numbers in this study appear higher than typical participation and retention rates in longitudinal studies with similar populations. The methods and lessons learned may be useful for other clinical trials that recruit vulnerable populations and wish to enhance participation, engagement, and retention.

The Indirect Effects of Trait Anxiety on Drug Use Via Emotion Dysregulation in a Low-Income Sample.

Background: Research has demonstrated consistent associations between anxiety and illicit drug use. However, few studies to date have examined the shared risk factors that may contribute to this common comorbidity. Therefore, the current investigation tested the indirect effect of trait anxiety on drug use disorder symptoms via emotion dysregulation, a widely recognized transdiagnostic risk factor found to be relevant across both anxiety and illicit drug use. Method: The sample was comprised of 241 adults (Mage = 50.56, SDage = 5.90; 76.8% Black) recruited from a community center serving low-income and homeless individuals. Results: Consistent with our hypothesis, structural equation modeling demonstrated an indirect effect of trait anxiety on drug use disorder symptoms through emotion dysregulation. Conclusions: The current findings show initial support for emotion dysregulation as an explanatory vulnerability factor indirectly underlying the relationship between anxiety and drug use.

Conscientiousness explains the link between childhood neglect and cigarette smoking in adults from a low-income, urban area-the differential effects of sex.

Cigarette smoking represents the leading cause of preventable morbidity and mortality in the US and understanding its risk factors remains a critical public health endeavor. Low-income individuals and individuals with a history of childhood maltreatment are at heightened risk for cigarette smoking, yet the underlying factors between this association are understudied. Conscientiousness is one construct with potential explanatory relevance to both smoking and childhood neglect. The current investigation examined the association between childhood physical and emotional neglect with smoking (i.e., self-reported cigarette smoking and breath carbon monoxide levels) via conscientiousness. The sample was comprised of 115 adults (Mage = 50.46, SDage = 5.86; 76.4% Black) recruited from a community center serving low-income and homeless individuals. Mediation analyses showed the indirect effect of childhood emotional neglect on cigarette smoking through conscientiousness; for physical neglect, this relationship was only present among males. The current study provides preliminary evidence that conscientiousness may be a particularly important vulnerability factor when examining the association between childhood neglect and smoking.

Molecular Recognition of Methionine-Terminated Peptides by Cucurbit[8]uril.

This Article describes the molecular recognition of peptides containing an N-terminal methionine (Met) by the synthetic receptor cucurbit[8]uril (Q8) in aqueous solution and with submicromolar affinity. Prior work established that Q8 binds with high affinity to peptides containing aromatic amino acids, either by simultaneous binding of two aromatic residues, one from each of two different peptides, or by simultaneous binding of an aromatic residue and its immediate neighbor on the same peptide. The additional binding interface of two neighboring residues suggested the possibility of targeting nonaromatic peptides, which have thus far bound only weakly to synthetic receptors. A peptide library designed to test this hypothesis was synthesized and screened qualitatively for Q8 binding using a fluorescent indicator displacement assay. The large fluorescence response observed for several Met-terminated peptides suggested strong binding, which was confirmed quantitatively by the determination of submicromolar equilibrium dissociation constant values for Q8 binding to MLA, MYA, and MFA using isothermal titration calorimetry (ITC). This discovery of high affinity binding to Met-terminated peptides and, more generally, to nonaromatic peptides prompted a detailed investigation of the determinants of binding in this system using ITC, electrospray ionization mass spectrometry, and 1H NMR spectroscopy for 25 purified peptides. The studies establish the sequence determinants required for high-affinity binding of Met-terminated peptides and demonstrate that cucurbit[ n]uril-mediated peptide recognition does not require an aromatic residue for high affinity. These results, combined with the known ability of cucurbit[ n]urils to target N-termini and disordered loops in folded proteins, suggest that Q8 could be used to target unmodified, Met-terminated proteins.