The transcription factor NF-κB orchestrates nucleosome remodeling during the primary response to Toll-like receptor 4 signaling.

Inducible nucleosome remodeling at hundreds of latent enhancers and several promoters shapes the transcriptional response to Toll-like receptor 4 (TLR4) signaling in macrophages. We aimed to define the identities of the transcription factors that promote TLR-induced remodeling. An analysis strategy based on ATAC-seq and single-cell ATAC-seq that enriched for genomic regions most likely to undergo remodeling revealed that the transcription factor nuclear factor κB (NF-κB) bound to all high-confidence peaks marking remodeling during the primary response to the TLR4 ligand, lipid A. Deletion of NF-κB subunits RelA and c-Rel resulted in the loss of remodeling at high-confidence ATAC-seq peaks, and CRISPR-Cas9 mutagenesis of NF-κB-binding motifs impaired remodeling. Remodeling selectivity at defined regions was conferred by collaboration with other inducible factors, including IRF3- and MAP-kinase-induced factors. Thus, NF-κB is unique among TLR4-activated transcription factors in its broad contribution to inducible nucleosome remodeling, alongside its ability to activate poised enhancers and promoters assembled into open chromatin.

The Pol II preinitiation complex (PIC) influences Mediator binding but not promoter-enhancer looping.

Knowledge of how Mediator and TFIID cross-talk contributes to promoter-enhancer (P-E) communication is important for elucidating the mechanism of enhancer function. We conducted an shRNA knockdown screen in murine embryonic stem cells to identify the functional overlap between Mediator and TFIID subunits on gene expression. Auxin-inducible degrons were constructed for TAF12 and MED4, the subunits eliciting the greatest overlap. Degradation of TAF12 led to a dramatic genome-wide decrease in gene expression accompanied by destruction of TFIID, loss of Pol II preinitiation complex (PIC) at promoters, and significantly decreased Mediator binding to promoters and enhancers. Interestingly, loss of the PIC elicited only a mild effect on P-E looping by promoter capture Hi-C (PCHi-C). Degradation of MED4 had a minor effect on Mediator integrity but led to a consistent twofold loss in gene expression, decreased binding of Pol II to Mediator, and decreased recruitment of Pol II to the promoters, but had no effect on the other PIC components. PCHi-C revealed no consistent effect of MED4 degradation on P-E looping. Collectively, our data show that TAF12 and MED4 contribute mechanistically in different ways to P-E communication but neither factor appears to directly control P-E looping, thereby dissociating P-E communication from physical looping.

Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods.

Metazoan chromosomes are sequentially partitioned into topologically associating domains (TADs) and then into smaller sub-domains. One class of sub-domains, insulated neighborhoods, are proposed to spatially sequester and insulate the enclosed genes through self-association and chromatin looping. However, it has not been determined functionally whether promoter-enhancer interactions and gene regulation are broadly restricted to within these loops. Here, we employed published datasets from murine embryonic stem cells (mESCs) to identify insulated neighborhoods that confine promoter-enhancer interactions and demarcate gene regulatory regions. To directly address the functionality of these regions, we depleted estrogen-related receptor ß (Esrrb), which binds the Mediator co-activator complex, to impair enhancers of genes within 222 insulated neighborhoods without causing mESC differentiation. Esrrb depletion reduces Mediator binding, promoter-enhancer looping, and expression of both nascent RNA and mRNA within the insulated neighborhoods without significantly affecting the flanking genes. Our data indicate that insulated neighborhoods represent functional regulons in mammalian genomes.

Mot1, Ino80C, and NC2 Function Coordinately to Regulate Pervasive Transcription in Yeast and Mammals.

Pervasive transcription initiates from cryptic promoters and is observed in eukaryotes ranging from yeast to mammals. The Set2-Rpd3 regulatory system prevents cryptic promoter function within expressed genes. However, conserved systems that control pervasive transcription within intergenic regions have not been well established. Here we show that Mot1, Ino80 chromatin remodeling complex (Ino80C), and NC2 co-localize on chromatin and coordinately suppress pervasive transcription in S. cerevisiae and murine embryonic stem cells (mESCs). In yeast, all three proteins bind subtelomeric heterochromatin through a Sir3-stimulated mechanism and to euchromatin via a TBP-stimulated mechanism. In mESCs, the proteins bind to active and poised TBP-bound promoters along with promoters of polycomb-silenced genes apparently lacking TBP. Depletion of Mot1, Ino80C, or NC2 by anchor away in yeast or RNAi in mESCs leads to near-identical transcriptome phenotypes, with new subtelomeric transcription in yeast, and greatly increased pervasive transcription in both yeast and mESCs.

Cbx3 maintains lineage specificity during neural differentiation.

Chromobox homolog 3 (Cbx3/heterochromatin protein 1γ [HP1γ]) stimulates cell differentiation, but its mechanism is unknown. We found that Cbx3 binds to gene promoters upon differentiation of murine embryonic stem cells (ESCs) to neural progenitor cells (NPCs) and recruits the Mediator subunit Med26. RNAi knockdown of either Cbx3 or Med26 inhibits neural differentiation while up-regulating genes involved in mesodermal lineage decisions. Thus, Cbx3 and Med26 together ensure the fidelity of lineage specification by enhancing the expression of neural genes and down-regulating genes specific to alternative fates.

A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling.

We describe a broad mechanistic framework for the transcriptional induction of mammalian primary response genes by Toll-like receptors and other stimuli. One major class of primary response genes is characterized by CpG-island promoters, which facilitate promiscuous induction from constitutively active chromatin without a requirement for SWI/SNF nucleosome remodeling complexes. The low nucleosome occupancy at promoters in this class can be attributed to the assembly of CpG islands into unstable nucleosomes, which may lead to SWI/SNF independence. Another major class consists of non-CpG-island promoters that assemble into stable nucleosomes, resulting in SWI/SNF dependence and a requirement for transcription factors that promote selective nucleosome remodeling. Some stimuli, including serum and tumor necrosis factor-alpha, exhibit a strong bias toward activation of SWI/SNF-independent CpG-island genes. In contrast, interferon-beta is strongly biased toward SWI/SNF-dependent non-CpG-island genes. By activating a diverse set of transcription factors, Toll-like receptors induce both classes and others for an optimal response to microbial pathogens.

EP400 Deposits H3.3 into Promoters and Enhancers during Gene Activation.

Gene activation in metazoans is accompanied by the presence of histone variants H2AZ and H3.3 within promoters and enhancers. It is not known, however, what protein deposits H3.3 into chromatin or whether variant chromatin plays a direct role in gene activation. Here we show that chromatin containing acetylated H2AZ and H3.3 stimulates transcription in vitro. Analysis of the Pol II pre-initiation complex on immobilized chromatin templates revealed that the E1A binding protein p400 (EP400) was bound preferentially to and required for transcription stimulation by acetylated double-variant chromatin. EP400 also stimulated H2AZ/H3.3 deposition into promoters and enhancers and influenced transcription in vivo at a step downstream of the Mediator complex. EP400 efficiently exchanged recombinant histones H2A and H3.1 with H2AZ and H3.3, respectively, in a chromatin- and ATP-stimulated manner in vitro. Our data reveal that EP400 deposits H3.3 into chromatin alongside H2AZ and contributes to gene regulation after PIC assembly.

Effects of stress management interventions on heart rate variability in adults with cardiovascular disease: a systematic review and meta-analysis.

Meta-analysis was used to investigate the potential benefits of stress management interventions (SMIs) on vagally-mediated heart rate variability (HRV) in adults with cardiovascular disease. Electronic bibliographic databases were searched through August 2022. Randomized controlled trials and quasi-experimental studies assessing effects of SMIs on HRV were included. Methodological quality was assessed with a standardized checklist. A pooled effect size was calculated for vagally-mediated HRV indices (standard deviation of normal-to-normal intervals, root mean square of the successive differences, and high frequency power) using random effects models. Fourteen studies (1202 participants, Mage: 59 ± 6.25 years; 25% ± 16% women; 61% ± 22% White) were included. Ten studies (11 effects) reported short-term HRV assessment; a small between-group difference emerged for vagally-mediated HRV (d+ = .27, 95% confidence interval [CI] 0.01-0.52, k = 11). Most interventions examined biofeedback; these studies yielded a small between-group difference on vagally-mediated HRV (d+ = 0.31, 95% CI 0.09-0.53, k = 7, Q [6] = 3.82, p = .70, I2 = 11%). This is the first systematic examination of the effect of SMIs on HRV in adults with CVD. Findings suggest a small effect of SMIs on vagally-mediated HRV, with biofeedback likely driving the effect. More research is required to fully understand whether this benefit on vagally-mediated HRV applies to other SMIs.

Investigating effects of climate-induced changes in water temperature and diet on mercury concentrations in an Arctic freshwater forage fish.

The amount of mercury (Hg) in Arctic lake food webs is, and will continue to be, affected by rapid, ongoing climate change. At warmer temperatures, fish require more energy to sustain growth; changes in their metabolic rates and consuming prey with potentially higher Hg concentrations could result in increased Hg accumulation. To examine the potential implications of climate warming on forage fish Hg accumulation in Arctic lakes, we quantified growth and Hg accumulation in Ninespine Stickleback Pungitius pungitius under different temperature and diet scenarios using bioenergetics models. Four scenarios were considered that examined the role of climate, diet, climate × diet, and climate × diet × elevated prey Hg. As expected, annual fish growth increased with warmer temperatures, but growth rates and Hg accumulation were largely diet dependent. Compared to current growth rates of 0.3 g⋅y-1, fish growth increased at least 200% for fish consuming energy-dense benthic prey and decreased at least 40% for fish consuming pelagic prey. Compared to baseline levels, the Hg burden per kilocalorie of Ninespine Stickleback declined up to 43% with benthic consumption - indicating strong somatic growth dilution - but no more than 4% with pelagic consumption; elevated prey Hg concentrations led to moderate Hg declines in benthic-foraging fish and Hg increases in pelagic-foraging fish. Bioenergetics models demonstrated the complex interaction of water temperature, growth, prey proportions, and prey Hg concentrations that respond to climate change. Further work is needed to resolve mechanisms and rates linking climate change to Hg availability and uptake in Arctic freshwater systems.

Fragile Nucleosomes Influence Pol II Promoter Function.

In this issue of Molecular Cell, Kubik et al. (2015) describe how the RSC chromatin remodeling complex collaborates with two DNA sequence motifs and sequence-specific general regulatory factors to assemble fragile nucleosomes at highly transcribed yeast Pol II promoters, and they distinguish these from promoters bearing stable nucleosomes.

The Ino80 complex prevents invasion of euchromatin into silent chromatin.

Here we show that the Ino80 chromatin remodeling complex (Ino80C) directly prevents euchromatin from invading transcriptionally silent chromatin within intergenic regions and at the border of euchromatin and heterochromatin. Deletion of Ino80C subunits leads to increased H3K79 methylation and noncoding RNA polymerase II (Pol II) transcription centered at the Ino80C-binding sites. The effect of Ino80C is direct, as it blocks H3K79 methylation by Dot1 in vitro. Heterochromatin stimulates the binding of Ino80C in vitro and in vivo. Our data reveal that Ino80C serves as a general silencing complex that restricts transcription to gene units in euchromatin.

Risk stratification through allergy history: single-centre experience of specialized COVID-19 vaccine clinic.

Anaphylaxis is a rare side-effect of COVID-19 vaccines. To (a) provide direct advice and reassurance to certain persons with a history of anaphylaxis/complex allergy, in addition to that available in national guidelines, and (b) to provide a medically supervised vaccination, a specialist regional vaccine allergy clinic was established. The main objective was to determine if risk stratification through history can lead to safe COVID-19 vaccination for maximum population coverage. A focused history was taken to establish contraindications to giving COVID-19 vaccines. People who reported a high-risk allergy history were given a vaccine not containing the excipient thought to have directly caused previous anaphylaxis. All vaccines were monitored for 30 min after administration. A total of 206 people were vaccinated between 6 July 2021 and 31 August 2021; Comirnaty (Pfizer-BioNTech) (n = 34), and Janssen (n = 172). In total, 78% were women. Ninety-two people (45%) reported a high-risk allergy history. There were no cases of anaphylaxis. Three people developed urticaria and one of these also developed transient tachycardia. One vaccinee developed a pseudoseizure. Two of 208 people (<1%) referred during this time declined vaccination based on personal preference, despite the assessment of low clinical risk. In our experience, all vaccines with high-risk allergy histories were administered Pfizer BioNTech or Janssen Covid-19 vaccines uneventfully following screening based on allergy-focussed history. Our data support that drug allergy is not associated with a higher risk of vaccine-related anaphylaxis but may act to guide the administration of alternate vaccines to people with polyethylene glycol/polysorbate 80/trometamol allergies or anaphylaxis after the first dose.

The Young Men and Media Study: A Pilot Randomized Controlled Trial of a Community-Informed, Online HIV Prevention Intervention for 14-17-Year-Old Sexual Minority Males.

The Young Men and Media study developed and pilot tested a community-informed, online HIV prevention program for adolescent sexual minority males (ASMM) in the United States. The developed intervention uses nine interactive modules to increase sexual health knowledge, promote critical examination of pornography, and decrease sexual risk among ASMM. Participants (N = 154, age 14-17 years) were recruited online in Spring 2020 and randomized to the intervention (n = 77) or other existing HIV websites (n = 77). Of the 65 intervention participants who logged in to the website, most completed all nine modules and found the content useful (average module score 4.3 out of 5 stars). The intervention also showed improved HIV/STI knowledge, increased pornography knowledge, and reduced beliefs that pornography is an accurate depiction of male-male sex. Results indicate that the Young Men and Media intervention is feasible, acceptable, and may positively impact sexual health outcomes.

The Lived Experience of Managing HIV and Chronic Pain: Qualitative Interviews with Patients and Healthcare Providers.

People living with HIV (PLWH) experience higher rates of comorbid chronic pain conditions compared to the general population. Managing HIV and chronic pain, two stigmatized health conditions, can exacerbate physical and psychological suffering. The current qualitative study was designed to increase our understanding of the experience of living with HIV and chronic pain. Twenty participants were recruited from a hospital-based immunology center to participate in individual in-depth qualitative interviews. The interviews focused on the experience of living with (or managing) chronic pain for PLWH. All interviews were audio recorded, transcribed and double-coded. Several themes emerged from our applied thematic analysis of the transcripts. The primary theme was that pain remained poorly managed among PLWH. Patients engaged in a variety of pain management strategies and described benefits from both traditional pain management interventions (e.g., pharmacology, physical therapy) as well as non-traditional approaches (e.g., medical marijuana, cannabidiol products, and spirituality). Other themes that emerged included barriers related to health insurance and the need to validate the patient pain experience. PLWH and chronic pain described compounding effects of managing two chronic health conditions, including perceived immune system over-activation, heightened awareness of illness, and negative mindset. More research is needed to improve care for those managing these often co-occurring health conditions.

Validated HIV Knowledge Scales for Use with Adults and Adolescents: A Systematic Review.

HIV knowledge - the information a person possesses about HIV - is essential for the prevention and management of HIV. Therefore, the accurate measurement of HIV knowledge is important for both science and practice. This systematic review identifies extant HIV knowledge scales that have been validated with adolescent and adult populations and summarizes the state of this research. We searched seven electronic databases, which resulted in 6,525 articles. After title/abstract and full-text review, 27 studies remained and underwent qualitative review of reported scale psychometric properties. Many studies were conducted in the last decade (n = 12), reflecting advances in scientific knowledge of HIV. Five were exclusively adolescent-based studies (sample age ≤ 18). Most studies reported reliability (n = 25) or at least one form of validity (n = 21). Future studies should develop or refine HIV knowledge scales so that they reflect recent scientific developments, use rigorous psychometric testing, and target samples that include those persons at highest risk for HIV.

Development of Long and Short Forms of the Multilevel Resilience Resource Measure for African American/Black Adults Living with HIV.

Understanding resilience in relation to HIV-related outcomes may help address racial/ethnic disparities, however, significant gaps in its measurement preclude in-depth study. Thus, this research aims to develop and evaluate the psychometric properties of long and short forms of the Multilevel Resilience Resource Measure for African American/Black Adults Living with HIV. To develop the items, we conducted a mixed methods study (N = 48) and reviewed published resilience measures. We completed content validity index analyses to ensure the items reflected the resilience construct. Next, we conducted 20 cognitive interviews and a field survey (N = 400). The long and short forms demonstrated acceptable to excellent psychometric properties based on factorial validity, internal consistency and convergent validity and on measurement invariance (conducted for the short form only). These measures provide a comprehensive framework to examine resilience and HIV-related outcomes and can inform resilience-building interventions to reduce racial and ethnic health disparities.

Resistance training for Black men with depressive symptoms: a pilot randomized controlled trial to assess acceptability, feasibility, and preliminary efficacy.

BACKGROUND: Depression is under-recognized in Black men, who are less likely to seek or have access to psychiatric treatment. Resistance training (RT; i.e., weight lifting) can improve depressive symptoms and may be more acceptable to Black men, but its effects have not been examined for Black men with depressive symptoms. METHODS: Fifty Black men with depressive symptoms were randomized to either (a) 12 weeks of RT (coupled with Behavioral Activation techniques to promote adherence) or (b) an attention-control group (Health, Wellness, and Education; HWE). Both groups met twice/week for 12 weeks, and follow-up assessments were done at end-of-treatment (EOT) and 6 months after enrollment. Changes in physical activity and muscular strength were collected as a manipulation check. The primary outcome was interviewer assessed symptoms of depression using the Quick Inventory of Depression Symptomology (QIDS). Secondary outcomes included self-reported depressive symptoms, anxiety, and stress. The association between change in QIDS from baseline to EOT and concurrent changes in physical activity and muscular strength in the RT group were explored as an initial assessment of mechanism. Longitudinal mixed effects regression models with subject-specific intercepts were used to examine intervention effects. RESULTS: A sample with high rates of medical comorbidities (e.g., 44% HIV positive), substance use (e.g., 34% smoking), and negative social determinates of health (e.g., 50% unemployed) was enrolled. Recruitment, engagement, and retention data indicate that the intervention and design were feasible. The RT group showed greater gains in self-reported exercise (b = 270.94, SE = 105.69, p = .01) and muscular strength (b = 11.71, SE = 4.23, p = .01 for upper body and b = 4.24, SE = 2.02, p = .04 for lower body) than the HWE group. The RT group had greater reductions in QIDS scores at both EOT (b = -3.00, SE = 1.34, p = .01) and 6 months (b = -2.63, SE = 1.81, p = .04). The RT group showed a greater reduction in anxiety at EOT (b = -2.67, SE = 1.06, p = .02). Findings regarding self-reported depressive symptoms and stress were non-significant, but in the expected direction with effect sizes in the small to medium range. In the RT group, improvement on the QIDS between baseline and EOT was associated with concurrent improvements in physical activity (b = 21.03, SE = 11.16, p = .02) and muscular strength (b = 1.27, SE = .44, p = .03 for upper body and b = .75, SE = .14, p = .03 for lower body). CONCLUSIONS: Results suggest that RT is feasible and may be efficacious for reducing depressive symptoms among underserved urban Black men. TRIAL REGISTRATION: ClinicalTrial.gov #: NCT03107039 (Registered 11/04/2017).

Subscribing to big data at scale.

Today, data is being actively generated by a variety of devices, services, and applications. Such data is important not only for the information that it contains, but also for its relationships to other data and to interested users. Most existing Big Data systems focus on passively answering queries from users, rather than actively collecting data, processing it, and serving it to users. To satisfy both passive and active requests at scale, application developers need either to heavily customize an existing passive Big Data system or to glue one together with systems like Streaming Engines and Pub-sub services. Either choice requires significant effort and incurs additional overhead. In this paper, we present the BAD (Big Active Data) system as an end-to-end, out-of-the-box solution for this challenge. It is designed to preserve the merits of passive Big Data systems and introduces new features for actively serving Big Data to users at scale. We show the design and implementation of the BAD system, demonstrate how BAD facilitates providing both passive and active data services, investigate the BAD system's performance at scale, and illustrate the complexities that would result from instead providing BAD-like services with a "glued" system.

A Concept Mapping Study to Understand Multilevel Resilience Resources Among African American/Black Adults Living with HIV in the Southern United States.

Resilience may help people living with HIV (PLWH) overcome adversities to disease management. This study identifies multilevel resilience resources among African American/Black (AA/B) PLWH and examines whether resilience resources differ by demographics and neighborhood risk environments. We recruited participants and conducted concept mapping at two clinics in the southeastern United States. Concept Mapping incorporates qualitative and quantitative methods to represent participant-generated concepts via two-dimensional maps. Eligible participants had to attend ≥ 75% of their scheduled clinic appointments and did not have ≥ 2 consecutive detectable HIV-1 viral load measurements in the past 2 years. Of the 85 AA/B PLWH who were invited, forty-eight participated. Twelve resilience resource clusters emerged-five individual, two interpersonal, two organizational/policy and three neighborhood level clusters. There were strong correlations in cluster ratings for demographic and neighborhood risk environment comparison groups (r ≥ 0.89). These findings could inform development of theories, measures and interventions for AA/B PLWH.

Telephone-delivered behavioral health interventions for people living with HIV: patients' perspectives from a qualitative study.

People living with HIV (PLWH) often experience mental health concerns as well as difficulties with medication adherence; they also report barriers to receipt of health services. Telephone-delivered interventions can overcome some of these barriers. To obtain patients' perspectives on telephone-delivered behavioral health services, we conducted a qualitative study with patients who participated in one of two telephone-delivered interventions (mindfulness training, health coaching) in a research trial. Patients (N = 42; M age = 46 years, 50% female, 26% Black) participated in semi-structured qualitative interviews after completing the study. They identified several advantages (e.g., being able to schedule sessions more flexibly compared to in-person appointments, ease of developing rapport with interventionists) as well as occasional challenges of phone delivery (e.g., network connectivity). Overall, PLWH view telephone-delivery as a convenient and flexible method to engage in behavioral health interventions.