LDB1 establishes multi-enhancer networks to regulate gene expression.

How specific enhancer-promoter pairing is established remains mostly unclear. Besides the CTCF/cohesin machinery, few nuclear factors have been studied for a direct role in physically connecting regulatory elements. Using a murine erythroid cell model, we show via acute degradation experiments that LDB1 directly and broadly promotes connectivity among regulatory elements.

Quantitative Liver Fat Assessment by Handheld Point-of-Care Ultrasound: A Technical Implementation and Pilot Study in Adults.

Objectives: To implement, examine the feasibility of, and evaluate the performance of quantitative ultrasound (QUS) with a handheld point-of-care US (POCUS) device for assessing liver fat in adults.

Materials And Methods: This prospective IRB-approved, HIPAA-compliant pilot study enrolled adults with overweight or obesity. Participants underwent chemical-shift-encoded magnetic resonance imaging to estimate proton density fat fraction (PDFF) and, within 1 mo, QUS with a POCUS device by expert sonographers and novice operators (no prior US scanning experience).

The DNA damage response and RNA Polymerase II regulator Def1 has posttranscriptional functions in the cytoplasm.

Yeast Def1 mediates RNA polymerase II degradation and transcription elongation during stress. Def1 is predominantly cytoplasmic, and DNA damage signals cause its proteolytic processing, liberating its N-terminus to enter the nucleus. Cytoplasmic functions for this abundant protein have not been identified.

LDB1 establishes multi-enhancer networks to regulate gene expression.

How specific enhancer-promoter pairing is established is still mostly unclear. Besides the CTCF/cohesin machinery, only a few nuclear factors have been studied for a direct role in physically connecting regulatory elements. Here, we show via acute degradation experiments that LDB1 directly and broadly promotes enhancer-promoter loops.

YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle.

Few transcription factors have been examined for their direct roles in physically connecting enhancers and promoters. Here acute degradation of Yin Yang 1 (YY1) in erythroid cells revealed its requirement for the maintenance of numerous enhancer-promoter loops, but not compartments or domains. Despite its reported ability to interact with cohesin, the formation of YY1-dependent enhancer-promoter loops does not involve stalling of cohesin-mediated loop extrusion.

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes.

Knowledge of locations and activities of -regulatory elements (CREs) is needed to decipher basic mechanisms of gene regulation and to understand the impact of genetic variants on complex traits. Previous studies identified candidate CREs (cCREs) using epigenetic features in one species, making comparisons difficult between species. In contrast, we conducted an interspecies study defining epigenetic states and identifying cCREs in blood cell types to generate regulatory maps that are comparable between species, using integrative modeling of eight epigenetic features jointly in human and mouse in our Validated Systematic Integration (VISION) Project.

Genome folding principles uncovered in condensin-depleted mitotic chromosomes.

During mitosis, condensin activity is thought to interfere with interphase chromatin structures. To investigate genome folding principles in the absence of chromatin loop extrusion, we codepleted condensin I and condensin II, which triggered mitotic chromosome compartmentalization in ways similar to that in interphase. However, two distinct euchromatic compartments, indistinguishable in interphase, emerged upon condensin loss with different interaction preferences and dependencies on H3K27ac.

Public Health Data Applications Using the CDC Tracking Network: Augmenting Environmental Hazard Information With Lower-Latency NASA Data.

Exposure to environmental hazards is an important determinant of health, and the frequency and severity of exposures is expected to be impacted by climate change. Through a partnership with the U.S.

Genome folding principles revealed in condensin-depleted mitotic chromosomes.

During mitosis, condensin activity interferes with interphase chromatin structures. Here, we generated condensin-free mitotic chromosomes to investigate genome folding principles. Co-depletion of condensin I and II, but neither alone, triggered mitotic chromosome compartmentalization in ways that differ from interphase.

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes.

Knowledge of locations and activities of cis-regulatory elements (CREs) is needed to decipher basic mechanisms of gene regulation and to understand the impact of genetic variants on complex traits. Previous studies identified candidate CREs (cCREs) using epigenetic features in one species, making comparisons difficult between species. In contrast, we conducted an interspecies study defining epigenetic states and identifying cCREs in blood cell types to generate regulatory maps that are comparable between species, using integrative modeling of eight epigenetic features jointly in human and mouse in our Validated Systematic Integration (VISION) Project.

Snapshot: a package for clustering and visualizing epigenetic history during cell differentiation.

Background: Epigenetic modification of chromatin plays a pivotal role in regulating gene expression during cell differentiation. The scale and complexity of epigenetic data pose significant challenges for biologists to identify the regulatory events controlling cell differentiation.

Results: To reduce the complexity, we developed a package, called Snapshot, for clustering and visualizing candidate cis-regulatory elements (cCREs) based on their epigenetic signals during cell differentiation.

Molecular basis of polycomb group protein-mediated fetal hemoglobin repression.

The switch from fetal hemoglobin (HbF) to adult hemoglobin (HbA) is a paradigm for developmental gene expression control with relevance to sickle cell disease and β-thalassemia. Polycomb repressive complex (PRC) proteins regulate this switch, and an inhibitor of PRC2 has entered a clinical trial for HbF activation. Yet, how PRC complexes function in this process, their target genes, and relevant subunit composition are unknown.

Nonalcoholic fatty liver disease (NAFLD) detection and deep learning in a Chinese community-based population.

Objectives: We aimed to develop and validate a deep learning system (DLS) by using an auxiliary section that extracts and outputs specific ultrasound diagnostic features to improve the explainable, clinical relevant utility of using DLS for detecting NAFLD.

Methods: In a community-based study of 4144 participants with abdominal ultrasound scan in Hangzhou, China, we sampled 928 (617 [66.5%] females, mean age: 56 years ± 13 [standard deviation]) participants (2 images per participant) to develop and validate DLS, a two-section neural network (2S-NNet).

Gene silencing dynamics are modulated by transiently active regulatory elements.

Transcriptional enhancers have been extensively characterized, but cis-regulatory elements involved in acute gene repression have received less attention. Transcription factor GATA1 promotes erythroid differentiation by activating and repressing distinct gene sets. Here, we study the mechanism by which GATA1 silences the proliferative gene Kit during murine erythroid cell maturation and define stages from initial loss of activation to heterochromatinization.

CLIMB: High-dimensional association detection in large scale genomic data.

Joint analyses of genomic datasets obtained in multiple different conditions are essential for understanding the biological mechanism that drives tissue-specificity and cell differentiation, but they still remain computationally challenging. To address this we introduce CLIMB (Composite LIkelihood eMpirical Bayes), a statistical methodology that learns patterns of condition-specificity present in genomic data. CLIMB provides a generic framework facilitating a host of analyses, such as clustering genomic features sharing similar condition-specific patterns and identifying which of these features are involved in cell fate commitment.

CTCF blocks antisense transcription initiation at divergent promoters.

Transcription at most promoters is divergent, initiating at closely spaced oppositely oriented core promoters to produce sense transcripts along with often unstable upstream antisense transcripts (uasTrx). How antisense transcription is regulated and to what extent it is coordinated with sense transcription is not well understood. Here, by combining acute degradation of the multi-functional transcription factor CTCF and nascent transcription measurements, we find that CTCF specifically suppresses antisense but not sense transcription at hundreds of divergent promoters.

Remote ex vivo lung perfusion at a centralized evaluation facility.

Background: In the US, only 23% of lungs offered for transplantation are transplanted. Ex vivo lung perfusion (EVLP) allows for evaluation of additional donor lungs; its adoption has been limited by resources and expertise. Dedicated facilities with a centralized lung evaluation system (CLES) could expand access to EVLP.

HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription.

The fetal-to-adult switch in hemoglobin production is a model of developmental gene control with relevance to the treatment of hemoglobinopathies. The expression of transcription factor BCL11A, which represses fetal β-type globin (HBG) genes in adult erythroid cells, is predominantly controlled at the transcriptional level but the underlying mechanism is unclear. We identify HIC2 as a repressor of BCL11A transcription.

NASA GEOS Composition Forecast Modeling System GEOS-CF v1.0: Stratospheric Composition.

The NASA Goddard Earth Observing System (GEOS) Composition Forecast (GEOS-CF) provides recent estimates and 5-day forecasts of atmospheric composition to the public in near-real time. To do this, the GEOS Earth system model is coupled with the GEOS-Chem tropospheric-stratospheric unified chemistry extension (UCX) to represent composition from the surface to the top of the GEOS atmosphere (0.01 hPa).

Aerosol-Radiation Interactions in China in Winter: Competing Effects of Reduced Shortwave Radiation and Cloud-Snowfall-Albedo Feedbacks Under Rapidly Changing Emissions.

Since 2013, Chinese policies have dramatically reduced emissions of particulates and their gas-phase precursors, but the implications of these reductions for aerosol-radiation interactions are unknown. Using a global, coupled chemistry-climate model, we examine how the radiative impacts of Chinese air pollution in the winter months of 2012 and 2013 affect local meteorology and how these changes may, in turn, influence surface concentrations of PM, particulate matter with diameter <2.5 μm.

Eisenmenger Syndrome in Case of Extended Goldenhar Complex Treated With Heart-Lung Transplantation.

A patient diagnosed with expanded Goldenhar complex with oculoauriculovertebral spectrum complicated with complex pulmonary and congenital heart disease, underwent successful heart-lung transplantation 21 years ago, with excellent functional outcome and good quality of life. Heart-lung transplantation can be an option of care for patients with expanded Goldenhar complex. ().