Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release.

During development, inflammation or tissue injury, macrophages may successively engulf and process multiple apoptotic corpses via efferocytosis to achieve tissue homeostasis1. How macrophages may rapidly adapt their transcription to achieve continuous corpse uptake is incompletely understood. Transcriptional pause/release is an evolutionarily conserved mechanism, in which RNA polymerase (Pol) II initiates transcription for 20-60 nucleotides, is paused for minutes to hours and is then released to make full-length mRNA2. Here we show that macrophages, within minutes of corpse encounter, use transcriptional pause/release to unleash a rapid transcriptional response. For human and mouse macrophages, the Pol II pause/release was required for continuous efferocytosis in vitro and in vivo. Interestingly, blocking Pol II pause/release did not impede Fc receptor-mediated phagocytosis, yeast uptake or bacterial phagocytosis. Integration of data from three genomic approaches-precision nuclear run-on sequencing, RNA sequencing, and assay for transposase-accessible chromatin using sequencing (ATAC-seq)-on efferocytic macrophages at different time points revealed that Pol II pause/release controls expression of select transcription factors and downstream target genes. Mechanistic studies on transcription factor EGR3, prominently regulated by pause/release, uncovered EGR3-related reprogramming of other macrophage genes involved in cytoskeleton and corpse processing. Using lysosomal probes and a new genetic fluorescent reporter, we identify a role for pause/release in phagosome acidification during efferocytosis. Furthermore, microglia from egr3-deficient zebrafish embryos displayed reduced phagocytosis of apoptotic neurons and fewer maturing phagosomes, supporting defective corpse processing. Collectively, these data indicate that macrophages use Pol II pause/release as a mechanism to rapidly alter their transcriptional programs for efficient processing of the ingested apoptotic corpses and for successive efferocytosis.

Decoding the Epigenetics and Chromatin Loop Dynamics of Androgen Receptor-Mediated Transcription.

Androgen receptor (AR)-mediated transcription plays a critical role in normal prostate development and prostate cancer growth. AR drives gene expression by binding to thousands of cis-regulatory elements (CRE) that loop to hundreds of target promoters. With multiple CREs interacting with a single promoter, it remains unclear how individual AR bound CREs contribute to gene expression. To characterize the involvement of these CREs, we investigated the AR-driven epigenetic and chromosomal chromatin looping changes. We collected a kinetic multi-omic dataset comprised of steady-state mRNA, chromatin accessibility, transcription factor binding, histone modifications, chromatin looping, and nascent RNA. Using an integrated regulatory network, we found that AR binding induces sequential changes in the epigenetic features at CREs, independent of gene expression. Further, we showed that binding of AR does not result in a substantial rewiring of chromatin loops, but instead increases the contact frequency of pre-existing loops to target promoters. Our results show that gene expression strongly correlates to the changes in contact frequency. We then proposed and experimentally validated an unbalanced multi-enhancer model where the impact on gene expression of AR-bound enhancers is heterogeneous, and is proportional to their contact frequency with target gene promoters. Overall, these findings provide new insight into AR-mediated gene expression upon acute androgen simulation and develop a mechanistic framework to investigate nuclear receptor mediated perturbations.

Inherited blood cancer predisposition through altered transcription elongation.

Despite advances in defining diverse somatic mutations that cause myeloid malignancies, a significant heritable component for these cancers remains largely unexplained. Here, we perform rare variant association studies in a large population cohort to identify inherited predisposition genes for these blood cancers. CTR9, which encodes a key component of the PAF1 transcription elongation complex, is among the significant genes identified. The risk variants found in the cases cause loss of function and result in a ∼10-fold increased odds of acquiring a myeloid malignancy. Partial CTR9 loss of function expands human hematopoietic stem cells (HSCs) by increased super elongation complex-mediated transcriptional activity, which thereby increases the expression of key regulators of HSC self-renewal. By following up on insights from a human genetic study examining inherited predisposition to the myeloid malignancies, we define a previously unknown antagonistic interaction between the PAF1 and super elongation complexes. These insights could enable targeted approaches for blood cancer prevention.

PRO-seq: Precise Mapping of Engaged RNA Pol II at Single-Nucleotide Resolution.

Gene regulation is dependent on the production of mRNAs and a repertoire of non-coding RNAs by RNA polymerase II (RNAPII). Precision run-on sequencing (PRO-seq) maps the position of engaged RNAPII complexes at single-nucleotide resolution and can reveal direct targets of regulation, locations of enhancers, and transcription mechanisms that are difficult or impossible to measure by analysis of total cellular RNA. Briefly, this method first involves permeabilizing cells with mild detergents to remove intracellular NTPs and halt transcription. Transcription is then resumed in the presence of biotin-NTPs and sarkosyl to allow transcriptional incorporation of a single biotinylated NTP by RNAPII. The biotin moiety is then bound to streptavidin beads to stringently enrich for nascent RNAs. Sequencing libraries are then generated such that the first base read corresponds to the 3' end of the nascent transcript. Here, we describe our current protocol for generating PRO-seq libraries from metazoan cells, including adaptations of previously published protocols to incorporate unique molecular identifiers, reduce ligation bias, and improve library yields. Additional commentary describes quality control and processing of PRO-seq data and references for more advanced downstream analysis such as gene and enhancer identification. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Cell permeabilization for PRO-seq Basic Protocol 2: Construction of PRO-seq libraries Support Protocol: Adenylation of 3' adapter.

Temporal resolution of gene derepression and proteome changes upon PROTAC-mediated degradation of BCL11A protein in erythroid cells.

Reactivation of fetal hemoglobin expression by the downregulation of BCL11A is a promising treatment for ß-hemoglobinopathies. A detailed understanding of BCL11A-mediated repression of γ-globin gene (HBG1/2) transcription is lacking, as studies to date used perturbations by shRNA or CRISPR-Cas9 gene editing. We leveraged the dTAG PROTAC degradation platform to acutely deplete BCL11A protein in erythroid cells and examined consequences by nascent transcriptomics, proteomics, chromatin accessibility, and histone profiling. Among 31 genes repressed by BCL11A, HBG1/2 and HBZ show the most abundant and progressive changes in transcription and chromatin accessibility upon BCL11A loss. Transcriptional changes at HBG1/2 were detected in <2 h. Robust HBG1/2 reactivation upon acute BCL11A depletion occurred without the loss of promoter 5-methylcytosine (5mC). Using targeted protein degradation, we establish a hierarchy of gene reactivation at BCL11A targets, in which nascent transcription is followed by increased chromatin accessibility, and both are uncoupled from promoter DNA methylation at the HBG1/2 loci.

A ubiquitous disordered protein interaction module orchestrates transcription elongation.

During eukaryotic transcription elongation, RNA polymerase II (RNAP2) is regulated by a chorus of factors. Here, we identified a common binary interaction module consisting of TFIIS N-terminal domains (TNDs) and natively unstructured TND-interacting motifs (TIMs). This module was conserved among the elongation machinery and linked complexes including transcription factor TFIIS, Mediator, super elongation complex, elongin, IWS1, SPT6, PP1-PNUTS phosphatase, H3K36me3 readers, and other factors. Using nuclear magnetic resonance, live-cell microscopy, and mass spectrometry, we revealed the structural basis for these interactions and found that TND-TIM sequences were necessary and sufficient to induce strong and specific colocalization in the crowded nuclear environment. Disruption of a single TIM in IWS1 induced robust changes in gene expression and RNAP2 elongation dynamics, which underscores the functional importance of TND-TIM surfaces for transcription elongation.

Informatics response to address the COVID-19 pandemic in a safety net healthcare system.

In service of particularly vulnerable populations, safety net healthcare systems must nimbly leverage health information technology (IT), including electronic health records (EHRs), to coordinate the medical and public health response to the novel coronavirus (COVID-19). Six months after the San Francisco Department of Public Health implemented a new EHR across its hospitals and citywide clinics, California declared a state of emergency in response to COVID-19. This paper describes how the IT and informatics teams supported San Francisco Department of Public Health's goals of expanding the safety net healthcare system capacity, meeting the needs of specific vulnerable populations, increasing equity in COVID-19 testing access, and expanding public health analytics and research capacity. Key enabling factors included critical partnerships with operational leaders, early identification of priorities, a clear governance structure, agility in the face of rapidly changing circumstances, and a commitment to vulnerable populations.

Novel Coronavirus (COVID-19) Infection-Attributed Acute Pancreatitis: A Case Report and Literature Review.

Novel coronavirus (COVID-19) has spread widely across the world inducing a global health crisis. Predominant signs of infection involve respiratory symptoms such as cough and dyspnea. Investigation into COVID-19 infection-associated gastrointestinal symptoms remains fluid. COVID-19-induced acute pancreatitis has been recorded from greater than 20 countries at this time. Herein, we submit a case of COVID-19-attributed acute pancreatitis, as well as a comprehensive assessment of previously reported cases of COVID-19-attributed acute pancreatitis.

Negative elongation factor regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation.

Negative elongation factor (NELF) is a critical transcriptional regulator that stabilizes paused RNA polymerase to permit rapid gene expression changes in response to environmental cues. Although NELF is essential for embryonic development, its role in adult stem cells remains unclear. In this study, through a muscle-stem-cell-specific deletion, we showed that NELF is required for efficient muscle regeneration and stem cell pool replenishment. In mechanistic studies using PRO-seq, single-cell trajectory analyses and myofiber cultures revealed that NELF works at a specific stage of regeneration whereby it modulates p53 signaling to permit massive expansion of muscle progenitors. Strikingly, transplantation experiments indicated that these progenitors are also necessary for stem cell pool repopulation, implying that they are able to return to quiescence. Thus, we identified a critical role for NELF in the expansion of muscle progenitors in response to injury and revealed that progenitors returning to quiescence are major contributors to the stem cell pool repopulation.

Systematic Collection of Sexual Orientation and Gender Identity in a Public Health System: The San Francisco Health Network SO/GI Systems-Change Initiative.

BACKGROUND: Lesbian, gay, bisexual, transgender, and queer (LGBTQ+) individuals experience disparate outcomes within health care that are often unacknowledged by health systems due to lack of systematic collection of sexual orientation/gender identity (SO/GI) data. METHODS: This article describes a San Francisco Department of Public Health (SFDPH) initiative to standardize SO/GI data collection for every patient/client utilizing SFDPH services, as well as the training development and implementation around this initiative. This initiative incorporated community engagement throughout and had an aim of meeting new regulatory requirements, improving patient experience and, ultimately, equipping staff with the needed data to uncover and reduce health disparities. RESULTS: Upon completion of the first wave of training (May 2019), a total of 5618 (69.1%) staff completed the online training and 2189 (26.7%) staff completed the optional in-person training. As of June 2020, SO/GI was collected in 35.0 percent of empanelled primary care patients and in 26.8 percent of the unique patient encounters overall throughout the health network. CONCLUSIONS: This initiative demonstrated the feasibility of implementing SO/GI data collection as an inclusive and community-driven culture change initiative, fully integrated with the complexities of operational change in a diverse public health network. Next steps include providing ongoing training and support for clinicians, staff, and patients, implementing SO/GI data collection for pediatric patients/clients, and identifying health disparities within the network to create targeted interventions and improve the care experience for our LGBTQ+ patients/clients.

Analysis of Bacterial Transcription by "Massively Systematic Transcript End Readout," MASTER.

A systems-level view of cellular gene expression requires understanding the mechanistic principles governing each step of transcription. In this chapter, we describe a massively multiplexed method for the analysis of the relationship between nucleic acid sequence and transcription termed "MASTER," for massively systematic transcript end readout. MASTER enables parallel measurements of transcription output from at least 410 (~1,000,000) individual template sequences in vitro and in vivo. MASTER involves constructing a DNA template library of barcoded sequences, generating RNA transcripts from the library during transcription in vitro or in vivo, and analyzing the relative abundance and 5'-end sequences of the RNA transcripts by high-throughput sequencing. MASTER provides a powerful, rapid, and versatile method to identify sequence determinants of each step of transcription and to define the mechanistic basis by which these sequence determinants dictate transcription output.

Acute Clinical Care for Transgender Patients: A Review.

Importance: Transgender is an umbrella term used to describe individuals whose gender identity and/or gender expression differs from assigned sex at birth. There are an estimated 1.4 million transgender adults in the United States, and this number is increasing. Clinicians will increasingly be caring for transgender patients. Topics considered in this narrative review include terminology, how to address transgender patients, obtaining an inclusive history that takes into account gender-affirming surgery, managing hormone therapy and other clinical issues, consideration for hospitalized patients, interpreting laboratory values in the setting of hormone use, legal issues, and considerations for health systems. Observations: Best practices in caring for a transgender patient include using a patient-identified name and pronoun, using gender-neutral terminology until the appropriate term is identified by the patient, and obtaining a surgical history inclusive of an anatomic inventory. Gender-affirming hormones can modify disease-specific risk factors or confer risk for in-hospital complications. They can also cause changes in laboratory values; however, studies are limited to observational studies and case series. Some data are derived and extrapolated from cisgender populations. There are also unique systems-based concerns, including lack of procedures for standardized collection of gender identity and lack of sufficiently comprehensive electronic health record platforms. Vulnerabilities exist for hospitalized transgender patients in the transition from the inpatient to outpatient care that require dedicated institutional efforts to address. Conclusions and Relevance: Clinicians should learn how to engage with transgender patients, appreciate that unique anatomy or the use of gender-affirming hormones may affect the prevalence of certain disease (eg, cardiovascular disease, venous thromboembolism, and osteoporosis), and be prepared to manage specific issues, including those related to hormone therapy. Health care facilities should work toward providing inclusive systems of care that correctly identify and integrate information about transgender patients into the electronic health record, account for the unique needs of these patients within the facility, and through education and policy create a welcoming environment for their care.

Improving best possible medication history with vulnerable patients at an urban safety net academic hospital using pharmacy technicians.

BACKGROUND: Best possible medication history (BPMH) enhances the care of safety net patients, especially those with limited English proficiency and limited health literacy who are most vulnerable to medication error during the hospital admission process. Our large urban academic safety net centre faced numerous barriers to achieve BPMH among hospitalised patients including communication barriers that increase the time and complexity of eliciting BPMH, frequent provider turnover at our training institution and lack of an electronic health record (EHR) medication reconciliation tool to facilitate BPMH collection and monitoring. DESIGN: Leveraging opportunities afforded by the US federal incentive EHR programme, our multidisciplinary team designed an EHR-facilitated medication reconciliation programme by which pharmacy technicians engaged newly admitted patients and their caregivers at the bedside to develop and electronically document the BPMH. STRATEGY: Prior to this intervention, pharmacy technicians had no role in BPMH. Providers collected home medications documented on paper notes without a consistent methodology. With each plan-do-study-act (PDSA) cycle since the programme began, the goal was to increase the per cent of BPMH completed by a pharmacy technician. Individual PDSA cycles targeted either the pharmacy technicians by expanding their pool of eligible patients or provider engagement with the pharmacy technician workflow. RESULTS: By optimising not only the health information technology platform but also the operational processes, the programme achieved a nearly 80% generation of BPMH completed by a highly trained pharmacy technician, surpassing its intended goal of 50% BPMH completion by a pharmacy technician on admission. CONCLUSION: An EHR-facilitated tool improved BPMH at an urban academic safety net hospital using pharmacy technicians.

Massively Systematic Transcript End Readout, "MASTER": Transcription Start Site Selection, Transcriptional Slippage, and Transcript Yields.

We report the development of a next-generation sequencing-based technology that entails construction of a DNA library comprising up to at least 4(7) (∼ 16,000) barcoded sequences, production of RNA transcripts, and analysis of transcript ends and transcript yields (massively systematic transcript end readout, "MASTER"). Using MASTER, we define full inventories of transcription start sites ("TSSomes") of Escherichia coli RNA polymerase for initiation at a consensus core promoter in vitro and in vivo; we define the TSS-region DNA sequence determinants for TSS selection, reiterative initiation ("slippage synthesis"), and transcript yield; and we define effects of DNA topology and NTP concentration. The results reveal that slippage synthesis occurs from the majority of TSS-region DNA sequences and that TSS-region DNA sequences have profound, up to 100-fold, effects on transcript yield. The results further reveal that TSSomes depend on DNA topology, consistent with the proposal that TSS selection involves transcription-bubble expansion ("scrunching") and transcription-bubble contraction ("anti-scrunching").

The primary σ factor in Escherichia coli can access the transcription elongation complex from solution in vivo.

The σ subunit of bacterial RNA polymerase (RNAP) confers on the enzyme the ability to initiate promoter-specific transcription. Although σ factors are generally classified as initiation factors, σ can also remain associated with, and modulate the behavior of, RNAP during elongation. Here we establish that the primary σ factor in Escherichia coli, σ(70), can function as an elongation factor in vivo by loading directly onto the transcription elongation complex (TEC) in trans. We demonstrate that σ(70) can bind in trans to TECs that emanate from either a σ(70)-dependent promoter or a promoter that is controlled by an alternative σ factor. We further demonstrate that binding of σ(70) to the TEC in trans can have a particularly large impact on the dynamics of transcription elongation during stationary phase. Our findings establish a mechanism whereby the primary σ factor can exert direct effects on the composition of the entire transcriptome, not just that portion that is produced under the control of σ(70)-dependent promoters.

A Conserved Pattern of Primer-Dependent Transcription Initiation in Escherichia coli and Vibrio cholerae Revealed by 5' RNA-seq.

Transcription initiation that involves the use of a 2- to ~4-nt oligoribonucleotide primer, "primer-dependent initiation," (PDI) has been shown to be widely prevalent at promoters of genes expressed during the stationary phase of growth in Escherichia coli. However, the extent to which PDI impacts E. coli physiology, and the extent to which PDI occurs in other bacteria is not known. Here we establish a physiological role for PDI in E. coli as a regulatory mechanism that modulates biofilm formation. We further demonstrate using high-throughput sequencing of RNA 5' ends (5' RNA-seq) that PDI occurs in the pathogenic bacterium Vibrio cholerae. A comparative global analysis of PDI in V. cholerae and E. coli reveals that the pattern of PDI is strikingly similar in the two organisms. In particular, PDI is detected in stationary phase, is not detected in exponential phase, and is preferentially apparent at promoters carrying the sequence T-1A+1 or G-1G+1 (where position +1 corresponds to the position of de novo initiation). Our findings demonstrate a physiological role for PDI and suggest PDI may be widespread among Gammaproteobacteria. We propose that PDI in both E. coli and V. cholerae occurs though a growth phase-dependent process that leads to the preferential generation of the linear dinucleotides 5´-UA-3´ and 5´-GG-3´.

Preparation of cDNA libraries for high-throughput RNA sequencing analysis of RNA 5' ends.

We provide a detailed protocol for preparing cDNA libraries suitable for high-throughput sequencing that are derived specifically from the 5' ends of RNA (5' specific RNA-seq). The protocol describes how cDNA libraries for 5' specific RNA-seq can be tailored to analyze specific classes of RNAs based upon the phosphorylation status of the 5' end. Thus, the analysis of cDNA libraries generated by these methods provides information regarding both the sequence and phosphorylation status of the 5' ends of RNAs. 5' specific RNA-seq can be used to analyze transcription initiation and posttranscriptional processing of RNAs with single base pair resolution on a genome-wide level.

Interactions between RNA polymerase and the "core recognition element" counteract pausing.

Transcription elongation is interrupted by sequences that inhibit nucleotide addition and cause RNA polymerase (RNAP) to pause. Here, by use of native elongating transcript sequencing (NET-seq) and a variant of NET-seq that enables analysis of mutant RNAP derivatives in merodiploid cells (mNET-seq), we analyze transcriptional pausing genome-wide in vivo in Escherichia coli. We identify a consensus pause-inducing sequence element, G₋10Y₋1G(+1) (where -1 corresponds to the position of the RNA 3' end). We demonstrate that sequence-specific interactions between RNAP core enzyme and a core recognition element (CRE) that stabilize transcription initiation complexes also occur in transcription elongation complexes and facilitate pause read-through by stabilizing RNAP in a posttranslocated register. Our findings identify key sequence determinants of transcriptional pausing and establish that RNAP-CRE interactions modulate pausing.

Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs.

Prokaryotic and eukaryotic RNA polymerases can use 2- to ∼4-nt RNAs, "nanoRNAs," to prime transcription initiation in vitro. It has been proposed that nanoRNA-mediated priming of transcription can likewise occur under physiological conditions in vivo and influence transcription start site selection and gene expression. However, no direct evidence of such regulation has been presented. Here we demonstrate in Escherichia coli that nanoRNAs prime transcription in a growth phase-dependent manner, resulting in alterations in transcription start site selection and changes in gene expression. We further define a sequence element that determines, in part, whether a promoter will be targeted by nanoRNA-mediated priming. By establishing that a significant fraction of transcription initiation is primed in living cells, our findings contradict the conventional model that all cellular transcription is initiated using nucleoside triphosphates (NTPs) only. In addition, our findings identify nanoRNAs as a previously undocumented class of regulatory small RNAs that function by being directly incorporated into a target transcript.

NanoRNAs prime transcription initiation in vivo.

It is often presumed that, in vivo, the initiation of RNA synthesis by DNA-dependent RNA polymerases occurs using NTPs alone. Here, using the model Gram-negative bacterium Pseudomonas aeruginosa, we demonstrate that depletion of the small-RNA-specific exonuclease, Oligoribonuclease, causes the accumulation of oligoribonucleotides 2 to ∼4 nt in length, "nanoRNAs," which serve as primers for transcription initiation at a significant fraction of promoters. Widespread use of nanoRNAs to prime transcription initiation is coupled with global alterations in gene expression. Our results, obtained under conditions in which the concentration of nanoRNAs is artificially elevated, establish that small RNAs can be used to initiate transcription in vivo, challenging the idea that all cellular transcription occurs using only NTPs. Our findings further suggest that nanoRNAs could represent a distinct class of functional small RNAs that can affect gene expression through direct incorporation into a target RNA transcript rather than through a traditional antisense-based mechanism.