Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing

Variations in transcription start site (TSS) selection reflect diversity of preinitiation complexes and can impact on post-transcriptional RNA fates. Most metazoan polymerase II-transcribed genes carry canonical initiation with pyrimidine/purine (YR) dinucleotide, while translation machinery-associated genes carry polypyrimidine initiator (5'-TOP or TCT). By addressing the developmental regulation of TSS selection in zebrafish we uncovered a class of dual-initiation promoters in thousands of genes, including snoRNA host genes. 5'-TOP/TCT initiation is intertwined with canonical initiation and used divergently in hundreds of dual-initiation promoters during maternal to zygotic transition. Dual-initiation in snoRNA host genes selectively generates host and snoRNA with often different spatio-temporal expression. Dual-initiation promoters are pervasive in human and fruit fly, reflecting evolutionary conservation. We propose that dual-initiation on shared promoters represents a composite promoter architecture, which can function both coordinately and divergently to diversify RNAs

A cell cycle-coordinated Polymerase II transcription compartment encompasses gene expression before global genome activation

© 2019, The Author(s). Most metazoan embryos commence development with rapid, transcriptionally silent cell divisions, with genome activation delayed until the mid-blastula transition (MBT). However, a set of genes escapes global repression and gets activated before MBT. Here we describe the formation and the spatio-temporal dynamics of a pair of distinct transcription compartments, which encompasses the earliest gene expression in zebrafish. 4D imaging of pri-miR430 and zinc-finger-gene activities by a novel, native transcription imaging approach reveals transcriptional sharing of nuclear compartments, which are regulated by homologous chromosome organisation. These compartments carry the majority of nascent-RNAs and active Polymerase II, are chromatin-depleted and represent the main sites of detectable transcription before MBT. Transcription occurs during the S-phase of increasingly permissive cleavage cycles. It is proposed, that the transcription compartment is part of the regulatory architecture of embryonic nuclei and offers a transcriptionally competent environment to facilitate early escape from repression before global genome activation

Acute diverticulitis in immunocompromised patients: evidence from an international multicenter observational registry (Web-based International Register of Emergency Surgery and Trauma, Wires-T)

Background: Immunocompromised patients with acute diverticulitis are at increased risk of morbidity and mortality. The aim of this study was to compare clinical presentations, types of treatment, and outcomes between immunocompromised and immunocompetent patients with acute diverticulitis. Methods: We compared the data of patients with acute diverticulitis extracted from the Web-based International Registry of Emergency Surgery and Trauma (WIRES-T) from January 2018 to December 2021. First, two groups were identified: medical therapy (A) and surgical therapy (B). Each group was divided into three subgroups: nonimmunocompromised (grade 0), mildly to moderately (grade 1), and severely immunocompromised (grade 2). Results: Data from 482 patients were analyzed—229 patients (47.5%) [M:F = 1:1; median age: 60 (24–95) years] in group A and 253 patients (52.5%) [M:F = 1:1; median age: 71 (26–94) years] in group B. There was a significant difference between the two groups in grade distribution: 69.9% versus 38.3% for grade 0, 26.6% versus 51% for grade 1, and 3.5% versus 10.7% for grade 2 (p < 0.00001). In group A, severe sepsis (p = 0.027) was more common in higher grades of immunodeficiency. Patients with grade 2 needed longer hospitalization (p = 0.005). In group B, a similar condition was found in terms of severe sepsis (p = 0.002), quick Sequential Organ Failure Assessment score > 2 (p = 0.0002), and Mannheim Peritonitis Index (p = 0.010). A Hartmann’s procedure is mainly performed in grades 1–2 (p < 0.0001). Major complications increased significantly after a Hartmann’s procedure (p = 0.047). Mortality was higher in the immunocompromised patients (p = 0.002). Conclusions: Immunocompromised patients with acute diverticulitis present with a more severe clinical picture. When surgery is required, immunocompromised patients mainly undergo a Hartmann’s procedure. Postoperative morbidity and mortality are, however, higher in immunocompromised patients, who also require a longer hospital stay

F-Spondin/spon1b Expression Patterns in Developing and Adult Zebrafish

F-spondin, an extracellular matrix protein, is an important player in embryonic morphogenesis and CNS development, but its presence and role later in life remains largely unknown. We generated a transgenic zebrafish in which GFP is expressed under the control of the F-spondin (spon1b) promoter, and used it in combination with complementary techniques to undertake a detailed characterization of the expression patterns of F-spondin in developing and adult brain and periphery. We found that F-spondin is often associated with structures forming long neuronal tracts, including retinal ganglion cells, the olfactory bulb, the habenula, and the nucleus of the medial longitudinal fasciculus (nMLF). F-spondin expression coincides with zones of adult neurogenesis and is abundant in CSF-contacting secretory neurons, especially those in the hypothalamus. Use of this new transgenic model also revealed F-spondin expression patterns in the peripheral CNS, notably in enteric neurons, and in peripheral tissues involved in active patterning or proliferation in adults, including the endoskeleton of zebrafish fins and the continuously regenerating pharyngeal teeth. Moreover, patterning of the regenerating caudal fin following fin amputation in adult zebrafish was associated with F-spondin expression in the blastema, a proliferative region critical for tissue reconstitution. Together, these findings suggest major roles for F-spondin in the CNS and periphery of the developing and adult vertebrate

Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish

Zebrafish, a popular model for embryonic development and for modelling human diseases, has so far lacked a systematic functional annotation programme akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created the first central repository to store and process zebrafish developmental functional genomic data. Our Data Coordination Center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and reanalysed published genomics data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements in development, including novel classes with distinct features dependent on their activity in time and space. We delineated the distinction between regulatory elements active during zygotic genome activation and those active during organogenesis, identifying new aspects of how they relate to each other. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predict functional relationships between them beyond sequence similarity, extending the utility of zebrafish developmental genomics to mammals

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

Spatiotemporal control of gene expression is central to animal development. Core promoters represent a previously unanticipated regulatory level by interacting with cis-regulatory elements and transcription initiation in different physiological and developmental contexts. Here, we provide a first and comprehensive description of the core promoter repertoire and its dynamic use during the development of a vertebrate embryo. By using cap analysis of gene expression (CAGE), we mapped transcription initiation events at single nucleotide resolution across 12 stages of zebrafish development. These CAGE-based transcriptome maps reveal genome-wide rules of core promoter usage, structure, and dynamics, key to understanding the control of gene regulation during vertebrate ontogeny. They revealed the existence of multiple classes of pervasive intra- and intergenic post-transcriptionally processed RNA products and their developmental dynamics. Among these RNAs, we report splice donor site-associated intronicRNA(sRNA) to be specific to genes of the splicing machinery. For the identification of conserved features, we compared the zebrafish data sets to the first CAGE promoter map of Tetraodon and the existing human CAGE data. We show that a number of features, such as promoter type, newly discovered promoter properties such as a specialized purine-rich initiator motif, as well as sRNAs and the genes in which they are detected, are conserved in mammalian and Tetraodon CAGE-defined promoter maps. The zebrafish developmental promoterome represents a powerful resource for studying developmental gene regulation and revealing promoter features shared across vertebrates

Time for a paradigm shift in shared decision-making in trauma and emergency surgery? Results from an international survey

Background: Shared decision-making (SDM) between clinicians and patients is one of the pillars of the modern patient-centric philosophy of care. This study aims to explore SDM in the discipline of trauma and emergency surgery, investigating its interpretation as well as the barriers and facilitators for its implementation among surgeons. Methods: Grounding on the literature on the topics of the understanding, barriers, and facilitators of SDM in trauma and emergency surgery, a survey was created by a multidisciplinary committee and endorsed by the World Society of Emergency Surgery (WSES). The survey was sent to all 917 WSES members, advertised through the society’s website, and shared on the society’s Twitter profile. Results: A total of 650 trauma and emergency surgeons from 71 countries in five continents participated in the initiative. Less than half of the surgeons understood SDM, and 30% still saw the value in exclusively engaging multidisciplinary provider teams without involving the patient. Several barriers to effectively partnering with the patient in the decision-making process were identified, such as the lack of time and the need to concentrate on making medical teams work smoothly. Discussion: Our investigation underlines how only a minority of trauma and emergency surgeons understand SDM, and perhaps, the value of SDM is not fully accepted in trauma and emergency situations. The inclusion of SDM practices in clinical guidelines may represent the most feasible and advocated solutions

Intraperitoneal drain placement and outcomes after elective colorectal surgery: international matched, prospective, cohort study

Despite current guidelines, intraperitoneal drain placement after elective colorectal surgery remains widespread. Drains were not associated with earlier detection of intraperitoneal collections, but were associated with prolonged hospital stay and increased risk of surgical-site infections.Background Many surgeons routinely place intraperitoneal drains after elective colorectal surgery. However, enhanced recovery after surgery guidelines recommend against their routine use owing to a lack of clear clinical benefit. This study aimed to describe international variation in intraperitoneal drain placement and the safety of this practice. Methods COMPASS (COMPlicAted intra-abdominal collectionS after colorectal Surgery) was a prospective, international, cohort study which enrolled consecutive adults undergoing elective colorectal surgery (February to March 2020). The primary outcome was the rate of intraperitoneal drain placement. Secondary outcomes included: rate and time to diagnosis of postoperative intraperitoneal collections; rate of surgical site infections (SSIs); time to discharge; and 30-day major postoperative complications (Clavien-Dindo grade at least III). After propensity score matching, multivariable logistic regression and Cox proportional hazards regression were used to estimate the independent association of the secondary outcomes with drain placement. Results Overall, 1805 patients from 22 countries were included (798 women, 44.2 per cent; median age 67.0 years). The drain insertion rate was 51.9 per cent (937 patients). After matching, drains were not associated with reduced rates (odds ratio (OR) 1.33, 95 per cent c.i. 0.79 to 2.23; P = 0.287) or earlier detection (hazard ratio (HR) 0.87, 0.33 to 2.31; P = 0.780) of collections. Although not associated with worse major postoperative complications (OR 1.09, 0.68 to 1.75; P = 0.709), drains were associated with delayed hospital discharge (HR 0.58, 0.52 to 0.66; P < 0.001) and an increased risk of SSIs (OR 2.47, 1.50 to 4.05; P < 0.001). Conclusion Intraperitoneal drain placement after elective colorectal surgery is not associated with earlier detection of postoperative collections, but prolongs hospital stay and increases SSI risk