Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets.

Gene expression governs cell fate, and is regulated via a complex interplay of transcription factors and molecules that change chromatin structure. Advances in sequencing-based assays have enabled investigation of these processes genome-wide, leading to large datasets that combine information on the dynamics of gene expression, transcription factor binding and chromatin structure as cells differentiate. While numerous studies focus on the effects of these features on broader gene regulation, less work has been done on the mechanisms of gene-specific transcriptional control. In this study, we have focussed on the latter by integrating gene expression data for the in vitro differentiation of murine ES cells to macrophages and cardiomyocytes, with dynamic data on chromatin structure, epigenetics and transcription factor binding. Combining a novel strategy to identify communities of related control elements with a penalized regression approach, we developed individual models to identify the potential control elements predictive of the expression of each gene. Our models were compared to an existing method and evaluated using the existing literature and new experimental data from embryonic stem cell differentiation reporter assays. Our method is able to identify transcriptional control elements in a gene specific manner that reflect known regulatory relationships and to generate useful hypotheses for further testing.

Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model.

Comprehensive study of transcriptional control processes will be required to enhance our understanding of both normal and malignant hematopoiesis. Modern sequencing technologies have revolutionized our ability to generate genome-scale expression and histone modification profiles, transcription factor (TF)-binding maps, and also comprehensive chromatin-looping information. Many of these technologies, however, require large numbers of cells, and therefore cannot be applied to rare hematopoietic stem/progenitor cell (HSPC) populations. The stem cell factor-dependent multipotent progenitor cell line HPC-7 represents a well-recognized cell line model for HSPCs. Here we report genome-wide maps for 17 TFs, 3 histone modifications, DNase I hypersensitive sites, and high-resolution promoter-enhancer interactomes in HPC-7 cells. Integrated analysis of these complementary data sets revealed TF occupancy patterns of genomic regions involved in promoter-anchored loops. Moreover, preferential associations between pairs of TFs bound at either ends of chromatin loops led to the identification of 4 previously unrecognized protein-protein interactions between key blood stem cell regulators. All HPC-7 data sets are freely available both through standard repositories and a user-friendly Web interface. Together with previously generated genome-wide data sets, this study integrates HPC-7 data into a genomic resource on par with ENCODE tier 1 cell lines and, importantly, is the only current model with comprehensive genome-scale data that is relevant to HSPC biology.

Parallel evolution of chordate cis-regulatory code for development.

Urochordates are the closest relatives of vertebrates and at the larval stage, possess a characteristic bilateral chordate body plan. In vertebrates, the genes that orchestrate embryonic patterning are in part regulated by highly conserved non-coding elements (CNEs), yet these elements have not been identified in urochordate genomes. Consequently the evolution of the cis-regulatory code for urochordate development remains largely uncharacterised. Here, we use genome-wide comparisons between C. intestinalis and C. savignyi to identify putative urochordate cis-regulatory sequences. Ciona conserved non-coding elements (ciCNEs) are associated with largely the same key regulatory genes as vertebrate CNEs. Furthermore, some of the tested ciCNEs are able to activate reporter gene expression in both zebrafish and Ciona embryos, in a pattern that at least partially overlaps that of the gene they associate with, despite the absence of sequence identity. We also show that the ability of a ciCNE to up-regulate gene expression in vertebrate embryos can in some cases be localised to short sub-sequences, suggesting that functional cross-talk may be defined by small regions of ancestral regulatory logic, although functional sub-sequences may also be dispersed across the whole element. We conclude that the structure and organisation of cis-regulatory modules is very different between vertebrates and urochordates, reflecting their separate evolutionary histories. However, functional cross-talk still exists because the same repertoire of transcription factors has likely guided their parallel evolution, exploiting similar sets of binding sites but in different combinations.

Activity of a heptad of transcription factors is associated with stem cell programs and clinical outcome in acute myeloid leukemia.

Aberrant transcriptional programs in combination with abnormal proliferative signaling drive leukemic transformation. These programs operate in normal hematopoiesis where they are involved in hematopoietic stem cell (HSC) proliferation and maintenance. Ets Related Gene (ERG) is a component of normal and leukemic stem cell signatures and high ERG expression is a risk factor for poor prognosis in acute myeloid leukemia (AML). However, mechanisms that underlie ERG expression in AML and how its expression relates to leukemic stemness are unknown. We report that ERG expression in AML is associated with activity of the ERG promoters and +85 stem cell enhancer and a heptad of transcription factors that combinatorially regulate genes in HSCs. Gene expression signatures derived from ERG promoter-stem cell enhancer and heptad activity are associated with clinical outcome when ERG expression alone fails. We also show that the heptad signature is associated with AMLs that lack somatic mutations in NPM1 and confers an adverse prognosis when associated with FLT3 mutations. Taken together, these results suggest that transcriptional regulators cooperate to establish or maintain primitive stem cell-like signatures in leukemic cells and that the underlying pattern of somatic mutations contributes to the development of these signatures and modulate their influence on clinical outcome.

Minor change, major difference: divergent functions of highly conserved cis-regulatory elements subsequent to whole genome duplication events.

Within the vertebrate lineage, a high proportion of duplicate genes have been retained after whole genome duplication (WGD) events. It has been proposed that many of these duplicate genes became indispensable because the ancestral gene function was divided between them. In addition, novel functions may have evolved, owing to changes in cis-regulatory elements. Functional analysis of the PAX2/5/8 gene subfamily appears to support at least the first part of this hypothesis. The collective role of these genes has been widely retained, but sub-functions have been differentially partitioned between the genes in different vertebrates. Conserved non-coding elements (CNEs) represent an interesting and readily identifiable class of putative cis-regulatory elements that have been conserved from fish to mammals, an evolutionary distance of 450 million years. Within the PAX2/5/8 gene subfamily, PAX2 is associated with the highest number of CNEs. An additional WGD experienced in the teleost lineage led to two copies of pax2, each of which retained a large proportion of these CNEs. Using a reporter gene assay in zebrafish embryos, we have exploited this rich collection of regulatory elements in order to determine whether duplicate CNEs have evolved different functions. Remarkably, we find that even highly conserved sequences exhibit more functional differences than similarities. We also discover that short flanking sequences can have a profound impact on CNE function. Therefore, if CNEs are to be used as candidate enhancers for transgenic studies or for multi-species comparative analyses, it is paramount that the CNEs are accurately delineated.

Managing patients with cervical spine injury.

Common measures to establish spinal immobilisation at the scene of an accident include keeping the patient's head still, applying a rigid cervical collar and transporting the patient on a rigid spinal board to an emergency department. This article reviews the literature about spinal immobilisation practices in emergency settings, including best-practice guidance and papers on immobilisation, imaging, rapport with patients and complications.

Management of patients with mental health needs.

This article presents findings from the first phase of a two-part study that examined the knowledge and experience of emergency department (ED) staff who work with people with mental health needs. In the first part of the study, 19 semi-structured interviews were conducted with multidisciplinary team (MDT) members and the results were analysed. The interviews covered the ED environment, participants' attitudes towards, ability to communicate with, and knowledge and experience of patients with mental health needs. One of the study's main findings was that MDT members require more appropriate training to raise their awareness of issues related to mental health. The findings informed the development of a questionnaire, which was distributed to a large cohort of ED staff and social workers.

Effects of stroke on informal carers.

Informal carers have a pivotal role in caring for patients who have had a stroke. Research has shown that informal carers have unmet information, psychological and social needs. There is a lack of research about how informal carers in Northern Ireland manage the role of caring for a patient who has experienced stroke, and what kind of support they need and receive. This literature review explores the experiences of informal carers providing stroke care in the home. The issues highlighted in the article are relevant worldwide, because the incidence of stroke is increasing in developed and developing countries.

Supporting older people following out of hours discharge from the Emergency Department: An integrative review of the literature.

BACKGROUND: For many older people the emergency department (ED) is an important but sometimes difficult step in their healthcare journey. They often attend the ED with co and multi morbidities. Discharge home at evenings and weekends when post-discharge support services are limited can result in a delay or failure to follow through on their discharge plan leading to adverse health outcomes and in some cases, readmission to ED. OBJECTIVE: The aim of this integrative review was to identify and appraise the support available to older people following discharge from the ED out of hours (OOH). METHODS: For this review, out of hours referred to those times after 17.30 until 08.00 a.m. on Mondays to Fridays, all hours on weekends and public holidays. Whittemore and Knafl's (Journal of Advanced Nursing, 2005;52:546), framework was used to guide all stages of the review process. Articles were retrieved following a rigorous search of published works using various databases, the grey literature and hand search of the reference lists of the studies included. RESULTS: In total 31 articles were included in the review. These comprised systematic reviews, randomised control studies, cohort studies and surveys. Main themes identified included processes that enable support, support provision by health and social care professionals and telephone follow-up. Results identified a significant dearth of out of hours discharge research and a strong recommendation for more concise and thorough research in this important area of care transition. CONCLUSION: Older person discharge home from the ED presents an associated risk as previous research has identified frequent readmission and periods of ill health and dependency. Out of hours discharge can be even more problematic when it may be difficult to arrange support services and ensure continuity of care. Further work in this area is required, taking cognisance of the findings and recommendations identified in this review.

Early evolution of conserved regulatory sequences associated with development in vertebrates.

Comparisons between diverse vertebrate genomes have uncovered thousands of highly conserved non-coding sequences, an increasing number of which have been shown to function as enhancers during early development. Despite their extreme conservation over 500 million years from humans to cartilaginous fish, these elements appear to be largely absent in invertebrates, and, to date, there has been little understanding of their mode of action or the evolutionary processes that have modelled them. We have now exploited emerging genomic sequence data for the sea lamprey, Petromyzon marinus, to explore the depth of conservation of this type of element in the earliest diverging extant vertebrate lineage, the jawless fish (agnathans). We searched for conserved non-coding elements (CNEs) at 13 human gene loci and identified lamprey elements associated with all but two of these gene regions. Although markedly shorter and less well conserved than within jawed vertebrates, identified lamprey CNEs are able to drive specific patterns of expression in zebrafish embryos, which are almost identical to those driven by the equivalent human elements. These CNEs are therefore a unique and defining characteristic of all vertebrates. Furthermore, alignment of lamprey and other vertebrate CNEs should permit the identification of persistent sequence signatures that are responsible for common patterns of expression and contribute to the elucidation of the regulatory language in CNEs. Identifying the core regulatory code for development, common to all vertebrates, provides a foundation upon which regulatory networks can be constructed and might also illuminate how large conserved regulatory sequence blocks evolve and become fixed in genomic DNA.

The PAX258 gene subfamily: a comparative perspective.

Whole genome duplication events are thought to have substantially contributed to organismal complexity, largely via divergent transcriptional regulation. Members of the vertebrate PAX2, PAX5 and PAX8 gene subfamily derived from an ancient class of paired box genes and arose from such whole genome duplication events. These genes are critical in establishing the midbrain-hindbrain boundary, specifying interneuron populations and for eye, ear and kidney development. Also PAX2 has adopted a unique role in pancreas development, whilst PAX5 is essential for early B-cell differentiation. The contribution of PAX258 genes to their collective role has diverged across paralogues and the animal lineages, resulting in a complex wealth of literature. It is now timely to provide a comprehensive comparative overview of these genes and their ancient and divergent roles. We also discuss their fundamental place within gene regulatory networks and the likely influence of cis-regulatory elements over their differential roles during early animal development.

The use of social media (some) as a learning tool in healthcare education: An integrative review of the literature.

OBJECTIVES: The exponential rise of social media (SoMe) has transformed how people connect, learn, and network. The use of SoMe in health education is in its infancy. The objective of the review was to examine the use of SoMe by healthcare students, professionals and educators to ascertain if the use of SoMe enhanced the learning experience. DESIGN: An integrative literature review was completed in February 2019. DATA SOURCES: Three databases were used to facilitate the literature search (Medline (Ovid), Cinahl, and Scopus). REVIEW METHODS: Inclusion and exclusion criteria for the literature search were applied and PRISMA guidelines followed. The search retrieved 316 citations. Forty-seven duplicate articles were removed at this stage. Titles and abstracts were screened and 215 excluded as they were not relevant. The remaining articles were assessed for eligibility and 37 were excluded for not meeting the review requirements. RESULTS: Critical Appraisal Skills Programme (CASP, 2019) checklists primarily guided the critique of the literature, with the Caldwell et al. (2011) approach used to supplement the critique of health-related research studies. 17 research studies are included in this review. Themes were developed using Braun and Clarke's (2006) approach. Five reoccurring themes emerged: communication and collaboration, a source of reference, personal development, pitfalls and ethical concerns. CONCLUSIONS: This review provides a synthesis of SoMe use in healthcare education. SoMe is an excellent educational resource which can provide advantages in education. Areas of concern were noted and the need for improved policy and guidance highlighted. Further research and education on SoMe use in healthcare education is essential for educators, students and practitioners.

Person-centred end-of-life curriculum design in adult pre-registration undergraduate nurse education: A three-year longitudinal evaluation study.

BACKGROUND: The need to provide quality end-of-life care is universally accepted. International research and policies encourage innovative ways that effective culturally appropriate care can be provided. Higher education institutions and practice settings are tasked with ensuring that nurse graduates have the knowledge, skills and insight to deliver person-centred end-of-life care. RESEARCH AIMS AND OBJECTIVES: The aim was to explore student evaluation of end-of-life care learning within a three-year undergraduate adult nursing degree programme. Objectives were to assess student perceptions of the content and level of learning achieved, explore usefulness of learning, highlight areas that were most useful, and identify suggestions to improve learning. DESIGN: A 3-year quantitative longitudinal design was used. A questionnaire containing open and closed questions was designed to incorporate the personal and professional learning strategies indicated by the Nursing and Midwifery Council (NMC) (2010). SETTING AND PARTICIPANTS: The evaluation was completed at the same time point over a three-year period from April 2015-April 2017. The participants were year three student nurses, from 3 consecutive years, enrolled on a pre-registration adult nursing course at one university. There was a 66% response rate (n = 336). METHODS: Participant information sheets and questionnaires were distributed and time to complete them facilitated. Responses from closed questions were coded and analysed using descriptive statistics (SPSS 24) and thematic analysis used for open questions. RESULTS: Students expressed satisfaction with their learning, 88.7-97% of students reported a positive impact on their knowledge. They developed an understanding of the impact the nurse can have on the patient and family experience, reporting more confidence and competence in most aspects of end-of-life care. They noted improved ability to utilise this in their subsequent practice experience 88.1-97%. CONCLUSIONS: Structured end-of-life care within the curriculum is essential to equip graduate nurses to provide effective evidence informed care. Planning should continue for curriculum development that encompasses person-centred end-of-life care across cultures.

Highly conserved non-coding sequences are associated with vertebrate development.

In addition to protein coding sequence, the human genome contains a significant amount of regulatory DNA, the identification of which is proving somewhat recalcitrant to both in silico and functional methods. An approach that has been used with some success is comparative sequence analysis, whereby equivalent genomic regions from different organisms are compared in order to identify both similarities and differences. In general, similarities in sequence between highly divergent organisms imply functional constraint. We have used a whole-genome comparison between humans and the pufferfish, Fugu rubripes, to identify nearly 1,400 highly conserved non-coding sequences. Given the evolutionary divergence between these species, it is likely that these sequences are found in, and furthermore are essential to, all vertebrates. Most, and possibly all, of these sequences are located in and around genes that act as developmental regulators. Some of these sequences are over 90% identical across more than 500 bases, being more highly conserved than coding sequence between these two species. Despite this, we cannot find any similar sequences in invertebrate genomes. In order to begin to functionally test this set of sequences, we have used a rapid in vivo assay system using zebrafish embryos that allows tissue-specific enhancer activity to be identified. Functional data is presented for highly conserved non-coding sequences associated with four unrelated developmental regulators (SOX21, PAX6, HLXB9, and SHH), in order to demonstrate the suitability of this screen to a wide range of genes and expression patterns. Of 25 sequence elements tested around these four genes, 23 show significant enhancer activity in one or more tissues. We have identified a set of non-coding sequences that are highly conserved throughout vertebrates. They are found in clusters across the human genome, principally around genes that are implicated in the regulation of development, including many transcription factors. These highly conserved non-coding sequences are likely to form part of the genomic circuitry that uniquely defines vertebrate development.

CONDOR: a database resource of developmentally associated conserved non-coding elements.

BACKGROUND: Comparative genomics is currently one of the most popular approaches to study the regulatory architecture of vertebrate genomes. Fish-mammal genomic comparisons have proved powerful in identifying conserved non-coding elements likely to be distal cis-regulatory modules such as enhancers, silencers or insulators that control the expression of genes involved in the regulation of early development. The scientific community is showing increasing interest in characterizing the function, evolution and language of these sequences. Despite this, there remains little in the way of user-friendly access to a large dataset of such elements in conjunction with the analysis and the visualization tools needed to study them. DESCRIPTION: Here we present CONDOR (COnserved Non-coDing Orthologous Regions) available at: http://condor.fugu.biology.qmul.ac.uk. In an interactive and intuitive way the website displays data on > 6800 non-coding elements associated with over 120 early developmental genes and conserved across vertebrates. The database regularly incorporates results of ongoing in vivo zebrafish enhancer assays of the CNEs carried out in-house, which currently number approximately 100. Included and highlighted within this set are elements derived from duplication events both at the origin of vertebrates and more recently in the teleost lineage, thus providing valuable data for studying the divergence of regulatory roles between paralogs. CONDOR therefore provides a number of tools and facilities to allow scientists to progress in their own studies on the function and evolution of developmental cis-regulation. CONCLUSION: By providing access to data with an approachable graphics interface, the CONDOR database presents a rich resource for further studies into the regulation and evolution of genes involved in early development.

Dynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation.

Metazoan development involves the successive activation and silencing of specific gene expression programs and is driven by tissue-specific transcription factors programming the chromatin landscape. To understand how this process executes an entire developmental pathway, we generated global gene expression, chromatin accessibility, histone modification, and transcription factor binding data from purified embryonic stem cell-derived cells representing six sequential stages of hematopoietic specification and differentiation. Our data reveal the nature of regulatory elements driving differential gene expression and inform how transcription factor binding impacts on promoter activity. We present a dynamic core regulatory network model for hematopoietic specification and demonstrate its utility for the design of reprogramming experiments. Functional studies motivated by our genome-wide data uncovered a stage-specific role for TEAD/YAP factors in mammalian hematopoietic specification. Our study presents a powerful resource for studying hematopoiesis and demonstrates how such data advance our understanding of mammalian development.

Evolution of lineage-specific functions in ancient cis-regulatory modules.

Morphological evolution is driven both by coding sequence variation and by changes in regulatory sequences. However, how cis-regulatory modules (CRMs) evolve to generate entirely novel expression domains is largely unknown. Here, we reconstruct the evolutionary history of a lens enhancer located within a CRM that not only predates the lens, a vertebrate innovation, but bilaterian animals in general. Alignments of orthologous sequences from different deuterostomes sub-divide the CRM into a deeply conserved core and a more divergent flanking region. We demonstrate that all deuterostome flanking regions, including invertebrate sequences, activate gene expression in the zebrafish lens through the same ancient cluster of activator sites. However, levels of gene expression vary between species due to the presence of repressor motifs in flanking region and core. These repressor motifs are responsible for the relatively weak enhancer activity of tetrapod flanking regions. Ray-finned fish, however, have gained two additional lineage-specific activator motifs which in combination with the ancient cluster of activators and the core constitute a potent lens enhancer. The exploitation and modification of existing regulatory potential in flanking regions but not in the highly conserved core might represent a more general model for the emergence of novel regulatory functions in complex CRMs.

Nurses perceptions of sleep in the intensive care unit environment: a literature review.

OBJECTIVES: Sleep deprivation within intensive care units (ICU) remains a recurring norm despite the extensive research highlighting a crucial need for sleep promotion. However, the degree to which sleep deprivation can be associated with the nurses' provision of care remains unclear. Therefore, this critical literature review aims to explore the nurses' knowledge and prioritisation of sleep whilst examining the nurses' use of sleep assessment skills and tools. The nurses' awareness and prioritisation of sleep promoting interventions and complimentary therapies will also be analysed. METHODS: The online databases Cochrane, CINAHL and Science Direct were searched for English language articles, published between 2003 and 2013 which were downloadable in full text format. A total of 378 articles were identified and 25 papers met all the inclusion criteria. CONCLUSIONS: It appears that ICU nurses lack a complex understanding of the importance of sleep and the interventions needed to promote it. Indeed, studies suggest that inattention to sufficient training and a lack of structured protocol within practice makes the provision of sleep for the ICU patient impossible. Therefore, whilst further empirical research is required it may be noted that evidence informed education programmes and sleep assessment tools require development within the ICU environment.

Capturing the regulatory interactions of eukaryote genomes.

A key finding from early genomics research is the remarkable consistency in the number of protein-coding regions across diverse species. This has led many researchers to look to the cis-regulatory elements of genes as the fundamental influence behind evolving gene function and subsequent species diversification. Historically, since these elements are often located in vast intergenic and intronic regions of the genome, their identification has been recalcitrant. Now, with the deluge of whole-genome data from representatives of numerous eukaryotic lineages, various approaches have enabled us to begin to recognize features that characterize regulatory regions of the genome. Here we endeavour to collate these approaches in order to give an overview of the complexities involved in extrapolating regulatory signatures. The resource provided by the escalating richness of whole-genome datasets enables more sophisticated modelling of these regulatory signatures yet at the same time introduces increasing potential for noise. While we are only at the advent of making these discoveries, the next decade promises to be a very exciting and rewarding time for genome researchers.

Single site-specific integration targeting coupled with embryonic stem cell differentiation provides a high-throughput alternative to in vivo enhancer analyses.

Comprehensive analysis of cis-regulatory elements is key to understanding the dynamic gene regulatory networks that control embryonic development. While transgenic animals represent the gold standard assay, their generation is costly, entails significant animal usage, and in utero development complicates time-course studies. As an alternative, embryonic stem (ES) cells can readily be differentiated in a process that correlates well with developing embryos. Here, we describe a highly effective platform for enhancer assays using an Hsp68/Venus reporter cassette that targets to the Hprt locus in mouse ES cells. This platform combines the flexibility of Gateway® cloning, live cell trackability of a fluorescent reporter, low background and the advantages of single copy insertion into a defined genomic locus. We demonstrate the successful recapitulation of tissue-specific enhancer activity for two cardiac and two haematopoietic enhancers. In addition, we used this assay to dissect the functionality of the highly conserved Ets/Ets/Gata motif in the Scl+19 enhancer, which revealed that the Gata motif is not required for initiation of enhancer activity. We further confirmed that Gata2 is not required for endothelial activity of the Scl+19 enhancer using Gata2(-/-) Scl+19 transgenic embryos. We have therefore established a valuable toolbox to study gene regulatory networks with broad applicability.