Probing instructions for expression regulation in gene nucleotide compositions.
ABSTRACT: Gene expression is orchestrated by distinct regulatory regions to ensure a wide variety of cell types and functions. A challenge is to identify which regulatory regions are active, what are their associated features and how they work together in each cell type. Several approaches have tackled this problem by modeling gene expression based on epigenetic marks, with the ultimate goal of identifying driving regions and associated genomic variations that are clinically relevant in particular in precision medicine. However, these models rely on experimental data, which are limited to specific samples (even often to cell lines) and cannot be generated for all regulators and all patients. In addition, we show here that, although these approaches are accurate in predicting gene expression, inference of TF combinations from this type of models is not straightforward. Furthermore these methods are not designed to capture regulation instructions present at the sequence level, before the binding of regulators or the opening of the chromatin. Here, we probe sequence-level instructions for gene expression and develop a method to explain mRNA levels based solely on nucleotide features. Our method positions nucleotide composition as a critical component of gene expression. Moreover, our approach, able to rank regulatory regions according to their contribution, unveils a strong influence of the gene body sequence, in particular introns. We further provide evidence that the contribution of nucleotide content can be linked to co-regulations associated with genome 3D architecture and to associations of genes within topologically associated domains.
Project description:Phenotypic differences between species are driven by changes in gene expression and, by extension, by modifications in the regulation of the transcriptome. Investigation of mammalian transcriptome divergence has been restricted to analysis of bulk gene expression levels and gene-internal splicing. Using allele-specific expression analysis in inter-strain hybrids of Mus musculus, we determined the contribution of multiple cellular regulatory systems to transcriptome divergence, including: alternative promoter usage, transcription start site selection, cassette exon usage, alternative last exon usage, and alternative polyadenylation site choice. Between mouse strains, a fifth of genes have variations in isoform usage that contribute to transcriptomic changes, half of which alter encoded amino acid sequence. Virtually all divergence in isoform usage altered the post-transcriptional regulatory instructions in gene UTRs. Furthermore, most genes with isoform differences between strains contain changes originating from multiple regulatory systems. This result indicates widespread cross-talk and coordination exists among different regulatory systems. Overall, isoform usage diverges in parallel with and independently to gene expression evolution, and the cis and trans regulatory contribution to each differs significantly.
Project description:Sequence changes in coding region and regulatory region of the gene itself (cis) determine most of gene expression divergence between closely related species. But gene expression divergence between yeast species is not correlated with evolution of primary nucleotide sequence. This indicates that other factors in cis direct gene expression divergence. Here, we studied the contribution of DNA three-dimensional structural evolution as cis to gene expression divergence. We found that the evolution of DNA structure in coding regions and gene expression divergence are correlated in yeast. Similar result was also observed between Drosophila species. DNA structure is associated with the binding of chromatin remodelers and histone modifiers to DNA sequences in coding regions, which influence RNA polymerase II occupancy that controls gene expression level. We also found that genes with similar DNA structures are involved in the same biological process and function. These results reveal the previously unappreciated roles of DNA structure as cis-effects in gene expression.
Project description:OBJECTIVES:In this study, we analysed patient information leaflets (PILs) of intranasal corticosteroid sprays (INCS) of different manufacturers in the UK to determine if instructions for the use of INCS are complete and uniform. SETTING:PILs of all INCS of all manufacturers, available for patients in the UK, were collected from the British National Formulary website and the Medicines and Healthcare products Regulatory Agency website. All instructions in these PILs were analysed. PARTICIPANTS:We identified PILs of INCS from 21 different manufacturers, available for patients in the UK. RESULTS:We analysed the instructions for the use of INCS in 21 different PILs and there is large variation in the PIL instructions for the technique of using INCS across PILs. CONCLUSION:Complete and uniform instructions for the use of INCS are lacking in PILs for registered preparations in the UK. Structured and standardised instructions to be used by both professionals and patients are essential in order to optimise daily use of INCS.
Project description:Regeneration requires both potential and instructions for tissue replacement. In planarians, pluripotent stem cells have the potential to produce all new tissue. The identities of the cells that provide regeneration instructions are unknown. Here, we report that position control genes (PCGs) that control regeneration and tissue turnover are expressed in a subepidermal layer of nonneoblast cells. These subepidermal cells coexpress many PCGs. We propose that these subepidermal cells provide a system of body coordinates and positional information for regeneration, and identify them to be muscle cells of the planarian body wall. Almost all planarian muscle cells express PCGs, suggesting a dual function: contraction and control of patterning. PCG expression is dynamic in muscle cells after injury, even in the absence of neoblasts, suggesting that muscle is instructive for regeneration. We conclude that planarian regeneration involves two highly flexible systems: pluripotent neoblasts that can generate any new cell type and muscle cells that provide positional instructions for the regeneration of any body region.
Project description:Background:Hospital readmissions are considered as the primary indicator of insufficient quality of care and are responsible of increasing annual medical costs by billions of dollars. Different factors tend to reduce readmissions, particularly instructions at discharge. Objectives:Our study objective was to evaluate discharge instructions given to hospitalized Lebanese patients and associated factors. Methods:Two hundred patients, aged between 21 and 79 years and admitted to the emergency department, were recruited from a Lebanese university hospital. Discharge instructions were evaluated by a face-to-face interview to fill a questionnaire with the patients immediately after their final contact with the physician or nurse in charge. We mainly focused on medications instructions and created two scores related to "instructions given" and "instructions appropriate" to later conduct bivariate analysis. Results:We found that discharge instructions were not completely given to all our study population. The degree of appropriateness fluctuated between 25% and 100%. The instructor in charge of giving discharge instructions had its significant influence on medication instructions given (p=0.014). In addition, the instructor and his experience influenced the degree of "appropriate instructions". In fact, our study showed that despite being capable of giving good medication advice, nurses' instructions were significantly less effective in comparison with physicians, fellows and residents. However, nurses gave 52% of the instructions, which questions the quality of those instructions. Conclusions:In conclusion, our observational study showed that in a Lebanese university hospital, patients' understanding of discharge instructions is poor. Careful attention should be drawn to other hospitals as well and interventions should be considered to improve instructions quality and limit later complications and readmissions. The intervention of clinical pharmacists and their medication-related advice might be crucial in order to improve instructions' quality.
Project description:Complex patterns of cell-type-specific gene expression are thought to be achieved by combinatorial binding of transcription factors (TFs) to sequence elements in regulatory regions. Predicting cell-type-specific expression in mammals has been hindered by the oftentimes unknown location of distal regulatory regions. To alleviate this bottleneck, we used DNase-seq data from 19 diverse human cell types to identify proximal and distal regulatory elements at genome-wide scale. Matched expression data allowed us to separate genes into classes of cell-type-specific up-regulated, down-regulated, and constitutively expressed genes. CG dinucleotide content and DNA accessibility in the promoters of these three classes of genes displayed substantial differences, highlighting the importance of including these aspects in modeling gene expression. We associated DNase I hypersensitive sites (DHSs) with genes, and trained classifiers for different expression patterns. TF sequence motif matches in DHSs provided a strong performance improvement in predicting gene expression over the typical baseline approach of using proximal promoter sequences. In particular, we achieved competitive performance when discriminating up-regulated genes from different cell types or genes up- and down-regulated under the same conditions. We identified previously known and new candidate cell-type-specific regulators. The models generated testable predictions of activating or repressive functions of regulators. DNase I footprints for these regulators were indicative of their direct binding to DNA. In summary, we successfully used information of open chromatin obtained by a single assay, DNase-seq, to address the problem of predicting cell-type-specific gene expression in mammalian organisms directly from regulatory sequence.
Project description:Regulatory single-nucleotide polymorphisms (rSNPs) alter gene expression. Common approaches for identifying rSNPs focus on sequence variants in conserved regions; however, it is unknown what fraction of rSNPs is undetectable using this approach. We present a systematic analysis of gene expression variation at the single-nucleotide level in the Saccharomyces cerevisiae GAL1-10 regulatory region. We exhaustively mutated nearly every base and measured the expression of each variant with a sensitive dual reporter assay. We observed an expression change for 7% (43/582) of the bases in this region, most of which (35/43, 81%) reside in conserved positions. The most dramatic changes were caused by variants that produced AUGs upstream of the translation start (uAUGs), and we sought to understand the consequences and molecular mechanisms underlying this class of mutations. A genome-wide analysis showed that genes with uAUGs display significantly lower mRNA and protein levels than genes without uAUGs. To determine the generality of this mechanism, we introduced uAUGs into S. cerevisiae genes and observed significantly reduced expression in 17/21 instances (p < 0.01), suggesting that uAUGs are functional in a wide variety of sequence contexts. Quantification of mRNA and protein levels for uAUG mutants showed that uAUGs affect both transcription and translation. Expression of uAUG mutants under the upf1Δ strain demonstrated that uAUGs stimulate the nonsense-mediated decay pathway. Our results suggest that uAUGs are potent and widespread regulators of gene expression that act by attenuating both protein and RNA levels.
Project description:Parents often manage complex instructions when their children are discharged from the inpatient setting or emergency department (ED); misunderstanding instructions can put children at risk for adverse outcomes. Parents' ability to manage discharge instructions has not been examined before in a systematic review.To perform a systematic review of the literature related to parental management (knowledge and execution) of inpatient and ED discharge instructions.We consulted PubMed/Medline, Embase, Cumulative Index to Nursing and Allied Health Literature, and Cochrane CENTRAL (from database inception to January 1, 2017).We selected experimental or observational studies in the inpatient or ED settings in which parental knowledge or execution of discharge instructions were evaluated.Two authors independently screened potential studies for inclusion and extracted data from eligible articles by using a structured form.Sixty-four studies met inclusion criteria; most (n = 48) were ED studies. Medication dosing and adherence errors were common; knowledge of medication side effects was understudied (n = 1). Parents frequently missed follow-up appointments and misunderstood return precaution instructions. Few researchers conducted studies that assessed management of instructions related to diagnosis (n = 3), restrictions (n = 2), or equipment (n = 1). Complex discharge plans (eg, multiple medicines or appointments), limited English proficiency, and public or no insurance were associated with errors. Few researchers conducted studies that evaluated the role of parent health literacy (ED, n = 5; inpatient, n = 0).The studies were primarily observational in nature.Parents frequently make errors related to knowledge and execution of inpatient and ED discharge instructions. Researchers in the future should assess parental management of instructions for domains that are less well studied and focus on the design of interventions to improve discharge plan management.
Project description:Regulation of gene expression involves the orchestrated interaction of a large number of proteins with transcriptional regulatory elements in the context of chromatin. Our understanding of gene regulation is limited by the lack of a protein measurement technology that can systematically detect and quantify the ensemble of proteins associated with the transcriptional regulatory elements of specific genes. Here, we introduce a set of selected reaction monitoring (SRM) assays for the systematic measurement of 464 proteins with known or suspected roles in transcriptional regulation at RNA polymerase II transcribed promoters in Saccharomyces cerevisiae. Measurement of these proteins in nuclear extracts by SRM permitted the reproducible quantification of 42% of the proteins over a wide range of abundances. By deploying the assay to systematically identify DNA binding transcriptional regulators that interact with the environmentally regulated FLO11 promoter in cell extracts, we identified 15 regulators that bound specifically to distinct regions along ?600 bp of the regulatory sequence. Importantly, the dataset includes a number of regulators that have been shown to either control FLO11 expression or localize to these regulatory regions in vivo. We further validated the utility of the approach by demonstrating that two of the SRM-identified factors, Mot3 and Azf1, are required for proper FLO11 expression. These results demonstrate the utility of SRM-based targeted proteomics to guide the identification of gene-specific transcriptional regulators.
Project description:The impact of discharge instructions on a patient's experience is not fully understood. This research explored whether nurse- and physician-generated discharge instructions had a positive effect on patient perceptions regarding their discharge experience.We compared Press Ganey discharge-related patient satisfaction scores for the year prior to and the year subsequent to implementing revised discharge instructions for all patients admitted to a 180-bed community-based hospital.Following the implementation of our revised discharge instructions, patient satisfaction significantly improved (84.7% vs 83%, P < .01). Patients responded that they felt ready for discharge (86.6% vs 84.9%, P = .01) and were satisfied with instructions for home care (87.8% vs 85.3%, P < .01).This study finds that a novel discharge instruction set produced by both the nursing and physician staff may improve patient perceptions with the discharge process.