Links between core promoter and basic gene features influence gene expression

<p>Abstract</p> <p>Background</p> <p>Diversity in rates of gene expression is essential for basic cell functions and is controlled by a variety of intricate mechanisms. Revealing general mechanisms that control gene expression is important for understanding normal and pathological cell functions and for improving the design of expression systems. Here we analyzed the relationship between general features of genes and their contribution to expression levels.</p> <p>Results</p> <p>Genes were divided into four groups according to their core promoter type and their characteristics analyzed statistically. Surprisingly we found that small variations in the TATA box are linked to large differences in gene length. Genes containing canonical TATA are generally short whereas long genes are associated with either non-canonical TATA or TATA-less promoters. These differences in gene length are primarily determined by the size and number of introns. Generally, gene expression was found to be tightly correlated with the strength of the TATA-box. However significant reduction in gene expression levels were linked with long TATA-containing genes (canonical and non-canonical) whereas intron length hardly affected the expression of TATA-less genes. Interestingly, features associated with high translation are prevalent in TATA-containing genes suggesting that their protein production is also more efficient.</p> <p>Conclusion</p> <p>Our results suggest that interplay between core promoter type and gene size can generate significant diversity in gene expression.</p

Informative material for patient empowerment in sensitive situations

Women diagnosed with HPV face a hard-to-understand disease that may impact their psychological and physical health and may pose challenges communicating with healthcare providers in sensitive settings. We posit patient empowerment through targeted educational materials can improve sensitive communication and lead to better health outcomes. This study measured the impact of a patient-empowerment process used in a gynecology clinic for HPV patients to improve sensitive communication during medical-related meetings and on subsequent patient empowerment outcomes. The empowerment process was based on expert-vetted informative material made accessible in the physician’s waiting room on tablet devices. Communication between physicians and patients was measured during medical visits via a direct observation, encoding process. Empowerment items were tested following medical visits. The results were compared to a control group that received non-medical, lifestyle material. 237 female, gynecology patients from a large, private clinic participated. Using expert-vetted, relevant material to enhance patient education in a clinical setting results in higher levels of patient empowerment. Physician interaction impacts patient empowerment as do various communication behaviors and this can lead to positive health outcomes. Experience Framework This article is associated with the Patient, Family & Community Engagement lens of The Beryl Institute Experience Framework (https://theberylinstitute.org/experience-framework/). Access other PXJ articles related to this lens. Access other resources related to this lens

Characteristics of Core Promoter Types with respect to Gene Structure and Expression in Arabidopsis thaliana

It is now well known that vertebrates use multiple types of core promoter to accomplish differentiated tasks in Pol II-dependent transcription. Several transcriptional characteristics are known to be associated with core types, including distribution patterns of transcription start sites (TSSs) and selection between tissue-specific and constitutive expression profiles. However, their relationship to gene structure is poorly understood. In this report, we carried a comparative analysis of three Arabidopsis core types, TATA, GA, and Coreless, with regard to gene structure. Our genome-wide investigation was based on the peak TSS positions in promoters that had been identified in a large-scale experimental analysis. This analysis revealed that the types of core promoter are related with the room for promoters that is measured as the distance from the TSS to the end of the upstream gene, the distance from the TSS to the start position of the coding sequence (CDS), and the number and species of the cis-regulatory elements. Of these, it was found that the distance from the TSS to the CDS has a tight, inverse correlation to the expression level, and thus the observed relationship to the core type appears to be indirect. However, promoter length and preference of cis-elements are thought to be a direct reflection of core type-specific transcriptional initiation mechanisms

Characterisation and microleakage of a new hydrophilic fissure sealant – UltraSeal XT® hydro™

Objectives: The new hydrophilic fissure sealant, UltraSeal XT® hydro™ (Ultradent Products, USA), was characterised and its in vitro resistance to microleakage after placement on conventionally acid etched and sequentially lased and acid etched molars was investigated. Materials and Methods: The sealant was characterised by Fourier transform infra-red spectroscopy, (FTIR), scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDX) and Vickers indentation test. Occlusal surfaces of extracted human molars were either conventionally acid etched (n = 10), or sequentially acid etched and laser irradiated (n = 10). UltraSeal XT® hydro™ was applied to both groups of teeth which were then subjected to 2500 thermocycles between 5 and 55 °C prior to microleakage assessment by fuchsin dye penetration. Results: UltraSeal XT® hydro™ is an acrylate-based sealant which achieved a degree of conversion of 50.6 ± 2.2% and a Vickers microhardness of 24.2 ± 1.5 under standard light curing (1000 mWcm-2 for 20 s). Fluoride ion release was negligible within a 14-day period. SEM and EDX analyses indicated that the sealant comprises irregular sub-micron and nano-sized silicon-, barium- and aluminium-bearing filler phases embedded within a ductile matrix. Laser preconditioning was found to significantly reduce microleakage (Mann-Whitney U test, p < 0.001). The lased teeth presented enhanced surface roughness on a 50 to 100 μm scale which caused the segregation and concentration of the filler particles at the enamel-sealant interface. Conclusion: Laser preconditioning significantly decreased microleakage and increased enamel surface roughness which caused zoning of the filler particles at the enamel-sealant interface

Characterization of sINR, a strict version of the Initiator core promoter element

The proximal promoter consists of binding sites for transcription regulators and a core promoter. We identified an overrepresented motif in the proximal promoter of human genes with an Initiator (INR) positional bias. The core of the motif fits the INR consensus but its sequence is more strict and flanked by additional conserved sequences. This strict INR (sINR) is enriched in TATA-less genes that belong to specific functional categories. Analysis of the sINR-containing DHX9 and ATP5F1 genes showed that the entire sINR sequence, including the strict core and the conserved flanking sequences, is important for transcription. A conventional INR sequence could not substitute for DHX9 sINR whereas, sINR could replace a conventional INR. The minimal region required to create the major TSS of the DHX9 promoter includes the sINR and an upstream Sp1 site. In a heterologous context, sINR substituted for the TATA box when positioned downstream to several Sp1 sites. Consistent with that the majority of sINR promoters contain at least one Sp1 site. Thus, sINR is a TATA-less-specific INR that functions in cooperation with Sp1. These findings support the idea that the INR is a family of related core promoter motifs

The impact of Er:YAG laser enamel conditioning on the microleakage of a new hydrophilic sealant — UltraSeal XT® hydro™

UltraSeal XT® hydro™ is a new hydrophilic, light-cured, methacrylate-based pit and fissure sealant which has been developed by Ultradent Products, USA. The sealant is highly filled with a 53 wt.% mixture of inorganic particles which confer both thixotropy and radiopacity. The principal purpose of this study was to investigate the microleakage of UltraSeal XT® hydro™ as a function of different enamel etching techniques. The occlusal surfaces of sound, extracted human molars were either acid etched, Er:YAG laser irradiated or successively laser irradiated and acid etched. UltraSeal XT® hydro™ was applied to each group of teeth (n=10) which were subjected to a thermocycling process consisting of 2500 cycles between 5 and 50°C with a dwell time of 30s. Microleakage assessments were then carried out using 0.5 % fuchsin dye and optical microscopy. The microleakage score data were analysed using the Kruskal-Wallis, Mann–Whitney U test with Bonferroni adjustment. No significant differences in microleakage were noted between the individually acid etched and laser-irradiated groups (p>0.05); however, teeth treated with a combination of laser irradiation and acid etching demonstrated significantly lower microleakage scores (p<0.001). Electron microscopy with energy-dispersive X-ray analysis revealed that the mineral filler component of UltraSeal XT® hydro™ essentially comprises micrometre-sized particles of inorganic silicon-, aluminium- and barium-bearing phases. Laser etching increases the roughness of the enamel surface which causes a concentrated zoning of the filler particles at the enamel-sealant interface

A Translation Initiation Element Specific to mRNAs with Very Short 5′UTR that Also Regulates Transcription

Transcription is controlled by cis regulatory elements, which if localized downstream to the transcriptional start site (TSS), in the 5′UTR, could influence translation as well. However presently there is little evidence for such composite regulatory elements. We have identified by computational analysis an abundant element located downstream to the TSS up to position +30, which controls both transcription and translation. This element has an invariable ATG sequence, which serves as the translation initiation codon in 64% of the genes bearing it. In these genes the initiating AUG is preceded by an extremely short 5′UTR. We show that translation in vitro and in vivo is initiated exclusively from the AUG of this motif, and that the AUG flanking sequences create a strong translation initiation context. This motif is distinguished from the well-known Kozak in its unique ability to direct efficient and accurate translation initiation from mRNAs with a very short 5′UTR. We therefore named it TISU for Translation Initiator of Short 5′UTR. Interestingly, this translation initiation element is also an essential transcription regulatory element of Yin Yang 1. Our characterization of a common transcription and translation element points to a link between mammalian transcription and translation initiation

Inferring Condition-Specific Modulation of Transcription Factor Activity in Yeast through Regulon-Based Analysis of Genomewide Expression

Background: A key goal of systems biology is to understand how genomewide mRNA expression levels are controlled by transcription factors (TFs) in a condition-specific fashion. TF activity is frequently modulated at the post-translational level through ligand binding, covalent modification, or changes in sub-cellular localization. In this paper, we demonstrate how prior information about regulatory network connectivity can be exploited to infer condition-specific TF activity as a hidden variable from the genomewide mRNA expression pattern in the yeast Saccharomyces cerevisiae. Methodology/Principal Findings: We first validate experimentally that by scoring differential expression at the level of gene sets or "regulons" comprised of the putative targets of a TF, we can accurately predict modulation of TF activity at the post-translational level. Next, we create an interactive database of inferred activities for a large number of TFs across a large number of experimental conditions in S. cerevisiae. This allows us to perform TF-centric analysis of the yeast regulatory network. Conclusions/Significance: We analyze the degree to which the mRNA expression level of each TF is predictive of its regulatory activity. We also organize TFs into "co-modulation networks" based on their inferred activity profile across conditions, and find that this reveals functional and mechanistic relationships. Finally, we present evidence that the PAC and rRPE motifs antagonize TBP-dependent regulation, and function as core promoter elements governed by the transcription regulator NC2. Regulon-based monitoring of TF activity modulation is a powerful tool for analyzing regulatory network function that should be applicable in other organisms. Tools and results are available online at http://bussemakerlab.org/RegulonProfiler/