IsoXpressor: A Tool to Assess Transcriptional Activity within Isochores.
Ontology highlight
ABSTRACT:
SUBMITTER: Ayad LAK
PROVIDER: S-EPMC7523728 | biostudies-literature | 2020 Sep
REPOSITORIES: biostudies-literature
Publications
IsoXpressor: A Tool to Assess Transcriptional Activity within Isochores.
Ayad Lorraine A K LAK Dourou Athanasia-Maria AM Arhondakis Stilianos S Pissis Solon P SP
Genome biology and evolution 20200901 9
Genomes are characterized by large regions of homogeneous base compositions known as isochores. The latter are divided into GC-poor and GC-rich classes linked to distinct functional and structural properties. Several studies have addressed how isochores shape function and structure. To aid in this important subject, we present IsoXpressor, a tool designed for the analysis of the functional property of transcription within isochores. IsoXpressor allows users to process RNA-Seq data in relation to ...[more]
Similar Datasets
Project description:BACKGROUND: Leptospirosis is a zoonotic infectious disease that affects both humans and animals. The existing genetic tools for Leptospira spp. have improved our understanding of the biology of this spirochete as well as the interaction of pathogenic leptospires with the mammalian host. However, new tools are necessary to provide novel and useful information to the field. METHODOLOGY AND PRINCIPAL FINDINGS: A series of promoter-probe vectors carrying a reporter gene encoding green fluorescent protein (GFP) were constructed for use in L. biflexa. They were tested by constructing transcriptional fusions between the lipL41, Leptospiral Immunoglobulin-like A (ligA) and Sphingomyelinase 2 (sph2) promoters from L. interrogans and the reporter gene. ligA and sph2 promoters were the most active, in comparison to the lipL41 promoter and the non-induced controls. The results obtained are in agreement with LigA expression from the L. interrogans Fiocruz L1-130 strain. CONCLUSIONS: The novel vectors facilitated the in vitro evaluation of L. interrogans promoter activity under defined growth conditions which simulate the mammalian host environment. The fluorescence and rt-PCR data obtained closely reflected transcriptional regulation of the promoters, thus demonstrating the suitability of these vectors for assessing promoter activity in L. biflexa.
| S-EPMC3060810 | biostudies-literature
Project description:BackgroundThe availability of fully sequenced genomes and the implementation of transcriptome technologies have increased the studies investigating the expression profiles for a variety of tissues, conditions, and species. In this study, using RNA-seq data for three distinct tissues (brain, liver, and muscle), we investigate how base composition affects mammalian gene expression, an issue of prime practical and evolutionary interest.ResultsWe present the transcriptome map of the mouse isochores (DNA segments with a fairly homogeneous base composition) for the three different tissues and the effects of isochores' base composition on their expression activity. Our analyses also cover the relations between the genes' expression activity and their localization in the isochore families.ConclusionsThis study is the first where next-generation sequencing data are used to associate the effects of both genomic and genic compositional properties to their corresponding expression activity. Our findings confirm previous results, and further support the existence of a relationship between isochores and gene expression. This relationship corroborates that isochores are primarily a product of evolutionary adaptation rather than a simple by-product of neutral evolutionary processes.
| S-EPMC3215772 | biostudies-literature
Project description:ObjectiveTo design and evaluate an interactive data quality (DQ) characterization tool focused on fitness-for-use completeness measures to support researchers' assessment of a dataset.Materials and methodsDesign requirements were identified through a conceptual framework on DQ, literature review, and interviews. The prototype of the tool was developed based on the requirements gathered and was further refined by domain experts. The Fitness-for-Use Tool was evaluated through a within-subjects controlled experiment comparing it with a baseline tool that provides information on missing data based on intrinsic DQ measures. The tools were evaluated on task performance and perceived usability.ResultsThe Fitness-for-Use Tool allows users to define data completeness by customizing the measures and its thresholds to fit their research task and provides a data summary based on the customized definition. Using the Fitness-for-Use Tool, study participants were able to accurately complete fitness-for-use assessment in less time than when using the Intrinsic DQ Tool. The study participants perceived that the Fitness-for-Use Tool was more useful in determining the fitness-for-use of a dataset than the Intrinsic DQ Tool.DiscussionIncorporating fitness-for-use measures in a DQ characterization tool could provide data summary that meets researchers needs. The design features identified in this study has potential to be applied to other biomedical data types.ConclusionA tool that summarizes a dataset in terms of fitness-for-use dimensions and measures specific to a research question supports dataset assessment better than a tool that only presents information on intrinsic DQ measures.
| S-EPMC9667174 | biostudies-literature
Project description:BackgroundSignificant differences in G+C content between different isochore types suggest that the nucleosome positioning patterns in DNA of the isochores should be different as well.ResultsExtraction of the patterns from the isochore DNA sequences by Shannon N-gram extension reveals that while the general motif YRRRRRYYYYYR is characteristic for all isochore types, the dominant positioning patterns of the isochores vary between TAAAAATTTTTA and CGGGGGCCCCCG due to the large differences in G+C composition. This is observed in human, mouse and chicken isochores, demonstrating that the variations of the positioning patterns are largely G+C dependent rather than species-specific. The species-specificity of nucleosome positioning patterns is revealed by dinucleotide periodicity analyses in isochore sequences. While human sequences are showing CG periodicity, chicken isochores display AG (CT) periodicity. Mouse isochores show very weak CG periodicity only.ConclusionsNucleosome positioning pattern as revealed by Shannon N-gram extension is strongly dependent on G+C content and different in different isochores. Species-specificity of the pattern is subtle. It is reflected in the choice of preferentially periodical dinucleotides.
| S-EPMC3097165 | biostudies-literature
Project description:The human genome is a mosaic of isochores, which are long (>200 kb) DNA sequences that are fairly homogeneous in base composition and can be assigned to five families comprising 33%-59% of GC composition. Although the compartmentalized organization of the mammalian genome has been investigated for more than 40 years, no satisfactory automatic procedure for segmenting the genome into isochores is available so far. We present a critical discussion of the currently available methods and a new approach called isoSegmenter which allows segmenting the genome into isochores in a fast and completely automatic manner. This approach relies on two types of experimentally defined parameters, the compositional boundaries of isochore families and an optimal window size of 100 kb. The approach represents an improvement over the existing methods, is ideally suited for investigating long-range features of sequenced and assembled genomes, and is publicly available at https://github.com/bunop/isoSegmenter.
| S-EPMC4662427 | biostudies-literature
Project description:Chromosome replication timing is biphasic (early-late) in the cell cycle of vertebrates and of most (possibly all) eukaryotes. In the present work we have compared the extended, detailed replication timing maps that are available, namely those of human chromosomes 6, 11q, and 21q, with chromosomal bands as visualized at low (400 bands), high (850 bands), and highest (3,200 isochores) resolution. We have observed that the replicons located in a given isochore practically always show either all early or all late replication timing and that early-replicating isochores are short and GC-rich and late-replicating isochores are long and GC-poor. In the vast majority of cases, replicons are clustered in isochores, which are themselves most often clustered in early- or late-replication timing zones and may often reach the size of high-resolution bands and, very rarely, even that of low-resolution bands. Finally, we show that our results should be representative for the whole human genome and thus help to predict replication timing zones in all chromosomes.
| S-EPMC2265141 | biostudies-other
Project description:ObjectivesSchools are an important setting to enable and promote physical activity. Researchers have created a variety of tools to perform objective environmental assessments (or 'audits') of other settings, such as neighborhoods and parks; yet, methods to assess the school physical activity environment are less common. The purpose of this study is to describe the approach used to objectively measure the school physical activity environment across 12 countries representing all inhabited continents, and to report on the reliability and feasibility of this methodology across these diverse settings.MethodsThe International Study of Childhood Obesity, Lifestyle and the Environment (ISCOLE) school audit tool (ISAT) data collection required an in-depth training (including field practice and certification) and was facilitated by various supporting materials. Certified data collectors used the ISAT to assess the environment of all schools enrolled in ISCOLE. Sites completed a reliability audit (simultaneous audits by two independent, certified data collectors) for a minimum of two schools or at least 5% of their school sample. Item-level agreement between data collectors was assessed with both the kappa statistic and percent agreement. Inter-rater reliability of school summary scores was measured using the intraclass correlation coefficient.ResultsAcross the 12 sites, 256 schools participated in ISCOLE. Reliability audits were conducted at 53 schools (20.7% of the sample). For the assessed environmental features, inter-rater reliability (kappa) ranged from 0.37 to 0.96; 18 items (42%) were assessed with almost perfect reliability (κ=0.80-0.96), and a further 24 items (56%) were assessed with substantial reliability (κ=0.61-0.79). Likewise, scores that summarized a school's support for physical activity were highly reliable, with the exception of scores assessing aesthetics and perceived suitability of the school grounds for sport, informal games and general play.ConclusionsThis study suggests that the ISAT can be used to conduct reliable objective audits of the school physical activity environment across diverse, international school settings.
| S-EPMC4850618 | biostudies-literature
Project description:Ratios of physical activity and sports participation in people with cerebral palsy (CP) are still low compared with people without a disability. For an adequate and useful practice, physical activity professionals should understand how different types of CP profiles constrain the performance of motor skills that are required during sports practice. This study aims to develop an observation-based assessment tool to evaluate activity limitations in individuals with a moderate level of CP when performing skills requiring jumping, sprinting, change of direction, coordination, and balance. Nineteen observers with different backgrounds from five world regions were recruited for this study, with accredited experience classifying/observing para-athletes with CP. All observers watched videos of 20 international para-athletes with different CP profiles (bilateral spasticity, athetosis/ataxia, unilateral spasticity; all Gross Motor Function Classification System level I) performing 16 motor tasks, and their observations were recorded throughout an ad-hoc data collection instrument. A total of 6080 units of qualitative information were recorded for data analysis. An observation-based tool with qualitative descriptors is derived from data analyses, describing how coordination and balance affected mainly in those with dyskinesia/ataxia, range of movement in those with diplegia, and asymmetries in those with hemiplegia. This tool would help sports practitioners and physical educators to better understand how different CP profiles constrain the performance of motor skills.
| S-EPMC7142872 | biostudies-literature
Project description:Two articles published 5 years ago concluded that the genome of the lizard Anolis carolinensis is an amniote genome without isochores. This claim was apparently contradicting previous results on the general presence of an isochore organization in all vertebrate genomes tested (including Anolis). In this investigation, we demonstrate that the Anolis genome is indeed heterogeneous in base composition, since its macrochromosomes comprise isochores mainly from the L2 and H1 families (a moderately GC-poor and a moderately GC-rich family, respectively), and since the majority of the sequenced microchromosomes consists of H1 isochores. These families are associated with different features of genome structure, including gene density and compositional correlations (e.g., GC3 vs flanking sequence GC and intron GC), as in the case of mammalian and avian genomes. Moreover, the assembled Anolis chromosomes have an enormous number of gaps, which could be due to sequencing problems in GC-rich regions of the genome. In conclusion, the Anolis genome is no exception to the general rule of an isochore organization in the genomes of vertebrates (and other eukaryotes).
| S-EPMC4860688 | biostudies-literature
Project description:The human genome, a typical mammalian genome, is made up of long (approximately 1-Mb, on average) regions, the isochores, that are fairly homogeneous in base composition and belong in five families characterized by different GC levels. An analysis of di- and tri-nucleotide densities in the isochores from the five families has shown large differences. These different "short-sequence designs:" (i) account for the fractionation of human DNA (and vertebrate DNA in general) when using sequence-specific ligands in density gradients, (ii) are very similar in whole isochores and in the corresponding intergenic sequences and introns, (iii) are reflected in different codon usages, (iv) lead to amino acid differences that increase the thermal stability of the proteins encoded by genes located in increasingly GC-rich isochore families, and (v) correspond to different chromatin structures.
| S-EPMC2532971 | biostudies-literature