Gene Transcription Data Research Articles

CUDA–MEME: Accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units

Motif discovery in biological sequences is of prime importance and a major challenge in computational biology. Consequently, numerous motif discovery tools have been developed to date. However, the rapid growth of both genomic sequence and gene transcription data, establishes the need for the development of scalable motif discovery tools. An approach to improve the runtime of motif discovery by an order-of-magnitude without losing sensitivity is to employ emerging many-core architectures such as CUDA-enabled GPUs. In this paper, we present a highly parallel formulation and implementation of the MEME motif discovery algorithm using the CUDA programming model. To achieve high efficiency, we introduce two parallelization approaches: sequence-level and substring-level parallelization. Furthermore, a hybrid computing framework is described to take advantage of both CPU and GPU compute resources. Our performance evaluation on a GeForce GTX 280 GPU, results in average runtime speedups of 21.4 (19.3) for the starting point search and 20.5 (16.4) for the overall runtime using the OOPS (ZOOPS) motif search model. The runtime speedups of CUDA–MEME on a single GPU are also comparable to those of ParaMEME running on 16 CPU cores of a high-performance workstation cluster. In addition to the fast speed, CUDA–MEME has the capability of finding motif instances consistent with the sequential MEME.

Inflammation-associated gene transcription and expression in mouse lungs induced by low molecular weight compounds from fungi from the built environment

Few metabolites from fungi found indoors have been tested for inflammatory mediators endpoints in primary cultures of alveolar macrophages or in vivo. In this study, mice were intratracheally instilled with a single dose comprising 4 × 10 −5 mole toxin/kg lung wt dose of either atranone C, brevianamide, cladosporin, mycophenolic acid, neoechinulin A & B, sterigmatocystin or TMC-120A. These toxins are from fungi common on damp building materials. The dose used was comparable to the estimated doses of possible human exposure. Hematoxylin and eosin (H&E) histology and Alcian Blue/Periodic Acid Schiff (AB/PAS) histochemistry were used to evaluate lungs for time course (4 h and 12 h post-exposure (PE)) inflammatory and toxic changes. Reverse-transcription (RT)-PCR based arrays were also employed to evaluate time course inflammation-associated gene transcription in lung tissues of the different toxins. Immunohistochemistry (IHC) was used to probe MIP-2 and Tnf-α protein expression in treatment lungs to determine whether responses correspond with gene transcription data. Both histology and histochemistry revealed that toxin exposed lungs at 12 h PE showed evidence of inflammation. H&E revealed that bronchioli were lined with irregularly thickened and sometimes sloughing epithelium and bronchiolar spaces supported infiltration of leukocytes, cellular and mucus-like debris while alveolar spaces supported swollen macrophages and modest amorphous debris accumulations. All toxin-instilled lungs exhibited copious mucus production and alveolar macrophages with red stained cytoplasm on bronchiolar surfaces, especially at 12 h PE. Array analysis of 83 inflammation-associated genes extracted from lung tissue demonstrated a number of patterns, compared to controls. 82 genes assayed at 4 h PE and 75 genes at 12 h PE were significantly altered ( p ≤ 0.05; ≥1.5-fold or ≤−1.5-fold change) in the different treatment animal groups. Expression of transcriptionally regulated genes was confirmed using immunohistochemistry that demonstrated MIP-2 and Tnf-α staining in respiratory bronchiolar epithelia, alveolar macrophages and alveolar type II cells. The transcriptional regulation in these genes in the treatment groups suggests that they may serve central roles in the immunomodulation of toxin-induced pro-inflammatory lung responses. Hierarchical cluster analysis revealed significant patterns of gene transcription linking the response of the toxins at equimolar doses in three groups: (1) brevianamide, mycophenolic acid and neoechinulin B, (2) neoechinulin A and sterigmatocystin, and (3) cladosporin, atranone C and TMC-120. The results further confirm the inflammatory nature of metabolites/toxins from such fungi can contribute to the development of non-allergenic respiratory health effects.

Functional annotations of diabetes nephropathy susceptibility loci through analysis of genome-wide renal gene expression in rat models of diabetes mellitus.

BackgroundHyperglycaemia in diabetes mellitus (DM) alters gene expression regulation in various organs and contributes to long term vascular and renal complications. We aimed to generate novel renal genome-wide gene transcription data in rat models of diabetes in order to test the responsiveness to hyperglycaemia and renal structural changes of positional candidate genes at selected diabetic nephropathy (DN) susceptibility loci.MethodsBoth Affymetrix and Illumina technologies were used to identify significant quantitative changes in the abundance of over 15,000 transcripts in kidney of models of spontaneous (genetically determined) mild hyperglycaemia and insulin resistance (Goto-Kakizaki-GK) and experimentally induced severe hyperglycaemia (Wistar-Kyoto-WKY rats injected with streptozotocin [STZ]).ResultsDifferent patterns of transcription regulation in the two rat models of diabetes likely underlie the roles of genetic variants and hyperglycaemia severity. The impact of prolonged hyperglycaemia on gene expression changes was more profound in STZ-WKY rats than in GK rats and involved largely different sets of genes. These included genes already tested in genetic studies of DN and a large number of protein coding sequences of unknown function which can be considered as functional and, when they map to DN loci, positional candidates for DN. Further expression analysis of rat orthologs of human DN positional candidate genes provided functional annotations of known and novel genes that are responsive to hyperglycaemia and may contribute to renal functional and/or structural alterations.ConclusionCombining transcriptomics in animal models and comparative genomics provides important information to improve functional annotations of disease susceptibility loci in humans and experimental support for testing candidate genes in human genetics.

Nitrogen Catabolite Repression-Sensitive Transcription as a Readout of Tor Pathway Regulation: The Genetic Background, Reporter Gene and GATA Factor Assayed Determine the Outcomes

Nitrogen catabolite repression (NCR)-sensitive genes, whose expression is highly repressed when provided with excess nitrogen and derepressed when nitrogen is limited or cells are treated with rapamycin, are routinely used as reporters in mechanistic studies of the Tor signal transduction pathway in Saccharomyces cerevisiae. Two GATA factors, Gln3 and Gat1, are responsible for NCR-sensitive transcription, but recent evidence demonstrates that Tor pathway regulation of NCR-sensitive transcription bifurcates at the level of GATA factor localization. Gln3 requires Sit4 phosphatase for nuclear localization and NCR-sensitive transcription while Gat1 does not. In this article, we demonstrate that the extent to which Sit4 plays a role in NCR-sensitive transcription depends upon whether or not (i) Gzf3, a GATA repressor homologous to Dal80, is active in the genetic background assayed; (ii) Gat1 is able to activate transcription of the assayed gene in the absence of Gln3 in that genetic background; and (iii) the gene chosen as a reporter is able to be transcribed by Gln3 or Gat1 in the absence of the other GATA factor. Together, the data indicate that in the absence of these three pieces of information, overall NCR-sensitive gene transcription data are unreliable as Tor pathway readouts.

Tobacco use induces anti-apoptotic, proliferative patterns of gene expression in circulating leukocytes of Caucasian males

BackgroundStrong epidemiologic evidence correlates tobacco use with a variety of serious adverse health effects, but the biological mechanisms that produce these effects remain elusive.ResultsWe analyzed gene transcription data to identify expression spectra related to tobacco use in circulating leukocytes of 67 Caucasian male subjects. Levels of cotinine, a nicotine metabolite, were used as a surrogate marker for tobacco exposure. Significance Analysis of Microarray and Gene Set Analysis identified 109 genes in 16 gene sets whose transcription levels were differentially regulated by nicotine exposure. We subsequently analyzed this gene set by hyperclustering, a technique that allows the data to be clustered by both expression ratio and gene annotation (e.g. Gene Ontologies).ConclusionOur results demonstrate that tobacco use affects transcription of groups of genes that are involved in proliferation and apoptosis in circulating leukocytes. These transcriptional effects include a repertoire of transcriptional changes likely to increase the incidence of neoplasia through an altered expression of genes associated with transcription and signaling, interferon responses and repression of apoptotic pathways.

Pathophysiological, Genetic and Gene Expression Features of a Novel Rodent Model of the Cardio-Metabolic Syndrome

BackgroundComplex etiology and pathogenesis of pathophysiological components of the cardio-metabolic syndrome have been demonstrated in humans and animal models.Methodology/Principal FindingsWe have generated extensive physiological, genetic and genome-wide gene expression profiles in a congenic strain of the spontaneously diabetic Goto-Kakizaki (GK) rat containing a large region (110 cM, 170 Mb) of rat chromosome 1 (RNO1), which covers diabetes and obesity quantitative trait loci (QTL), introgressed onto the genetic background of the normoglycaemic Brown Norway (BN) strain. This novel disease model, which by the length of the congenic region closely mirrors the situation of a chromosome substitution strain, exhibits a wide range of abnormalities directly relevant to components of the cardio-metabolic syndrome and diabetes complications, including hyperglycaemia, hyperinsulinaemia, enhanced insulin secretion both in vivo and in vitro, insulin resistance, hypertriglyceridemia and altered pancreatic and renal histological structures. Gene transcription data in kidney, liver, skeletal muscle and white adipose tissue indicate that a disproportionately high number (43–83%) of genes differentially expressed between congenic and BN rats map to the GK genomic interval targeted in the congenic strain, which represents less than 5% of the total length of the rat genome. Genotype analysis of single nucleotide polymorphisms (SNPs) in strains genetically related to the GK highlights clusters of conserved and strain-specific variants in RNO1 that can assist the identification of naturally occurring variants isolated in diabetic and hypertensive strains when different phenotype selection procedures were applied.ConclusionsOur results emphasize the importance of rat congenic models for defining the impact of genetic variants in well-characterised QTL regions on in vivo pathophysiological features and cis-/trans- regulation of gene expression. The congenic strain reported here provides a novel and sustainable model for investigating the pathogenesis and genetic basis of risks factors for the cardio-metabolic syndrome.

Genomewide Identification of Genes Under Directional Selection: Gene TranscriptionQST Scan in Diverging Atlantic Salmon Subpopulations

Evolutionary genomics has benefited from methods that allow identifying evolutionarily important genomic regions on a genomewide scale, including genome scans and QTL mapping. Recently, genomewide scanning by means of microarrays has permitted assessing gene transcription differences among species or populations. However, the identification of differentially transcribed genes does not in itself suffice to measure the role of selection in driving evolutionary changes in gene transcription. Here, we propose and apply a "transcriptome scan" approach to investigating the role of selection in shaping differential profiles of gene transcription among populations. We compared the genomewide transcription levels between two Atlantic salmon subpopulations that have been diverging for only six generations. Following assessment of normality and unimodality on a gene-per-gene basis, the additive genetic basis of gene transcription was estimated using the animal model. Gene transcription h(2) estimates were significant for 1044 (16%) of all detected cDNA clones. In an approach analogous to that of genome scans, we used the distribution of the Q(ST) values estimated from intra- and intersubpopulation additive genetic components of the transcription profiles to identify 16 outlier genes (average Q(ST) estimate = 0.11) whose transcription levels are likely to have evolved under the influence of directional selection within six generations only. Overall, this study contributes both empirically and methodologically to the quantitative genetic exploration of gene transcription data.

Aerobic Exercise Bout Effects on Gene Transcription in the Rat Soleus

This study was designed to identify changes in gene transcription that occur in the soleus muscle of untrained, 10-wk-old rats after a single aerobic exercise bout, and to identify which families of genes are most likely affected. Rats were either run for 2 h and killed 1 h after exercise, or they remained sedentary and were killed at a matched time. Soleus muscles from each animal were examined using DNA microarrays, four genes related to RONS were analyzed by PCR, and two proteins were checked by Western blot analysis. The microarray identified 52 genes significantly altered by the exercise. The major gene families altered were metabolism, apoptosis, muscle contraction, transcription/cell signaling, tissue generation, and inflammation. Real-time PCR was performed on four genes (NFkappaB, TNFalpha, Atf3, and Mgst1), and the results from PCR analysis agreed with the microarray results. NFkappaB and TNFalpha were unaltered, whereas Atf3 was upregulated and Mgst1 was downregulated in the exercised soleus muscles. NFkappaB protein level was not different between the two groups, whereas Atf3 protein level was elevated in the exercise group according to Western blot analysis. These data suggest that 1 h after a 2-h run at approximately 65% of VO2max, the soleus muscle undergoes significant gene-transcript changes. Also, the genes examined with the real-time PCR matched the microarray results and the measured protein concentration concentrations agreed with gene-transcript data at the 1-h postexercise time point.

Quantitative profiling of housekeeping and Epstein-Barr virus gene transcription in Burkitt lymphoma cell lines using an oligonucleotide microarray

BackgroundThe Epstein-Barr virus (EBV) is associated with lymphoid malignancies, including Burkitt's lymphoma (BL), and can transform human B cells in vitro. EBV-harboring cell lines are widely used to investigate lymphocyte transformation and oncogenesis. Qualitative EBV gene expression has been extensively described, but knowledge of quantitative transcription is lacking. We hypothesized that transcription levels of EBNA1, the gene essential for EBV persistence within an infected cell, are similar in BL cell lines.ResultsTo compare quantitative gene transcription in the BL cell lines Namalwa, Raji, Akata, Jijoye, and P3HR1, we developed an oligonucleotide microarray chip, including 17 housekeeping genes, six latent EBV genes (EBNA1, EBNA2, EBNA3A, EBNA3C, LMP1, LMP2), and four lytic EBV genes (BZLF1, BXLF2, BKRF2, BZLF2), and used the cell line B95.8 as a reference for EBV gene transcription. Quantitative polymerase chain reaction assays were used to validate microarray results. We found that transcription levels of housekeeping genes differed considerably among BL cell lines. Using a selection of housekeeping genes with similar quantitative transcription in the tested cell lines to normalize EBV gene transcription data, we showed that transcription levels of EBNA1 were quite similar in very different BL cell lines, in contrast to transcription levels of other EBV genes. As demonstrated with Akata cells, the chip allowed us to accurately measure EBV gene transcription changes triggered by treatment interventions.ConclusionOur results suggest uniform EBNA1 transcription levels in BL and that microarray profiling can reveal novel insights on quantitative EBV gene transcription and its impact on lymphocyte biology.

EPINEPHRINE INCREASES MKP-1 IN LPS-STIMULATED THP-1 CELLS

Objective: MKP-1 is a type II dual specific MAPK phosphatase that dephosphorylates MAP kinases, especially p38 and JNK, decreasing their activity. Epinephrine, through cAMP, suppresses inflammation, in part by decreasing TNFα and increasing IL-10 gene transcription. We sought to determine the role for MKP-1 in cAMP mediated suppression of TNFα. Methods: Differentiated THP-1 cells were treated under the following conditions: (1) epinephrine alone, (2) LPS alone, (3) both and, (4) untreated. Cells were harvested at various time points to 4 hours. Using real time PCR, mRNA levels of MKP-1 and TNFα were measured. pJNK was analyzed by immunoblot. RTPCR data is presented as fold increase over time 0 controls. All data were expressed as mean ± SD and were analyzed by ANOVA. Results: Epinephrine decreased LPS induced TNFα gene transcription (data not shown). Epinephrine alone increased MKP-1 gene transcription over untreated controls at 20, 40, 60 and 120 minutes (P <.001 at all time points). The addition of epinephrine to LPS increased MKP-1 mRNA at 20, 40, 60 and 120 minutes vs LPS alone (P <.001 at all time points). MKP-1 transcription was short lived, reaching its peak at 40 minutes and falling close to baseline by 2 hours. Western blot revealed earlier deactivation of JNK in samples treated with LPS and epinephrine vs LPS alone (data not shown).FigureConclusions: Our work demonstrates a novel observation, which may represent the mechanism by which cAMP activation results in early suppression of TNFα gene transcription. Increased MKP-1 activity is known to dephosphorylate MAPKs, specifically p38 and JNK, decreasing their activity. It is possible that decreased JNK activity, through a reduction in AP-1 activation, a known transcription factor, is responsible for the decrease in TNFα transcription. Manipulation of this pathway may represent a potential treatment avenue during times of sepsis and trauma.

A dynamic model of Rubisco turnover in cereal leaves

A simple, improved model of Rubisco synthesis and degradation in cereal leaves is developed using data obtained over the leaf lifespan to return maximum likelihood values for Rubisco proteolysis and biosynthesis. It assumes that the time course of leaf Rubisco content can be described using a log-normal curve, and degradation of the Rubisco pool occurs exponentially. Curve parameters give an insight into how Rubisco dynamics differ among treatments or genotypes; also, statistical analyses can be performed more easily, requiring fewer data and allowing more flexibility in sampling than previous studies. Predicted patterns of synthesis correlate well with independent rbc gene transcript data. Rubisco degradation is a first-order decay process, and biosynthesis correlates with leaf elongation rates. As Rubisco degradation takes place according to first-order kinetics, control of leaf Rubisco concentration must be exerted by adjustment of biosynthetic, rather than proteolytic, rates.

Organization of the MASP2 locus and its expression profile in mouse and rat

The mouse, rat, and human MASP2 loci are situated on syntenic chromosome regions and are highly conserved. They comprise the genes for MASP-2/ MAp19, TAR DNA binding protein of 43 kDa, FRAP kinase, CDT6, Polymyositis-Scleroderma 100-kDa autoantigen, spermidine synthase, and TERE which were analyzed by annotation of available gene transcript data and cross-species comparison of available genomic sequences. The human and rat genes for spermidine synthase have an additional intron compared to the mouse gene. The mouse and rat genes for Polymyositis-Scleroderma 100-kDa autoantigen have an additional exon compared to the human gene. We find support for the hypothesis that the MAp19-specific exon within the MASP2 gene may have originated in a transposable element. Blocks of highly conserved intronic sequences were found in the MASP2 gene and the TARDBP gene. The expression of all genes within the MASP2 locus was analyzed in mouse and rat. The restricted expression of MASP-2 and MAp19 mRNA in liver contrasts with the ubiquitous expression of all neighboring genes studied.

Previtamin D3 with a trans-Fused Decalin CD-ring Has Pronounced Genomic Activity

Deletion of C19 in the structure of 1 alpha,25-dihydroxyvitamin D3 [1,25(OH)2D3] does not substantially alter the biological potency but prevents the conversion between the vitamin and the previtamin form. Hence, this modification allows the study of locked previtamin and vitamin forms. The locked 19-nor-1,25(OH)2-previtamin D3 analog (19-nor-previtamin D) had a low biological activity and was a rather weak activator of the genomic signal transduction pathway. 19-Nor-trans-decalin-1,25(OH)2-vitamin D3 (19-nor-TD-vitamin D), characterized by the presence of a trans-fused decalin CD-ring system, was 10-fold more potent than the parent compound and was a potent activator of the genomic signal transduction pathway. Surprisingly, the previtamin, 19-nor-trans-decalin-1,25(OH)2-previtamin D3 (19-nor-TD-previtamin D), was as potent as 1,25(OH)2D3 in inhibiting cell proliferation and inducing cell differentiation and represents the first previtamin structure with pronounced vitamin D-like activity. Furthermore, this compound interacted as efficiently as 1,25(OH)2D3 with the vitamin D receptor (VDR), retinoid X receptor (RXR), coactivators, and DNA, which illustrated its potent ability to activate the genomic signal transduction pathway. Analysis of the transactivation potency of 12 VDR point mutants after stimulation with 19-nor-TD-previtamin D revealed that this analog used the same contact points within the receptor as did 1,25(OH)2D3. This could be confirmed by modeling analysis of this compound in the ligand binding pocket of VDR. In conclusion, a previtamin D3 analog is presented with genomic activities equivalent to 1,25(OH)2D3.