Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “transcriptome sequencing”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,639 records · Page 91Linked to original sources
PubMed2006

Aging in legume symbiosis. A molecular view on nodule senescence in Medicago truncatula.

Rhizobia reside as symbiosomes in the infected cells of legume nodules to fix atmospheric nitrogen. The symbiotic relation is strictly controlled, lasts for some time, but eventually leads to nodule senescence. We present a comprehensive transcriptomics study to understand the onset of nodule senescence in the legume Medicago truncatula. Distinct developmental stages with characteristic gene expression were delineated during which the two symbiotic partners were degraded consecutively, marking the switch in nodule tissue status from carbon sink to general nutrient source. Cluster analysis discriminated an early expression group that harbored regulatory genes that might be primary tools to interfere with pod filling-related or stress-induced nodule senescence, ultimately causing prolonged nitrogen fixation. Interestingly, the transcriptomes of nodule and leaf senescence had a high degree of overlap, arguing for the recruitment of similar pathways.

Cluster Analysis↗
PubMed2004

Toxicogenomics of subchronic hexachlorobenzene exposure in Brown Norway rats.

Hexachlorobenzene (HCB) is a persistent environmental pollutant with toxic effects in man and rat. Reported adverse effects are hepatic porphyria, neurotoxicity, and adverse effects on the reproductive and immune system. To obtain more insight into HCB-induced mechanisms of toxicity, we studied gene expression levels using DNA microarrays. For 4 weeks, Brown Norway rats were fed a diet supplemented with 0, 150, or 450 mg HCB/kg. Spleen, mesenteric lymph nodes (MLN), thymus, blood, liver, and kidney were collected and analyzed using the Affymetrix rat RGU-34A GeneChip microarray. Most significant (p < 0.001) changes, compared to the control group, occurred in spleen, followed by liver, kidney, blood, and MLN, but only a few genes were affected in thymus. This was to be expected, as the thymus is not a target organ of HCB. Transcriptome profiles confirmed known effects of HCB such as stimulatory effects on the immune system and induction of enzymes involved in drug metabolism, porphyria, and the reproductive system. In line with previous histopathological findings were increased transcript levels of markers for granulocytes and macrophages. New findings include the upregulation of genes encoding proinflammatory cytokines, antioxidants, acute phase proteins, mast cell markers, complements, chemokines, and cell adhesion molecules. Generally, gene expression data provide evidence that HCB induces a systemic inflammatory response, accompanied by oxidative stress and an acute phase response. In conclusion, this study confirms previously observed (immuno)toxicological effects of HCB but also reveals several new and mechanistically relevant gene products. Thus, transcriptome profiles can be used as markers for several of the processes that occur after HCB exposure.

Acute-Phase Reaction↗
PubMed2005

Doxycycline, the drug used to control the tet-regulatable promoter system, has no effect on global gene expression in Saccharomyces cerevisiae.

The tet-regulatable promoter system is commonly used for genetic studies in many eukaryotic organisms. The promoter is regulated using doxycycline. There are no obvious phenotypic effects observed when doxycycline is added to the growth medium of yeast to control expression from the promoter. It is widely accepted that doxycycline is innocuous to yeast. Global genetic studies are now commonplace and the tetO-system is being used in transcriptome studies. Hence, we wanted to ensure that the absence of phenotypic effects, on addition of doxycycline to the growth medium, is mirrored in transcriptome data. We have demonstrated that doxycycline has no significant effect on global transcription levels and will continue to use the tetO-regulatable promoter system for genetic studies.

Culture Media↗
PubMed2006

The transcriptome of the uterine cervix before and after spontaneous term parturition.

OBJECTIVE: This study was designed to identify genes differentially expressed in the human uterine cervix after spontaneous term labor. STUDY DESIGN: The transcriptome of cervical tissue was characterized using Affymetrix HG-U133 plus 2 microarrays. Samples were collected from patients at term not in labor (n = 7) and after spontaneous labor (n = 9). Microarray statistical analysis included robust multiarray average, reduction of invariant probes, and permutation analysis for differential expression. Real-time quantitative reverse transcriptase-polymerase chain reaction assays of selected genes were performed on a new set of samples from term patients without labor (n = 10) and patients after spontaneous labor (n = 9). RESULTS: (1) The cervical transcriptome of term patients without labor was dramatically different from that of patients who underwent labor; (2) unique genes (n = 1192) were differentially expressed in the cervical tissue from patients after spontaneous labor, compared with that of the term patients without labor (false discovery rate less than 0.05, absolute fold change greater than 2); (3) Gene Ontology analysis indicated that multiple "Biological Process" categories were enriched, including "response to biotic stimulus," "apoptosis," "epidermis development," and "steroid metabolism"; (4) of major interest, genes involved in neutrophil chemotaxis were dramatically up-regulated in specimens from women after spontaneous labor; (5) real-time quantitative reverse transcriptase-polymerase chain reaction confirmed the increased expression of interleukin-8, interleukin-6, and vascular endothelial growth factor in patients after spontaneous labor; and (6) Toll-like receptor-3 and Toll-like receptor-5 showed decreased gene expression in patients after spontaneous labor. This was confirmed by real-time quantitative reverse transcriptase-polymerase chain reaction. CONCLUSION: (1) Cervical dilatation in term labor is associated with a stereotypic gene expression pattern determined by microarray, which is characterized by overexpression of genes involved in neutrophil chemotaxis, apoptosis, extracellular matrix regulation, and steroid metabolism; (2) Toll-like receptor-3 and Toll-like receptor-5 are differentially regulated during spontaneous parturition at term; and (3) this study provides an unbiased and comprehensive description of the changes in the cervical transcriptome before and after spontaneous term labor.

Adolescent↗
PubMed2004

Alcohol and gene expression in the central nervous system.

AIMS: To describe recent research focusing on the analysis of gene and protein expression relevant to understanding ethanol consumption, dependence and effects, in order to identify common themes. METHODS: A selective literature search was used to collate the relevant data. RESULTS: Over 160 genes have been individually assessed before or after ethanol administration, as well as in genetically selected lines. Techniques for studying gene expression include northern blots, differential display, real time reverse transcriptase-polymerase chain reaction (RT-PCR) and in situ hybridization. More recently, high throughput functional genomic technology, such as DNA microarrays, has been used to examine gene expression. Recent gene expression analyses have dramatically increased the number of candidate genes (nine array papers have illuminated 600 novel gene transcripts that may contribute to alcohol abuse and alcoholism). CONCLUSIONS: Although functional genomic experiments (transcriptome analysis) have failed to identify a single alcoholism gene, they have illuminated important pathways and gene products that may contribute to the risk of alcohol abuse and alcoholism.

Alcoholism↗
PubMed2006

Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray.

Small non-coding RNAs (ncRNAs) are encoded by genes that function at the RNA level, and several hundred ncRNAs have been identified in various organisms. Here we describe an analysis of the small non-coding transcriptome of Caenorhabditis elegans, microRNAs excepted. As a substantial fraction of the ncRNAs is located in introns of protein-coding genes in C.elegans, we also analysed the relationship between ncRNA and host gene expression. To this end, we designed a combined microarray, which included probes against ncRNA as well as host gene mRNA transcripts. The microarray revealed pronounced differences in expression profiles, even among ncRNAs with housekeeping functions (e.g. snRNAs and snoRNAs), indicating distinct developmental regulation and stage-specific functions of a number of novel transcripts. Analysis of ncRNA-host mRNA relations showed that the expression of intronic ncRNA loci with conserved upstream motifs was not correlated to (and much higher than) expression levels of their host genes. Even promoter-less intronic ncRNA loci, though showing a clear correlation to host gene expression, appeared to have a surprising amount of 'expressional freedom', depending on host gene function. Taken together, our microarray analysis presents a more complete and detailed picture of a non-coding transcriptome than hitherto has been presented for any other multicellular organism.

Animals↗
PubMed2004

Characterization of the Bacillus subtilis YxdJ response regulator as the inducer of expression for the cognate ABC transporter YxdLM.

The genome of Bacillus subtilis, like those of some other AT-rich Gram-positive bacteria, has the uncommon feature of containing several copies of arrangements in which the genes encoding two-component and cognate ABC transporter systems are adjacent. As the function of one of these systems, the product of the yxd locus, is still unknown, it was analysed further in order to get some clues on the physiological role of the gene products it encodes. The yxdJ gene was shown to encode a DNA-binding protein that directly controls transcription of the neighbouring operon encoding the ABC transporter YxdLM. Primer extension and DNase protection experiments allowed precise definition of the yxdLM transcription start and controlling region. Two putative direct repeats were identified that are proposed to be the YxdJ response regulator binding sites. Whole-cell transcriptome analyses revealed that the YxdJ regulon is extremely restricted. In addition to the yxdJKLMyxeA operon, only a few genes involved in modifications of the bacterial cell wall were shown to be regulated by YxdJ.

ATP-Binding Cassette Transporters↗
PubMed2006

Genome-wide analysis of spatial and temporal gene expression in rice panicle development.

The basic structure of a rice inflorescence (the panicle) is determined by the pattern of branch formation, which is established at the early stages of panicle development. In this study we conducted global transcriptome profiling of the early stages of rice panicle development from phase transition to floral organ differentiation. To generate a meristem-specific gene-expression profile, shoot apical meristems (SAMs) and subsequently formed, very young panicles were collected manually and used for cDNA microarray analysis. We identified 357 out of 22,000 genes that are expressed differentially in the early stages of panicle development, and the 357 genes were classified into seven groups based on their temporal expression patterns. The most noticeable feature is that a fairly small number of genes, which are extensively enriched in transcription factors, are upregulated in the SAM immediately after phase transition. In situ hybridization analysis showed that each gene analysed exhibits a unique and interesting localization of mRNA. Remarkably, one of the transcription factors was proven to be a close downstream component of the pathway in which LAX, a major regulator of panicle branching, acts. These results suggest that our strategy--careful collection of meristems, global transcriptome analysis and subsequent in situ hybridization analysis--is useful not only to obtain a genome-wide view of gene expression, but also to reveal genetic networks controlling rice panicle development.

Gene Expression Profiling↗
PubMed2001

Extracting biological information from DNA arrays: an unexpected link between arginine and methionine metabolism in Bacillus subtilis.

BACKGROUND: In global gene expression profiling experiments, variation in the expression of genes of interest can often be hidden by general noise. To determine how biologically significant variation can be distinguished under such conditions we have analyzed the differences in gene expression when Bacillus subtilis is grown either on methionine or on methylthioribose as sulfur source. RESULTS: An unexpected link between arginine metabolism and sulfur metabolism was discovered, enabling us to identify a high-affinity arginine transport system encoded by the yqiXYZ genes. In addition, we tentatively identified a methionine/methionine sulfoxide transport system which is encoded by the operon ytmIJKLMhisP and is presumably used in the degradation of methionine sulfoxide to methane sulfonate for sulfur recycling. Experimental parameters resulting in systematic biases in gene expression were also uncovered. In particular, we found that the late competence operons comE, comF and comG were associated with subtle variations in growth conditions. CONCLUSIONS: Using variance analysis it is possible to distinguish between systematic biases and relevant gene-expression variation in transcriptome experiments. Co-variation of metabolic gene expression pathways was thus uncovered linking nitrogen and sulfur metabolism in B. subtilis.

Arginine↗
PubMed2005

KEGG-based pathway visualization tool for complex omics data.

Pathway-level visualization of omics data provides an essential means for systems biology, to capture the systematic properties of the inner activities of cells. Here we describe a web-based resource consisting of a web-application for the visualization of complex omics data onto KEGG pathways to overview all entities in the context of cellular pathways, and databases created with the software to visualize a series of microarray data. The web-application accepts transcriptome, proteome, metabolome, or the combination of these data as input, and because of this scalability it is advantageous for the visualization of cell simulation results. The web server can be accessed at http://www.g-language.org/data/marray/.

Computer Graphics↗
PubMed2007

Snake venomics of Bitis gabonica gabonica. Protein family composition, subunit organization of venom toxins, and characterization of dimeric disintegrins bitisgabonin-1 and bitisgabonin-2.

The protein composition of the venom of the East African Gaboon viper (Bitis gabonica gabonica) was analyzed using RP-HPLC, N-terminal sequencing, MALDI-TOF peptide mass fingerprinting, and CID-MS/MS. In total, 35 proteins of molecular masses in the range of 7-160 kDa and belonging to 12 toxin families were identified. The most abundant proteins were serine proteinases (26.4%), Zn2+-metalloproteinases (22.9%), C-type lectin-like proteins (14.3%), PLA2s (11.4%), and bitiscystatin (9.8%). Other protein classes, that is, bradykinin-potentiating peptides, dimeric disintegrins, Kunitz-type inhibitor, DC-fragments, sv-VEGF, CRISP, and L-amino acid oxidase, comprised between 1.3 and 3.4% of the total venom proteome. Only 11 venom-secreted proteins matched any of the previously reported 22 partial or full-length venom gland transcripts. In addition, venome and transcriptome depart in their relative abundances of different toxin families. The proteomic characterization of purified B. gabonica gabonica proteins run under nonreducing and reducing SDS-PAGE conditions revealed their aggregation state and subunit composition. Multimeric proteins included heterodimeric disintegrins, homodimeric sv-VEGF-A, heterodimeric (alphabeta) and tetrameric (alphabeta)4 C-type lectins, and multimeric PIII Zn2+-metalloproteinases. Determination of the complete primary structure and subunit composition of the two major dimeric disintegrins, bitisgabonin-1 and bitisgabonin-2, showed that each comprised a distinct RGD- and MLD-bearing subunit and a common, N-terminal-blocked, RGD-containing subunit identical to the disintegrin domain of the PII Zn2+-metalloproteinase 4. Cell adhesion inhibition assays showed that bitisgabonin-1 (RGD-RGD) is a potent inhibitor of integrin alpha5beta1, whereas bitisgabonin-2 (MLD-RGD) is a better antagonist of integrins alpha4beta1 and alpha9beta1.

Amino Acid Sequence↗
PubMed2005

Elucidating effects of long-term expression of HIV-1 Nef on astrocytes by microarray, promoter, and literature analyses.

The challenge of microarray analysis is to unveil the biological mechanisms behind the chip data. Due to the sometimes counteracting influences of de novo transcription, RNA processing and degradation, the discovery of any particular mechanism is difficult. Therefore, a combination of data- and knowledge-driven analysis appears to be the best way to attack the problem. We analyzed human astrocytes stably expressing the HIV-1 nef gene by microarray analyses to elucidate the effects of constitutive HIV-1 Nef expression on the transcriptome of astrocytes. Statistical evaluation of microarray results revealed small clusters of genes specifically up-regulated by native Nef protein in contrast to astrocytes expressing a non-myristoylated Nef variant. At least three significantly overrepresented gene ontology groups (small GTPase signaling, regulation of apoptosis and lipid metabolism) were detected. The JAK/STAT pathway was clearly associated with those genes. This finding agreed well with a literature-based approach, where a network was derived by combined literature and promoter sequence analysis. Promoter organization suggested potentially coordinated transcriptional regulation of some of these genes. Both results were in line with previously reported phenotypic changes.

Apoptosis↗
PubMed2026

Cis-regulatory variation in the MdCKX6 promoter is associated with allele-specific expression and fruit size in apple.

Fruit size is a key determinant of apple fruit quality and market value and is strongly influenced by phytohormone-regulated cell proliferation and expansion during early fruit development. Cytokinin oxidase/dehydrogenase (CKX) enzymes regulate cytokinin homeostasis by irreversibly degrading active cytokinins, but the contribution of natural variation in CKX genes to fruit size remains poorly understood. Here, we identified MdCKX6 as a candidate regulator of fruit growth in apple (Malus domestica). MdCKX6 exhibited pronounced allele-specific expression during fruit development in the cultivar 'Royal Gala'. Sequence analysis identified a promoter SNP associated with differential promoter activity and allele-specific expression. Genotyping of diverse apple cultivars and wild Malus accessions revealed a significant association between MdCKX6 promoter genotype and fruit size. Cultivars carrying low-expression alleles produced larger fruits, whereas high-expression alleles were associated with smaller fruits. To investigate gene function, MdCKX6 was overexpressed in tomato, resulting in reduced fruit size. Histological analyses of the transgenic tomato fruit revealed smaller pericarp cells. Transcriptome analysis of transgenic fruits revealed widespread changes in genes associated with cell-cycle regulation, cell wall modification, hormone-related processes, and transcriptional regulation. Together, these results identify MdCKX6 as a potential negative regulator of apple fruit growth and reveal an association between cis-regulatory variants, gene expression, and fruit size. This study provides new insights into the role of cytokinin metabolism in fruit development and highlights regulatory variation in MdCKX6 as a potential target for apple breeding.

Malus↗
PubMed2004

Dual-genome primer design for construction of DNA microarrays.

MOTIVATION: Microarray experiments using probes covering a whole transcriptome are expensive to initiate, and a major part of the costs derives from synthesizing gene-specific PCR primers or hybridization probes. The high costs may force researchers to limit their studies to a single organism, although comparing gene expression in different species would yield valuable information. RESULTS: We have developed a method, implemented in the software DualPrime, that reduces the number of primers required to amplify the genes of two different genomes. The software identifies regions of high sequence similarity, and from these regions selects PCR primers shared between the genomes, such that either one or, preferentially, both primers in a given PCR can be used for amplification from both genomes. To assure high microarray probe specificity, the software selects primer pairs that generate products of low sequence similarity to other genes within the same genome. We used the software to design PCR primers for 2182 and 1960 genes from the hyperthermophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius, respectively. Primer pairs were shared among 705 pairs of genes, and single primers were shared among 1184 pairs of genes, resulting in a saving of 31% compared to using only unique primers. We also present an alternative primer design method, in which each gene shares primers with two different genes of the other genome, enabling further savings. 3. AVAILABILITY: The software is freely available at http://www.biotech.kth.se/molbio/microarray/.

Algorithms↗
PubMed2026

Bacteria and phage consortia modulate cecal SCFA production and host metabolism to enhance feed efficiency in ducks.

BACKGROUND: The gut microbiota influences poultry health, nutrition, feed efficiency (FE), and overall productivity. However, the relationship between gut microbes, including bacteria and phages, and FE in ducks remains underexplored. To address this, we integrated cecal 16S amplicon, metagenome, microbiota-derived short-chain fatty acids (SCFAs) profiling, liver transcriptome, and serum metabolome data to illustrate the contribution of the gut microbiome (bacteria and viruses) to duck FE. RESULTS: We reconstructed viral genomes and prokaryotic metagenome-assembled genomes (MAGs) and annotated their genes using comprehensive databases. Prokaryotic hosts of viruses were also predicted to understand virus-host dynamics within the gut ecosystem. Our results revealed that high-FE ducks have higher concentration of propionate and butyrate in cecum compared with low-FE ducks. The metagenome sequencing revealed distinct cecal microbiota profiles between two groups, with increased relative abundance of representative SCFA producers, especially Paraprevotella sp905215575 and Bacteroides sp944322345, and enhanced SCFA-biosynthesis pathways in high-FE ducks. Virome genome assembly identified two phages encoding auxiliary metabolic genes (AMGs) involved in pyruvate metabolism, enhancing nutrient availability for host bacteria to produce SCFAs (e.g., temperate phage-encoded pyruvate phosphate dikinase) or exploiting host central metabolic pathways for viral replication (e.g., lytic phage-encoded formate C-acetyltransferase). Furthermore, these representative SCFA-producing bacteria and phage consortia were associated with serum metabolites (including L-histidine and 4-hydroxydecanedioylcarnitine) linked to duck FE. CONCLUSION: Collectively, these findings provide novel insights into the gut microbial factors regulating FE in ducks, offering potential strategies to optimize poultry nutrition and productivity. Video Abstract.

Animals↗
PubMed2004

Identification of changes in the transcriptome profile of human hepatoma HepG2 cells stimulated with interleukin-1 beta.

Interleukin-1 (IL-1) is the principal pro-inflammatory cytokine participating in the initiation of acute phase response. Human hepatoma HepG2 cells were exposed to 15 ng/ml of IL-1beta for times ranging from 1 to 24 h and the total RNA was isolated. Then cDNA was obtained and used for differential display with 10 arbitrary primers and 9 oligo(dT) primers designed by Clontech. Validation of observed changes of differentially expressed known genes was carried out by RT-PCR or Northern blot analysis. Out of 90 cDNA strands modulated by IL-1, 46 have been successfully reamplified and their sequencing indicates that they represent 36 different cDNA templates. By GenBank search, 26 cDNA clones were identified as already known genes while 10 showed no homology to any known gene. The identified transcripts modulated by IL-1 in HepG2 cells code for intracellular proteins of various function: trafficking/motor proteins (3 genes), proteins participating in the translation machinery or posttranscriptional/posttranslational modifications (7 genes), proteases (1 gene), proteins involved in metabolism (6 genes), activity modulators (3 genes), proteins of the cell cycle machinery (2 genes) and those functionally unclassified (4 genes). Majority of genes responded to IL-1 within 1 to 6 h (early genes), while two were late response genes (12-24 h) and four showed prolonged response over the whole 24-h period. Most of the observed changes of expression were in the range of two- to threefold increase in comparison to control untreated cells. Among identified genes, no typical secretory acute phase protein was found. The obtained results suggest that IL-1 affects the expression of several genes in HepG2 cells, especially those engaged in the synthesis and modifications of proteins.

Carcinoma, Hepatocellular↗
PubMed2004

The Mycobacterium tuberculosis complex transcriptome of attenuation.

Although the deletion of RD1 is likely correlated to attenuation from virulence for members of the Mycobacterium tuberculosis (MTB) complex, the reasons for this phenotype remain to be fully explained. As genomic variation is responsible for at least a component of variability in gene expression, we looked to the in vitro global expression profile of the RD1 artificial knockout from M. tuberculosis H37Rv (H37Rv:deltaRD1) for clues to elucidate its phenotypic shift towards attenuation. By comparing the transcriptome of H37Rv:deltaRD1 to that of virulent H37Rv, 15 regulated genes located in nine different regions outside of RD1 have been identified, capturing an effect of RD1's deletion on the rest of the genome. To assess whether these regulations are characteristic of attenuated MTB in general, expression profiles of natural RD1 mutants (BCG Russia, BCG Pasteur, and M. microti) as well as the 'avirulent' M. tuberculosis H37Ra, whose RD1 region is genomically intact, were obtained. Results indicate that attenuated strains lack the expression of RD1 genes including cfp10 and esat6, whether through deletion or reduced expression. Furthermore, comparative transcriptomics reveals the concurrent down-regulation of several gene neighborhoods beyond RD1. The potential relevance of these other expression changes towards MTB virulence is discussed.

DNA, Bacterial↗
PubMed2001

How many nuclear hormone receptors are there in the human genome?

The sequence of the human genome now allows the definition of the complete set of genes for specific protein families in humans. Because of their involvement in many physiological and pathological processes, the nuclear hormone receptors are a superfamily of crucial medical significance. Although 48 human nuclear receptor genes were identified previously, their total number is unclear from early human genome reports. Here, we report the identification and classification of all nuclear receptor genes in the human genome, and we discuss corresponding transcriptome and proteome diversity.

Alternative Splicing↗