Transcriptome analysis of Saccharomyces cerevisiae using serial analysis of gene expression.
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Biotinylation↗
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Results for “transcriptome sequencing”
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Mutation accumulation of the transcriptome.
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Animals↗
[Transcriptome; full-length cDNA project].
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Animals↗
The heavy metal hyperaccumulator Thlaspi caerulescens expresses many species-specific genes, as identified by comparative expressed sequence tag analysis.
Thlaspi caerulescens is a natural zinc (Zn), cadmium (Cd) and nickel (Ni) hyperaccumulator and an emerging plant model species to study heavy metal hyperaccumulation and tolerance. This paper describes the analysis of the first expressed sequence tag (EST) collection from T. caerulescens. This collection is a new resource to unravel the molecular basis of plant metal homeostasis, tolerance and hyperaccumulation. In total, 4289 ESTs were generated originating from Zn-exposed root and shoot tissues, leading to 3709 T. caerulescens assembled partial cDNA sequences (unigenes). In comparison to Arabidopsis or other publicly available plant sequences, a fraction of c. 8% of the T. caerulescens unigenes (TcUGs) had no significant similarity with any known DNA sequence and, so far, these sequences are T. caerulescens specific. Three per cent of the TcUGs correspond to Arabidopsis thaliana orthologues that, as yet, have not been found to be expressed. The T. caerulescens transcriptome generally relates very well to the A. thaliana transcriptome, although, compared with other closely related species, a relatively large number of T. caerulescens-specific transcripts were found. T. caerulescens also expresses a relatively large number of genes which are expressed at a very low level in A. thaliana.
Adaptation, Physiological↗
Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes.
LINE-1 (L1) elements are the most abundant autonomous retrotransposons in the human genome, accounting for about 17% of human DNA. The L1 retrotransposon encodes two proteins, open reading frame (ORF)1 and the ORF2 endonuclease/reverse transcriptase. L1 RNA and ORF2 protein are difficult to detect in mammalian cells, even in the context of overexpression systems. Here we show that inserting L1 sequences on a transcript significantly decreases RNA expression and therefore protein expression. This decreased RNA concentration does not result from major effects on the transcription initiation rate or RNA stability. Rather, the poor L1 expression is primarily due to inadequate transcriptional elongation. Because L1 is an abundant and broadly distributed mobile element, the inhibition of transcriptional elongation by L1 might profoundly affect expression of endogenous human genes. We propose a model in which L1 affects gene expression genome-wide by acting as a 'molecular rheostat' of target genes. Bioinformatic data are consistent with the hypothesis that L1 can serve as an evolutionary fine-tuner of the human transcriptome.
Animals↗
Trophoblastic cDNA cloning of porcine Pregnancy-Associated Glycoprotein genes (pPAG) and in silico analysis of coded polypeptide precursors.
Multiple Pregnancy-Associated Glycoprotein (PAG) genes, coding various chorionic products that belong to the aspartic proteinase family (AP), have been discovered in various eutherians (Placentalia). This paper presents cloning of five novel porcine PAG (pPAG) cDNAs: pPAG3, pPAG4, pPAG5, pPAG6, pPAG8 and pPAG10. All cDNAs have been identified by trophoblastic library screening on 13-17 days post coitum (dpc). These cloned and sequenced pPAG cDNAs have been deposited in GenBank database of National Institute of Heath/ National Center of Biotechnology Information (NIH/NCBI) with various accession numbers: AF315377, AF272734, AY188554, AF272735, AY373029 and one during submission. The open reading frames (ORF) of cloned cDNA sequences allowed for identification and in silico analysis of polypeptide pPAG precursors, including their identity content and various amino acid substitutions, which caused hypothetical structure changes of the pPAG precursors. In conclusion, our results concerning transcriptomal cloning and in silico analyses of the novel identified trophoblastic cDNA of the pPAG genes provided contributive data regarding porcine genome identification and physiology of the gestation in this species.
Amino Acid Sequence↗
Analysis of expressed sequence tags from a naked foraminiferan Reticulomyxa filosa.
Foraminifers are a major component of modern marine ecosystems and one of the most important oceanic producers of calcium carbonate. They are a key phylogenetic group among amoeboid protists, but our knowledge of their genome is still mostly limited to a few conserved genes. Here, we report the first study of expressed genes by means of expressed sequence tag (EST) from the freshwater naked foraminiferan Reticulomyxa filosa. Cluster analysis of 1630 valid ESTs enabled the identification of 178 groups of related sequences and 871 singlets. Approximately 50% of the putative unique 1059 ESTs could be annotated using Blast searches against the protein database SwissProt + TrEMBL. The EST database described here is the first step towards gene discovery in Foraminifera and should provide the basis for new insights into the genomic and transcriptomic characteristics of these interesting but poorly understood protists.
Animals↗
Comparative analysis of human genome assemblies reveals genome-level differences.
Previous comparative analysis has revealed a significant disparity between the predicted gene sets produced by the International Human Genome Sequencing Consortium (HGSC) and Celera Genomics. To determine whether the source of this discrepancy was due to underlying differences in the genomic sequences or different gene prediction methodologies, we analyzed both genome assemblies in parallel. Using the GENSCAN gene prediction algorithm, we generated predicted transcriptomes that could be directly compared. BLAST-based comparisons revealed a 20-30% difference between the transcriptomes. Further differences between the two genomes were revealed with protein domain PFAM analyses. These results suggest that fundamental differences between the two genome assemblies are likely responsible for a significant portion of the discrepancy between the transcript sets predicted by the two groups.
Chromosome Mapping↗
Coalescing single-cell genomes and transcriptomes to decode breast cancer progression.
Understanding epithelial lineages of breast cancer and genotype-phenotype relationships requires direct measurements of the genome and transcriptome of the same single cells at scale. To achieve this, we developed wellDR-seq, a high-genomic-resolution, high-throughput method to simultaneously profile the genome and transcriptome of thousands of single cells. We profiled 33,646 single cells from 12 estrogen-receptor-positive breast cancers and identified ancestral subclones in multiple patients that showed a luminal hormone-responsive lineage, indicating a potential cell of origin. In contrast to bulk studies, wellDR-seq enabled the study of subclone-level gene-dosage relationships, which showed near-linear correlations in large chromosomal segments and extensive variation at the single-gene level. We identified dosage-sensitive and dosage-insensitive genes, including many breast cancer genes as well as sporadic copy-number aberrations in non-cancer cells. Overall, these data reveal complex relationships between copy number and gene expression in single cells, improving our understanding of breast cancer progression.
Breast Neoplasms↗
Transcriptome analysis of O3-exposed Arabidopsis reveals that multiple signal pathways act mutually antagonistically to induce gene expression.
To analyze cellular responses to ozone (O3), we performed a large-scale analysis of the Arabidopsis transcriptome after plants were exposed to O3 for 12 h. By using cDNA macroarray technology, we identified 205 non-redundant expressed sequence tags (ESTs) that were regulated by O3. Of these, 157 were induced and 48 were suppressed by O3. A substantial proportion of these ESTs had predicted functions in cell rescue/defense processes. Using these isolated ESTs, we also undertook a comprehensive investigation of how three hormones, ethylene (ET), jasmonic acid (JA), and salicylic acid (SA), interact to regulate O3-induced genes in various genetic backgrounds of Arabidopsis, such as the ET-insensitive ein2-1, JA-resistant jar1-1, and SA-insensitive npr1-1. The expression of half of the 157 induced genes, especially cell rescue/defense genes, was controlled by ET and JA signaling, indicating that O3-induced defense gene expression at this stage was mainly regulated by ET and JA. Clustering analysis of the 157 O3-induced gene expressions revealed that multiple signal pathways act mutually antagonistically to induce the expression of these genes, and many cell rescue/defense genes induced by ET and JA signal pathways were suppressed by SA signaling, suggesting that the SA pathway acts as a strong antagonist to gene expression induced by ET and JA signaling.
Arabidopsis↗
Post-genomics approaches for the elucidation of plant adaptive mechanisms to sulphur deficiency.
With the genome sequence of Arabidopsis and rice now available, plant science has stepped forward into a new phase. Post-genomics studies such as transcriptomics, proteomics, and metabolomics will bring about a breakthrough for the functional elucidation of genes and for an understanding of a whole process of living cells. Concerning studies of sulphur (S) metabolism, several reports have recently been published describing the transcript profiles of S-starved Arabidopsis. In this review, these -omics studies that have revealed the network linking several pathways related to jasmonic acid (JA), oxidative stress response, auxin, and flavonoid to S metabolic pathway are summarized.
Adaptation, Physiological↗
Heat shock proteome analysis of wild-type Corynebacterium glutamicum ATCC 13032 and a spontaneous mutant lacking GroEL1, a dispensable chaperone.
Proteome analysis of Corynebacterium glutamicum ATCC 13032 showed that levels of several proteins increased drastically in response to heat shock. These proteins were identified as DnaK, GroEL1, GroEL2, ClpB, GrpE, and PoxB, and their heat response was in agreement with previous transcriptomic results. A major heat-induced protein was absent in the proteome of strain 13032B of C. glutamicum, used for genome sequencing in Germany, compared with the wild-type ATCC 13032 strain. The missing protein was identified as GroEL1 by matrix-assisted laser desorption ionization-time of flight peptide mass fingerprinting, and the mutation was found to be due to an insertion sequence, IsCg1, that was integrated at position 327 downstream of the translation start codon of the groEL1 gene, resulting in a truncated transcript of this gene, as shown by Northern analysis. The GroEL1 chaperone is, therefore, dispensable in C. glutamicum. On the other hand, GroEL2 appears to be essential for growth. Based on these results, the role of the duplicate groEL1 and groEL2 genes is analyzed.
Bacterial Proteins↗
DNA chip technology in cardiovascular research.
Global and/or dynamic analysis of the cardiac transcriptome may improve our understanding of the adaptation of cardiac tissue or cells to different physiological or pathological conditions. The achievement of sequencing projects on mammalian genomes and the development of DNA chip technology have dramatically extended the scale of gene expression studies from a candidate gene approach to a system approach. In current DNA chip experiments, expression levels of thousands of genes can be determined simultaneously. Obviously, the huge quantities of objects and information generated by these experiments require a computational management of the expression data with adequate mathematical (mostly statistical) algorithms. Here, we will discuss the principle and experimental key points of DNA chips. Four examples will be cited to illustrate applications in the cardiovascular system.
Animals↗
[Serial analysis of gene expression].
Serial analysis of gene expression (SAGE) is recently developed, a sequenced-based technique, which permits comprehensive and quantitative gene expression profiles from specific tissues or cells. SAGE has been successfully applied for transcriptome research and identification of differentially expressed genes between mRNA populations. This article mainly reviews the principle,development and application of SAGE.
English Abstract↗
LocustDB: a relational database for the transcriptome and biology of the migratory locust (Locusta migratoria).
BACKGROUND: The migratory locust (Locusta migratoria) is an orthopteran pest and a representative member of hemimetabolous insects for biological studies. Its transcriptomic data provide invaluable information for molecular entomology and pave a way for the comparative research of other medically, agronomically, and ecologically relevant insects. We developed the first transcriptomic database of the locust (LocustDB), building necessary infrastructures to integrate, organize, and retrieve data that are either currently available or to be acquired in the future. DESCRIPTION: LocustDB currently hosts 45,474 high-quality EST sequences from the locust, which were assembled into 12,161 unigenes. It, through user-friendly web interfaces, allows investigators to freely access sequence data, including homologous/orthologous sequences, functional annotations, and pathway analysis, based on conserved orthologous groups (COG), gene ontology (GO), protein domain (InterPro), and functional pathways (KEGG). It also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, including the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. The website address of LocustDB is http://locustdb.genomics.org.cn/. CONCLUSION: LocustDB starts with the first transcriptome information for an orthopteran and hemimetabolous insect and will be extended to provide a framework for incorporating in-coming genomic data of relevant insect groups and a workbench for cross-species comparative studies.
Animals↗
Transposable elements as modulators of homoeologous gene expression in bread wheat: lessons from the pan-transcriptome era.
Bread wheat (Triticum aestivum L.) is an allohexaploid (AABBDD) whose three ancestral subgenomes generate complex patterns of gene regulation. Most genes exist as homoeologous triads, and the relative expression balance among copies, homoeolog expression bias, is central to polyploid evolution and adaptation. Recent high-quality assemblies, long-read transcriptomics, and pan-transcriptome resources have uncovered extensive cultivar-specific transcriptional diversity. Because transposable elements (TEs) compose over 80% of the wheat genome, they are prime candidates for shaping subgenome asymmetry. We synthesize recent pan-genomic and transcriptomic evidence, including genome-wide associations between TE insertions and genome-specific expression, and propose a unifying framework in which TEs modulate homoeolog expression by donating cis-regulatory sequences, altering chromatin states, producing small RNAs, and driving structural variation. We discuss experimental and computational challenges for establishing causality, and outline future functional and translational strategies to leverage TE-associated regulatory diversity in wheat breeding.
Triticum↗
Use of Scots pine seedling roots as an experimental model to investigate gene expression during interaction with the conifer pathogen Heterobasidion annosum (P-type).
The root-rot fungus Heterobasidion annosum is a major pathogen of woody trees in temperate regions of the world. In this study, seedling root of Scots pine was used as an experimental model to investigate gene expression in conifer trees during challenge with H. annosum. Initial cellular and histochemical studies have established the systems and indicated the key sequence of events during the infection process. Also, to correlate histochemical observations with the time-dependent pattern of events in host gene expression, a transcriptome profiling of a selected set of host genes from a pine-root subtraction cDNA library was conducted. Differential screening of the subset of genes arrayed on nylon membrane with cDNA probes made from seedling roots infected for 1, 3, 7 and 15 days revealed a number of up-regulated genes [disease-resistance gene analog, antimicrobial peptide (AMP) gene homolog etc.] following inoculation. The results also showed strong expression of genes involved in cell defense and protein synthesis at the early stages of the infection (3-7 days) with a decline at late stages of infection (15 days). The decline in expression of key defense genes at late stages of infection correlated well with the period of vascular colonization and subsequent loss of root turgor. Northern analyses with two of the major induced genes (AMP homolog and disease-resistance gene analog) indicated a several-fold increase in host gene expression following infection. In addition, a particular single gene (thaumatin-like protein) was consistently expressed throughout the four sampling periods of the experiment. BlastX analyses revealed that the Scots-pine thaumatin-like gene shared 51-77% sequence homology with other thaumatin-like proteins in GenBank. The importance of these results in tree defense and use of conifer seedling root in host-parasite interaction in forest trees is discussed.
Amino Acid Sequence↗
A pilot-scale expressed sequence tag analysis of Beauveria bassiana gene expression reveals a tripeptidyl peptidase that is differentially expressed in vivo.
The entomopathogen Beauveria bassiana is a dimorphic fungus that displays an in vivo-specific, yeast-like parasitic phase. In order to study the transcriptome of B. bassiana during this unique developmental phase, we developed a method to harvest in vivo B. bassiana cells from infected Manduca sexta larvae. The infected hemolymph was collected just prior to insect death and subjected to gradient centrifugation, which allowed for separation of the B. bassiana in vivo-produced cells from remaining insect hemocytes. Total RNA was extracted from the harvested fungal cells and used to construct a cDNA library that is representative of B. bassiana gene expression in vivo. Expressed Sequence Tags (ESTs) were generated and led to the cloning of two protease genes. One of these proteases was identified as a tripeptidyl peptidase (Bb TPP). The Bb TPP protease was shown to be up-regulated during infection, and identification of a signal peptide suggested that the enzyme is secreted in the host hemolymph. Although its activity and role have yet to be characterized, the Bb TPP protease appears as a likely candidate for being involved in B. bassiana pathogenesis. The identification of this novel, up-regulated protease also suggests that random sequencing from our in vivo cDNA library may be a valuable step towards identifying biologically active metabolites produced in vivo by B. bassiana.
Aminopeptidases↗