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Results for “comparative transcriptomics”

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PubMed2006

Regulation of the cadmium stress response through SCF-like ubiquitin ligases: comparison between Saccharomyces cerevisiae, Schizosaccharomyces pombe and mammalian cells.

Saccharomyces cerevisiae has developed several mechanisms to cope with exposure to cadmium. In particular, the sulfur compound glutathione plays a pivotal role in cadmium detoxification, and exposure to cadmium leads to a wide reorganization of S. cerevisiae transcriptome and proteome, resulting in a significant increase in glutathione synthesis. Met4, the transcriptional activator of the sulfur metabolism enzymes, is a critical actor in this reorganization. Recent work has uncovered a part of the mechanism of cadmium-induced Met4 regulation, and showed that it occurs trough the SCF ubiquitin ligase complex SCF(Met30). We discuss this regulation in S. cerevisiae and compare it with the regulation of two other transcriptional activators involved in cadmium detoxification: the Schizosaccharomyces pombe Zip1, regulated by SCF(Pof1), and the mammalian Nrf2, regulated by the SCF-like ubiquitin ligase Cul3:Rbx1:Keap1.

Animals↗

PubMed2005

Advanced glycation endproduct-induced aging of the retinal pigment epithelium and choroid: a comprehensive transcriptional response.

Advanced glycation endproduct (AGE) formation is a trigger for the onset of age-related disease. To evaluate AGE-induced change in the ocular fundus, 5-mo-old C57BL/6 mice were given low-dose D-galactose (D-gal) for 8 wk and evaluated by AGE fluorescence, electroretinography (ERG), electron microscopy, and microarray analysis for 20 wk. Although AGE fluorescence was increased in D-gal-treated retinal pigment epithelium (RPE)-choroid compared with controls at all time points, ERG showed no AGE-induced functional toxicity. Progressive ultrastructural aging in the RPE-choroid was associated temporally with a transcriptional response of early inflammation, matrix expansion, and aberrant lipid processing and, later, down-regulation of energy metabolism genes, up-regulation of crystallin genes, and altered expression of cell structure genes. The overall transcriptome is similar to the generalized aging response of unrelated cell types. A subset of transcriptional changes is similar to early atherosclerosis, a chronic inflammatory disease characterized by matrix expansion and lipid deposition. These changes suggest an important contribution of a single environmental stimulus to the complex aging response.

Animals↗

PubMed2026

MAdLandExpression: integrating sexual reproduction into the Physcomitrium patens expression atlas.

Physcomitrium patens is a bryophyte model system particularly valuable for evolutionary developmental and comparative genomics studies. Sexual reproduction in bryophytes offers unique insights into the evolution of land plant reproduction. Unlike seed plants, bryophytes have a dominant gametophyte phase and provide significant advantages for studying sexual reproduction, such as the possibility to maintain embryo-lethal mutants through vegetative propagation or the presence of motile male gametes. More than 25 years after the first publications of transcriptomic data for P. patens, expression data of most developmental stages of P. patens as well as its responses to various biotic and abiotic perturbations have been represented by microarrays or RNA-seq datasets. To facilitate the use of such data, we introduce the MAdLandExpression atlas as a successor of PEATmoss (Physcomitrium Expression Atlas Tool), integrating its 109 P. patens expression experiments and expanding it with 20 recently published RNA-seq samples of sexual reproduction stages, thus completing the coverage of the P. patens life cycle. The MAdLandExpression atlas also introduces new features for data visualization and analysis, such as the comparison of samples from multiple datasets and gene set normalization. Using this tool, the sexual reproduction dataset was analyzed, identifying genes potentially important for egg and sperm cell development, and confirming the behavior of known key genes in sexual development observed in previous studies.

Bryopsida↗

PubMed2005

Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags.

The fraction of the genome associated with male reproduction in Drosophila may be unusually dynamic. For example, male reproduction-related genes show higher-than-average rates of protein divergence and gene expression evolution compared to most Drosophila genes. Drosophila male reproduction may also be enriched for novel genetic functions. Our earlier work, based on accessory gland protein genes (Acp's) in D. simulans and D. melanogaster, suggested that the melanogaster subgroup Acp's may be lost and/or gained on a relatively rapid timescale. Here we investigate this possibility more thoroughly through description of the accessory gland transcriptome in two melanogaster subgroup species, D. yakuba and D. erecta. A genomic analysis of previously unknown genes isolated from cDNA libraries of these species revealed several cases of genes present in one or both species, yet absent from ingroup and outgroup species. We found no evidence that these novel genes are attributable primarily to duplication and divergence, which suggests the possibility that Acp's or other genes coding for small proteins may originate from ancestrally noncoding DNA.

Animals↗

PubMed2026

Cell-of-origin Discovery in Infant Leukemia through Integration of 3D Models and Patient Transcriptomic Data.

Pediatric hematological malignancies remain challenging to investigate and model due to the age group-specificity of certain genetic abnormalities. In utero origin has been demonstrated for a subset of pediatric leukemias, placing their respective cell of origin (CoO) during embryonic development. We recently reported a 3D hemogenic gastruloid (haemGx) model of embryonic blood formation derived from mouse embryonic stem cells, resolving the spatio-temporal complexity of developmental hematopoiesis. Importantly, it allows genetic engineering to introduce disease-relevant mutations. Using haemGx, we modeled the most common acute myeloid leukemia exclusive to infants (infAML), subtype t(7;12)(q36;p13), which arises in utero and is characterized by MNX1 overexpression. Here, we detail a method to define susceptibility to specific mutations that integrate phenotypic and transcriptional changes in the haemGx system and compares them with patient data. By proxy of our MNX1-overexpression haemGx, we show a pipeline from cell engineering to downstream analyses of leukemogenic potential. In particular, we focus on the clinical relevance of the model by integrating single-cell and/or bulk RNA sequencing from the haemGx platform with patient data to extract cellular composition and temporal placement of the putative CoO. This method is adaptable to the introduction of other oncogenic mutations, chromosomal rearrangements, or epigenetic modifications, as well as to chemical perturbations, including drug vulnerability and growth factor dependence. This flexibility allows for broad application across diverse disease contexts, enabling mechanistic dissection of how specific alterations disrupt early developmental trajectories with clinical relevance.

Humans↗

PubMed2025

Comparative analysis of DREB gene family in buckwheat: the role of FtDREB02 in the delphinidin biosynthesis and drought stress response.

Dehydration response element binding (DREB) transcription factors play a pivotal role in plant abiotic stress responses, but its evolutionary and functional characterization in buckwheat remains unexplored. Here, we conducted a comprehensive analysis of the DREB gene family across three buckwheat species, revealing segmental duplication as the primary driver of family expansion and potential purifying selection during evolution. A FtDREB02 gene, classified as group A2, was identified through genome-wide association analysis (GWAS) on drought tolerance and delphinidin content. Functional validation in Arabidopsis thaliana and the hairy root of Tartary buckwheat (Fagopyrum tataricum) demonstrated that overexpression of this gene promotes delphinidin biosynthesis and enhances plant resistance to water scarcity. Through the integration of DAP-seq and PEG transcriptome cluster analysis, a FtANS candidate was screened. Functional studies showed that FtDREB02 regulates delphinidin content by binding directly to DRE elements of the FtANS promoter. This research identifies and comprehensively analyzes the DREB family within buckwheat species, elucidating the regulatory mechanisms of FtDREB02 in controlling flavonoid biosynthesis and drought resistance, providing potential genetic resources for breeding buckwheat varieties with excellent agronomic traits.

Anthocyanins↗

PubMed2026

Antennal transcriptome analysis of chemosensory proteins in the raspberry weevil, Aegorhinus superciliosus (Coleoptera: Curculionidae).

Aegorhinus superciliosus (Coleoptera: Curculionidae) is a polyphagous pest of economic importance in southern Chile, the chemical ecology of which remains poorly characterized. Across insect species, chemosensory proteins, including odorant receptors (ORs), gustatory receptors (GRs), ionotropic receptors (IRs), odorant-binding proteins (OBPs), chemosensory proteins (CSPs), and sensory neuron membrane proteins (SNMPs), mediate the detection of chemical cues involved in host selection, reproduction, and other ecologically relevant behaviors. In this study, the antennal transcriptome of adult A. superciliosus was sequenced and analyzed using a de novo RNA-seq approach. Three independent biological replicates per sex were used for RNA-seq, and the same number of independent biological replicates was used for RT-qPCR validation; sequencing yielded 147,409,936 high-quality reads after quality filtering. A total of 112 candidate chemosensory genes were identified, comprising 43 ORs, 34 OBPs, 10 CSPs, 18 IRs, 5 GRs, and 2 SNMPs. Phylogenetic analyses assigned these candidate proteins to established clades, providing a comparative framework for functional inference for ORs and OBPs. Sex- and tissue-biased expression analyses revealed that several ORs, including AsupOR4, AsupOR19, and AsupOBP13, exhibit antennal enrichment and sex-specific expression patterns. Notably, AsupOR19 and AsupOBP13 displayed strong female-biased expression. In addition, transcripts of selected ORs and OBPs were detected in non-antennal tissues, such as the rostrum and legs, suggesting potential functional versatility beyond canonical olfaction. Together, these findings represent the first molecular identification of the chemosensory repertoire of A. superciliosus. This study establishes a foundation for reverse chemical ecology approaches aimed at identifying behaviorally active volatile organic compounds (VOCs) toward environmentally sustainable strategies for integrated pest management.

Animals↗

PubMed2005

Genetic basis of phenotypic plasticity for predator-induced morphological defenses in anuran tadpole, Rana pirica, using cDNA subtraction and microarray analysis.

Anuran tadpoles (Rana pirica) are induced to develop a higher tail and a bulgy body as predator-specific morphological responses when they are exposed to predatory larval salamanders. Subtractive hybridization was performed using induced tadpole body skin and normal tadpoles' body skin. A total of 196 clones showed higher expression, and 104 clones showed lower expression, when they formed bulgy bodies. In the subtraction, carboxypeptidase B, trypsinogen, elastase I, fibrinogen, elastase II, triacyl-glycerol lipase, and alpha1-antitrypsin genes showed lower expression. In contrast, RT-like protein, bullous pemphigoid antigen, phosphoserine aminotransferase, uromodulin, tetranectin, chaperonin-like protein, zinc finger protein, osteonectin, aldehyde dehydrogenase, Sec 23A protein, and ribosomal protein showed higher gene expression. Microarray analysis was also performed using this subtracted cDNA (nine replicates). Results of the microarray data essentially corresponded with those of the subtraction data, and the degree of the suppressed genes was much stronger than that of the expressed genes. Carboxypeptidase B showed the strongest suppression, and its inhibition range was from 1/100 to 3/100 compared with that of control body skin. Strong suppression was also observed with trypsinogen, elastase I, fibrinogen, and elastase II as well. These results can be interpreted as increases of fibrinolysis by strong depression of both carboxypeptidase B and other genes simultaneously, resulting in the retention of blood vessels and facilitating the circulation of blood. Expression was observed in phosphoserine aminotransferase, aldehyde dehydrogenase, RT-related protein, chaperonin-like protein, tetranectin, bullous pemphigoid antigen, uromodulin, and Sec 23A protein. They were significantly (p<0.05) increased and were at least 1.5 times greater compared with the control. From the appearance, it seems that the bulgy shaped body is highly connecting to the bullous pemphigoid (BP) antigen that causes the skin blistering disorder, and tetranectin and uromodulin may be related to the extracell matrix through myogenesis, protein secretion, and ion transport, respectively. Since the RT-related protein gene derived from retrotransposon (L1) is known to disrupt mammalian transcriptomes, retrotransposon may be involved with phenotypic plasticity for morphological defense by Rana prica against predator threat.

Animals↗

PubMed2026

Genomic and transcriptomic quality control for an autologous iPSC-derived cell therapy for Parkinson's disease.

Toward development of an autologous, induced pluripotent stem cell (iPSC)-based cell therapy for Parkinson's disease (PD), we demonstrate successful, reproducible genomic and transcriptomic qualification of patient-derived dopaminergic neuron precursor cells (DANPCs) across multiple donors. Our analysis includes whole-genome sequencing data from fibroblasts, iPSCs, and DANPCs and the development of NeuriTest, an RNAseq-based bioinformatic analysis of DANPCs designed to predict cell quality based on empirical animal data. Autologous cell therapies are immune matched to the patient, potentially augmenting durability of benefit compared to allogeneic cells while negating the need for immunosuppression and accompanying side effects. Patient-specific iPSCs are an autologous cell source that can be differentiated to dopaminergic neurons, the cell type lost in PD. We report here our preclinical manufacturing strategy and results demonstrating efficacy in a PD rodent model and safety in a 9-month GLP toxicology study.

Parkinson’s disease↗

PubMed2006

Comprehensive analysis of differential gene expression profiles on D-galactosamine-induced acute mouse liver injury and regeneration.

Microarray analysis of RNA from d-galactosamine (GalN)-administered mouse livers was performed to establish a global gene expression profile during injury and regeneration stages at two different doses. A single dose of GalN at 266 or 26.6 mg/kg body weight was given intraperitoneally, and the liver samples were obtained after 6, 24, and 72 h. Histopathologic studies enabled the classification of the D-galactosamine effect into injury (6, 24 h) and regeneration (72 h) stages. By using the Applied Biosystems mouse genome survey microarray, a total of 7267 out of 33,315 (21.8%) genes were found to be statistically reliable at p<0.05 by two-way ANOVA, and 1469 (4.4%) probes at false discovery rate <5% by significance analysis of microarray. Among the statistically reliable clones by both analytical methods, 389 genes were differentially expressed when compared with non-treated control, with more than a 1.625-fold difference (which equals 0.7 in log(2) scale) at one or more GalN treatment conditions and with less than 1.625-fold difference at all three vehicle-treated conditions. Three hundred thirty six genes and 13 genes were identified as injury- and regeneration-specific genes, respectively, showing that most of the transcriptomic changes were seen during the injury stage. Furthermore, multiple genes involved in protein synthesis and degradation, mRNA processing and binding, and cell cycle regulation showed variable transcript levels upon acute GalN administration.

Acute Disease↗

PubMed2003

Nuclear genes in mitochondrial disorders.

Nuclear genes encode hundreds of proteins involved in mitochondrial biogenesis and oxidative phosphorylation (OXPHOS). Nevertheless, the identification of nuclear genes responsible for OXPHOS-related disorders has proceeded at a much slower pace, compared with the discovery and characterization of mtDNA mutations. Reasons for such a gap include rarity of syndromes, genetic heterogeneity, and ignorance on this nuclear gene repertoire in humans. This scenario is changing rapidly, thanks to the discovery of several OXPHOS-related human genes, and to the identification in some of them of disease-associated mutations. In addition, new strategies - based on transcriptome and proteome analysis, and functional complementation assays - have been applied successfully to mitochondrial medicine.

Cell Nucleus↗

PubMed2003

Rank order metrics for quantifying the association of sequence features with gene regulation.

MOTIVATION: Genome sequences and transcriptome analyses allow the correlation between gene regulation and DNA sequence features to be studied at the whole-genome level. To quantify these correlations, metrics are needed that can be applied to any sequence feature, regardless of its statistical distribution. It is also desirable for the metric values to be determined objectively, that is, without the use of subjective threshold values. RESULTS: We compare two metrics for quantifying the correlation of DNA sequence features with gene regulation. Each of the metrics is calculated from a rank-ordering of genes based on the value of the sequence feature of interest. The first metric is the area under the curve for a receiver operator characteristic plot (ROC AUC), a common way of summarizing the tradeoff between sensitivity and specificity for different values of a prediction criterion. We call the second metric the mean normalized conditional probability (MNCP). The MNCP can be thought of as the predictive value of the sequence feature averaged over all regulated genes. The statistical significance (P-value) of each metric can be estimated from simulations. Importantly, the P-value of the MNCP metric is less dramatically affected by the presence of false positives among the set of co-regulated genes than is the ROC AUC. This is especially useful in analyzing gene sets identified by DNA microarray analysis because such data cannot distinguish direct regulation by transcription factor binding from indirect regulation. We demonstrate that these two metrics, taken together, are useful tools for defining the binding site representation and regulatory control regions that best explain the difference between genes that are regulated by a given transcription factor and those that are not. Applications to other gene features are also described. AVAILABILITY: A Python program for calculating the ROC AUC and MNCP metric values given input rank orders is available from ftp://ftp.bs.jhmi.edu/users/nclarke/MNCP/

Algorithms↗

PubMed2026

Transcriptional and phytohormonal regulation of positional ear development reveals yield strategies in maize.

Maize (Zea mays L.) is a vital global crop, contributing ∼37% of annual grain production. Enhancing yield per unit area is crucial for food security, yet research has primarily focused on single-ear traits, overlooking the regulation of double ears-a key determinant of prolificacy. While secondary ears drive yield variability under prolificacy-favoring conditions, the mechanisms governing ear formation across shoot positions remain poorly understood. Here, we performed high-resolution transcriptomic analysis of 66 samples from three ear types (primary, secondary and third) in maize inbred B73. We uncovered distinct hormonal developmental dynamics: strigolactone (SL) signaling genes, particularly SBP transcription factors, dominated in primary (I) ears, whereas ethylene-related genes (e.g., ZmEREB131, ZmACCO35) were enriched in third (III) ears. Functional validation confirmed that knockout of ZmEREB131 and ZmACCO35 accelerated development and elongated ears compared to wild-type, implicating ethylene (ETH) signaling in ear maturation arrest. Notably, SL inhibitor application synchronized primary and secondary ear development, boosting total yield by >20% without compromising primary ear performance. Our study elucidates the transcriptional networks underlying differential ear development and provides actionable strategies for yield improvement through targeted hormonal modulation. These findings advance the understanding of maize inflorescence biology and offer molecular tools for breeding high-yielding varieties.

RNA-seq↗

PubMed2004

Combining transcriptome data with genomic and cDNA sequence alignments to make confident functional assignments for Aspergillus nidulans genes.

Whole genome sequencing of several filamentous ascomycetes is complete or in progress; these species, such as Aspergillus nidulans, are relatives of Saccharomyces cerevisiae. However, their genomes are much larger and their gene structure more complex, with genes often containing multiple introns. Automated annotation programs can quickly identify open reading frames for hypothetical genes, many of which will be conserved across large evolutionary distances, but further information is required to confirm functional assignments. We describe a comparative and functional genomics approach using sequence alignments and gene expression data to predict the function of Aspergillus nidulans genes. By highlighting examples of discrepancies between the automated genome annotation and cDNA or EST sequencing, we demonstrate that the greater complexity of gene structure in filamentous fungi demands independent data on gene expression and the gene sequence be used to make confident functional assignments.

Aspergillus nidulans↗

PubMed2006

Green light adjusts the plastid transcriptome during early photomorphogenic development.

During the transition from darkness to light, a suite of light sensors guides gene expression, biochemistry, and morphology to optimize acclimation to the new environment. Ultraviolet, blue, red, and far-red light all have demonstrated roles in modulating light responses, such as changes in gene expression and suppression of stem growth rate. However, green wavebands induce stem growth elongation, a response not likely mediated by known photosensors. In this study, etiolated Arabidopsis (Arabidopsis thaliana) seedlings were treated with a short, dim, single pulse of green light comparable in fluence and duration to that previously shown to excite robust stem elongation. Genome microarrays were then used to monitor coincident changes in gene expression. As anticipated, phytochrome A-regulated, nuclear-encoded transcripts were induced, confirming proper function of the sensitive phytochrome system. In addition, a suite of plastid-encoded transcripts decreased in abundance, including several typically up-regulated after phytochrome and/or cryptochrome activation. Further analyses using RNA gel-blot experiments demonstrated that the response is specific to green light, fluence dependent, and detectable within 30 min. The response obeys reciprocity and persists in the absence of known photosensors. Plastid transcript down-regulation was also observed in tobacco (Nicotiana tabacum) with similar temporal and fluence-response kinetics. Together, the down-regulation of plastid transcripts and increase in stem growth rate represent a mechanism that tempers progression of early commitment to the light environment, helping tailor seedling development during the critical process of establishment.

Arabidopsis↗

PubMed2003

Phosphoregulators: protein kinases and protein phosphatases of mouse.

With the completion of the human and mouse genome sequences, the task now turns to identifying their encoded transcripts and assigning gene function. In this study, we have undertaken a computational approach to identify and classify all of the protein kinases and phosphatases present in the mouse gene complement. A nonredundant set of these sequences was produced by mining Ensembl gene predictions and publicly available cDNA sequences with a panel of InterPro domains. This approach identified 561 candidate protein kinases and 162 candidate protein phosphatases. This cohort was then analyzed using TribeMCL protein sequence similarity clustering followed by CLUSTALV alignment and hierarchical tree generation. This approach allowed us to (1) distinguish between true members of the protein kinase and phosphatase families and enzymes of related biochemistry, (2) determine the structure of the families, and (3) suggest functions for previously uncharacterized members. The classifications obtained by this approach were in good agreement with previous schemes and allowed us to demonstrate domain associations with a number of clusters. Finally, we comment on the complementary nature of cDNA and genome-based gene detection and the impact of the FANTOM2 transcriptome project.

Animals↗

PubMed2025

Trajectory inference from single-cell genomics data with a process time model.

Single-cell transcriptomics experiments provide gene expression snapshots of heterogeneous cell populations across cell states. These snapshots have been used to infer trajectories and dynamic information even without intensive, time-series data by ordering cells according to gene expression similarity. However, while single-cell snapshots sometimes offer valuable insights into dynamic processes, current methods for ordering cells are limited by descriptive notions of "pseudotime" that lack intrinsic physical meaning. Instead of pseudotime, we propose inference of "process time" via a principled modeling approach to formulating trajectories and inferring latent variables corresponding to timing of cells subject to a biophysical process. Our implementation of this approach, called Chronocell, provides a biophysical formulation of trajectories built on cell state transitions. The Chronocell model is identifiable, making parameter inference meaningful. Furthermore, Chronocell can interpolate between trajectory inference, when cell states lie on a continuum, and clustering, when cells cluster into discrete states. By using a variety of datasets ranging from cluster-like to continuous, we show that Chronocell enables us to assess the suitability of datasets and reveals distinct cellular distributions along process time that are consistent with biological process times. We also compare our parameter estimates of degradation rates to those derived from metabolic labeling datasets, thereby showcasing the biophysical utility of Chronocell. Nevertheless, based on performance characterization on simulations, we find that process time inference can be challenging, highlighting the importance of dataset quality and careful model assessment.

Single-Cell Analysis↗

PubMed2002

Global/temporal gene expression in diaphragm and hindlimb muscles of dystrophin-deficient (mdx) mice.

The mdx mouse is a model for human Duchenne muscular dystrophy (DMD), an X-linked degenerative disease of skeletal muscle tissue characterized by the absence of the dystrophin protein. The mdx mice display a much milder phenotype than DMD patients. After the first week of life when all mdx muscles evolve like muscles of young DMD patients, mdx hindlimb muscles substantially compensate for the lack of dystrophin, whereas mdx diaphragm muscle becomes progressively affected by the disease. We used cDNA microarrays to compare the expression profile of 1,082 genes, previously selected by a subtractive method, in control and mdx hindlimb and diaphragm muscles at 12 time points over the first year of the mouse life. We determined that 1) the dystrophin gene defect induced marked expression remodeling of 112 genes encoding proteins implicated in diverse muscle cell functions and 2) two-thirds of the observed transcriptomal anomalies differed between adult mdx hindlimb and diaphragm muscles. Our results showed that neither mdx diaphram muscle nor mdx hindlimb muscles evolve entirely like the human DMD muscles. This finding should be taken under consideration for the interpretation of future experiments using mdx mice as a model for therapeutic assays.

Aging↗