Gene expression profiles of bovine genital ridges during sex determination and early differentiation of the gonads†

AbstractMost current knowledge of sex determination in mammals has emerged from mouse and human studies. To investigate the molecular regulation of the sex determination process in cattle, we used an RNA sequencing strategy to analyze the transcriptome landscape of male and female bovine fetal gonads collected in vivo at key developmental stages: before, during, and after SRY gene activation on fetal days D35 (bipotential gonad formation), D39 (peak SRY expression), and D43 (early gonad differentiation). Differentially expressed genes (DEGs) were identified in male vs. female germinal ridges and among group genes showing similar expression profiles during the three periods. There were 143, 96, and 658 DEG between males and female fetuses at D35, D39, and D43, respectively. On D35, genes upregulated in females were enriched in translation, nuclear export, RNA localization, and mRNA splicing events, whereas those upregulated in males were enriched in cell proliferation regulation and male sex determination terms. In time-course experiments, 767 DEGs in males and 545 DEGs in females were identified between D35 vs. D39, and 3157 DEGs in males and 2008 in females were identified between D39 vs. D43. Results highlight unique aspects of sex determination in cattle, such as the expression of several Y chromosome genes (absent in mice and humans) before SRY expression and an abrupt increase in the nuclear expression of SOX10 (instead of SOX9 expression in the Sertoli cell cytoplasm as observed in mice) during male determination and early differentiation.

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The Diverse Roles of the Global Transcriptional Regulator PhoP in the Lifecycle of Yersinia pestis

Pathogens ◽

10.3390/pathogens9121039 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1039

Author(s):

Hana S. Fukuto ◽

Gloria I. Viboud ◽

Viveka Vadyvaloo

Keyword(s):

Yersinia Pestis ◽

Current Knowledge ◽

Response Regulator ◽

Expression Profiles ◽

Critical Role ◽

Gene Expression Profiles ◽

Acanthamoeba Castellanii ◽

Wide Range

Yersinia pestis, the causative agent of plague, has a complex infectious cycle that alternates between mammalian hosts (rodents and humans) and insect vectors (fleas). Consequently, it must adapt to a wide range of host environments to achieve successful propagation. Y. pestis PhoP is a response regulator of the PhoP/PhoQ two-component signal transduction system that plays a critical role in the pathogen’s adaptation to hostile conditions. PhoP is activated in response to various host-associated stress signals detected by the sensor kinase PhoQ and mediates changes in global gene expression profiles that lead to cellular responses. Y. pestis PhoP is required for resistance to antimicrobial peptides, as well as growth under low Mg2+ and other stress conditions, and controls a number of metabolic pathways, including an alternate carbon catabolism. Loss of phoP function in Y. pestis causes severe defects in survival inside mammalian macrophages and neutrophils in vitro, and a mild attenuation in murine plague models in vivo, suggesting its role in pathogenesis. A Y. pestisphoP mutant also exhibits reduced ability to form biofilm and to block fleas in vivo, indicating that the gene is also important for establishing a transmissible infection in this vector. Additionally, phoP promotes the survival of Y. pestis inside the soil-dwelling amoeba Acanthamoeba castellanii, a potential reservoir while the pathogen is quiescent. In this review, we summarize our current knowledge on the mechanisms of PhoP-mediated gene regulation in Y. pestis and examine the significance of the roles played by the PhoP regulon at each stage of the Y. pestis life cycle.

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Analysis of temporal changes in the expression of estrogen-regulated genes in the uterus

Journal of Molecular Endocrinology ◽

10.1677/jme.0.0300347 ◽

2003 ◽

Vol 30 (3) ◽

pp. 347-358 ◽

Cited By ~ 59

Author(s):

H Watanabe ◽

A Suzuki ◽

M Kobayashi ◽

E Takahashi ◽

M Itamoto ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Expression Profiles ◽

Gene Activation ◽

Gene Expression Profiles ◽

Ovariectomized Mice ◽

Two Phases ◽

Er Alpha ◽

Inducible Genes

In order to understand early events caused by estrogen in vivo, temporal uterine gene expression profiles at early stages were examined using DNA microarray analysis. Ovariectomized mice were exposed to 17beta-estradiol and the temporal mRNA expression changes of ten thousand various genes were analyzed. Clustering analysis revealed that there are at least two phases of gene activation during the period up to six hours. One involved immediate-early genes, which included certain transcription factors and growth factors as well as oncogenes. The other involved early-late genes, which included genes related to RNA and protein synthesis. In clusters of down-regulated genes, transcription factors, proteases, apoptosis and cell cycle genes were found. These hormone-inducible genes were not induced in estrogen receptor (ER) alpha knockout mice. Although expression of ERbeta is known in the uterus, these findings indicate the importance of ERalpha in the changes in gene expression in the uterus.

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Pre- and postnatal hepatic gene expression profiles of two pig breeds differing in body composition: insight into pathways of metabolic regulation

Physiological Genomics ◽

10.1152/physiolgenomics.00178.2006 ◽

2007 ◽

Vol 29 (3) ◽

pp. 267-279 ◽

Cited By ~ 27

Author(s):

Siriluck Ponsuksili ◽

Eduard Murani ◽

Christina Walz ◽

Manfred Schwerin ◽

Klaus Wimmers

Keyword(s):

Body Composition ◽

Metabolic Regulation ◽

Time Course ◽

Developmental Stages ◽

Expression Profiles ◽

Cell Activity ◽

Gene Expression Profiles ◽

Prenatal Development ◽

Glycogen Accumulation ◽

Insight Into

The liver plays a central role in the regulation of the metabolic status, partitioning of nutrients, and expenditure of energy. To gain insight into hepatic metabolic pathways and key transcripts affecting traits related to body composition, liver expression profiles were compared of pigs of two breeds, the obese German Landrace (DL) and the lean Pietrain (Pi). Porcine oligonucleotide microarray were hybridized with liver cRNAs obtained at peripubertal age (180 days of age) and prenatal stages (35, 63, and 91 days postconception) that represent three developmental stages of liver, i.e., period of differentiation, period of metabolic activity, and period of glycogen accumulation. In terms of the number of genes regulated between DL and Pi, the most striking distinctions were found at peripubertal age with upregulation of key genes of lipid metabolism pathways (FASN, ACSS2, ACACA) in obese DL pigs and upregulation of genes of cell growth and/or maintenance, and protein syntheses, as well as cell proliferation pathways (PPARD, POU1F1, IGF2R), in lean Pi pigs. Moreover, time course analysis of breed-dependent expression profiles revealed breed-typical temporal regulation from prenatal stages to peripubertal age of genes assigned to biological processes involving lipid pathways and cell activity, i.e., breed differences are already initiated during early prenatal development. Information about mRNA expression levels of the two breeds differing in body composition, partitioning and utilization of nutrients and energy reveals functional candidate genes for traits related to obesity and leanness.

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Pathogen Recognition and Activation of the Innate Immune Response in Zebrafish

Advances in Hematology ◽

10.1155/2012/159807 ◽

2012 ◽

Vol 2012 ◽

pp. 1-19 ◽

Cited By ~ 65

Author(s):

Michiel van der Vaart ◽

Herman P. Spaink ◽

Annemarie H. Meijer

Keyword(s):

Immune Response ◽

Innate Immune Response ◽

Current Knowledge ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Innate Immune ◽

Model Systems ◽

Immune Effector ◽

Innate Immune Effector

The zebrafish has proven itself as an excellent model to study vertebrate innate immunity. It presents us with possibilities forin vivoimaging of host-pathogen interactions which are unparalleled in mammalian model systems. In addition, its suitability for genetic approaches is providing new insights on the mechanisms underlying the innate immune response. Here, we review the pattern recognition receptors that identify invading microbes, as well as the innate immune effector mechanisms that they activate in zebrafish embryos. We compare the current knowledge about these processes in mammalian models and zebrafish and discuss recent studies using zebrafish infection models that have advanced our general understanding of the innate immune system. Furthermore, we use transcriptome analysis of zebrafish infected withE. tarda, S. typhimurium, andM. marinumto visualize the gene expression profiles resulting from these infections. Our data illustrate that the two acute disease-causing pathogens,E. tardaandS. typhimurium, elicit a highly similar proinflammatory gene induction profile, while the chronic disease-causing pathogen,M. marinum, induces a weaker and delayed innate immune response.

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Alterations in Chromatin Structure and Function in the Microglia

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2020.626541 ◽

2021 ◽

Vol 8 ◽

Author(s):

Yuki Fujita ◽

Toshihide Yamashita

Keyword(s):

Gene Expression ◽

Neural Development ◽

Developmental Stages ◽

Current Knowledge ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Electrophysiological Properties ◽

Coordinate Gene Expression ◽

The Central Nervous System ◽

And Function

Microglia are resident immune cells in the central nervous system (CNS). Microglia exhibit diversity in their morphology, density, electrophysiological properties, and gene expression profiles, and play various roles in neural development and adulthood in both physiological and pathological conditions. Recent transcriptomic analysis using bulk and single-cell RNA-seq has revealed that microglia can shift their gene expression profiles in various contexts, such as developmental stages, aging, and disease progression in the CNS, suggesting that the heterogeneity of microglia may be associated with their distinct functions. Epigenetic changes, including histone modifications and DNA methylation, coordinate gene expression, thereby contributing to the regulation of cellular state. In this review, we summarize the current knowledge regarding the epigenetic mechanisms underlying spatiotemporal and functional diversity of microglia that are altered in response to developmental stages and disease conditions. We also discuss how this knowledge may lead to advances in therapeutic approaches for diseases.

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Genome-Wide Gene Expression Profiles Reveal Distinct Molecular Characteristics of the Goose Granulosa Cells

Frontiers in Genetics ◽

10.3389/fgene.2021.786287 ◽

2021 ◽

Vol 12 ◽

Author(s):

Guangliang Gao ◽

Silu Hu ◽

Keshan Zhang ◽

Haiwei Wang ◽

Youhui Xie ◽

...

Keyword(s):

Granulosa Cells ◽

Time Course ◽

Developmental Stages ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Follicular Development ◽

Egg Laying ◽

Molecular Characteristics ◽

Genome Wide ◽

Laying Performance

Granulosa cells (GCs) are decisive players in follicular development. In this study, the follicle tissues and GCs were isolated from the goose during the peak-laying period to perform hematoxylin-eosin staining and RNA-seq, respectively. Moreover, the dynamic mRNA and lncRNA expression profiles and mRNA-lncRNA network analysis were integrated to identify the important genes and lncRNAs. The morphological analysis showed that the size of the GCs did not significantly change, but the thickness of the granulosa layer cells differed significantly across the developmental stages. Subsequently, 14,286 mRNAs, 3,956 lncRNAs, and 1,329 TUCPs (transcripts with unknown coding potential) were detected in the GCs. We identified 37 common DEGs in the pre-hierarchical and hierarchical follicle stages, respectively, which might be critical for follicle development. Moreover, 3,089 significant time-course DEGs (Differentially expressed genes) and 13 core genes in 4 clusters were screened during goose GCs development. Finally, the network lncRNA G8399 with CADH5 and KLF2, and lncRNA G8399 with LARP6 and EOMES were found to be important for follicular development in GCs. Thus, the results would provide a rich resource for elucidating the reproductive biology of geese and accelerate the improvement of the egg-laying performance of geese.

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Bayesian approach for predicting responses to therapy from high-dimensional time-course gene expression profiles

BMC Bioinformatics ◽

10.1186/s12859-021-04052-4 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Arika Fukushima ◽

Masahiro Sugimoto ◽

Satoru Hiwa ◽

Tomoyuki Hiroyasu

Keyword(s):

Gene Expression ◽

Time Course ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Response To Therapy ◽

Hcv Infection ◽

Entire Treatment Period ◽

Time Points ◽

Time Course Data ◽

Conventional Methods

Abstract Background Historical and updated information provided by time-course data collected during an entire treatment period proves to be more useful than information provided by single-point data. Accurate predictions made using time-course data on multiple biomarkers that indicate a patient’s response to therapy contribute positively to the decision-making process associated with designing effective treatment programs for various diseases. Therefore, the development of prediction methods incorporating time-course data on multiple markers is necessary. Results We proposed new methods that may be used for prediction and gene selection via time-course gene expression profiles. Our prediction method consolidated multiple probabilities calculated using gene expression profiles collected over a series of time points to predict therapy response. Using two data sets collected from patients with hepatitis C virus (HCV) infection and multiple sclerosis (MS), we performed numerical experiments that predicted response to therapy and evaluated their accuracies. Our methods were more accurate than conventional methods and successfully selected genes, the functions of which were associated with the pathology of HCV infection and MS. Conclusions The proposed method accurately predicted response to therapy using data at multiple time points. It showed higher accuracies at early time points compared to those of conventional methods. Furthermore, this method successfully selected genes that were directly associated with diseases.

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Genome-Wide Identification of Soybean ABC Transporters Relate to Aluminum Toxicity

International Journal of Molecular Sciences ◽

10.3390/ijms22126556 ◽

2021 ◽

Vol 22 (12) ◽

pp. 6556

Author(s):

Junjun Huang ◽

Xiaoyu Li ◽

Xin Chen ◽

Yaru Guo ◽

Weihong Liang ◽

...

Keyword(s):

Gene Expression ◽

Abc Transporters ◽

Developmental Stages ◽

Aluminum Toxicity ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Purifying Selection ◽

Biotic Stresses ◽

Genome Wide ◽

New Germplasm

ATP-binding cassette (ABC) transporter proteins are a gene super-family in plants and play vital roles in growth, development, and response to abiotic and biotic stresses. The ABC transporters have been identified in crop plants such as rice and buckwheat, but little is known about them in soybean. Soybean is an important oil crop and is one of the five major crops in the world. In this study, 255 ABC genes that putatively encode ABC transporters were identified from soybean through bioinformatics and then categorized into eight subfamilies, including 7 ABCAs, 52 ABCBs, 48 ABCCs, 5 ABCDs, 1 ABCEs, 10 ABCFs, 111 ABCGs, and 21 ABCIs. Their phylogenetic relationships, gene structure, and gene expression profiles were characterized. Segmental duplication was the main reason for the expansion of the GmABC genes. Ka/Ks analysis suggested that intense purifying selection was accompanied by the evolution of GmABC genes. The genome-wide collinearity of soybean with other species showed that GmABCs were relatively conserved and that collinear ABCs between species may have originated from the same ancestor. Gene expression analysis of GmABCs revealed the distinct expression pattern in different tissues and diverse developmental stages. The candidate genes GmABCB23, GmABCB25, GmABCB48, GmABCB52, GmABCI1, GmABCI5, and GmABCI13 were responsive to Al toxicity. This work on the GmABC gene family provides useful information for future studies on ABC transporters in soybean and potential targets for the cultivation of new germplasm resources of aluminum-tolerant soybean.

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Transcriptome analysis of gravitational effects on mouse skeletal muscles under microgravity and artificial 1 g onboard environment

Scientific Reports ◽

10.1038/s41598-021-88392-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Risa Okada ◽

Shin-ichiro Fujita ◽

Riku Suzuki ◽

Takuto Hayashi ◽

Hirona Tsubouchi ◽

...

Keyword(s):

Gene Expression ◽

Muscle Mass ◽

Muscle Atrophy ◽

Transcriptome Analysis ◽

Fiber Type ◽

Expression Profiles ◽

Space Station ◽

Gene Expression Profiles

AbstractSpaceflight causes a decrease in skeletal muscle mass and strength. We set two murine experimental groups in orbit for 35 days aboard the International Space Station, under artificial earth-gravity (artificial 1 g; AG) and microgravity (μg; MG), to investigate whether artificial 1 g exposure prevents muscle atrophy at the molecular level. Our main findings indicated that AG onboard environment prevented changes under microgravity in soleus muscle not only in muscle mass and fiber type composition but also in the alteration of gene expression profiles. In particular, transcriptome analysis suggested that AG condition could prevent the alterations of some atrophy-related genes. We further screened novel candidate genes to reveal the muscle atrophy mechanism from these gene expression profiles. We suggest the potential role of Cacng1 in the atrophy of myotubes using in vitro and in vivo gene transductions. This critical project may accelerate the elucidation of muscle atrophy mechanisms.

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Discovery of novel mechanosensitive genes in vivo using mouse carotid artery endothelium exposed to disturbed flow

Blood ◽

10.1182/blood-2010-04-278192 ◽

2010 ◽

Vol 116 (15) ◽

pp. e66-e73 ◽

Cited By ~ 104

Author(s):

Chih-Wen Ni ◽

Haiwei Qiu ◽

Amir Rezvan ◽

Kihwan Kwon ◽

Douglas Nam ◽

...

Keyword(s):

Carotid Artery ◽

Ex Vivo ◽

Expression Profiles ◽

Quantitative Polymerase Chain Reaction ◽

Gene Expression Profiles ◽

Disturbed Flow ◽

A Genome ◽

Pattern Comparison

Abstract Recently, we showed that disturbed flow caused by a partial ligation of mouse carotid artery rapidly induces atherosclerosis. Here, we identified mechanosensitive genes in vivo through a genome-wide microarray study using mouse endothelial RNAs isolated from the flow-disturbed left and the undisturbed right common carotid artery. We found 62 and 523 genes that changed significantly by 12 hours and 48 hours after ligation, respectively. The results were validated by quantitative polymerase chain reaction for 44 of 46 tested genes. This array study discovered numerous novel mechanosensitive genes, including Lmo4, klk10, and dhh, while confirming well-known ones, such as Klf2, eNOS, and BMP4. Four genes were further validated for protein, including LMO4, which showed higher expression in mouse aortic arch and in human coronary endothelium in an asymmetric pattern. Comparison of in vivo, ex vivo, and in vitro endothelial gene expression profiles indicates that numerous in vivo mechanosensitive genes appear to be lost or dysregulated during culture. Gene ontology analyses show that disturbed flow regulates genes involved in cell proliferation and morphology by 12 hours, followed by inflammatory and immune responses by 48 hours. Determining the functional importance of these novel mechanosensitive genes may provide important insights into understanding vascular biology and atherosclerosis.

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