Characterisation of mouse interferon-induced transmembrane protein-1 gene expression in the mouse uterus during the oestrous cycle and pregnancy

2011 ◽  
Vol 23 (6) ◽  
pp. 798 ◽  
Author(s):  
Hyun Jung Park ◽  
In Sun Kuk ◽  
Jin Hoi Kim ◽  
Jae Hwan Kim ◽  
Sang Jin Song ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Transmembrane Protein ◽  
Post Partum ◽  
Expression Patterns ◽  
Prostaglandin F2α ◽  
Oestrous Cycle ◽  
Signalling Pathway ◽  
Mouse Uterus ◽  
Functional Changes

During the oestrous cycle, pregnancy and parturition, the uterus undergoes marked morphological, physiological and functional changes. Amid these changes, the Wnt/β-catenin signalling pathway has been identified as having a crucial role in regulating associated biological events. Recently, based on results from a mouse embryo study, interferon-induced transmembrane protein 1 (Ifitm1) was reported as a downstream molecule of the Wnt/β-catenin signalling pathway. Differential expression patterns of the Ifitm1 gene during the oestrous cycle, pregnancy and parturition were identified in the present study. Quantitative real-time polymerase chain reaction data from uterine samples of mice induced start the oestrous cycle by injection of human chorionic gonadotropin (hCG) and revealed that Ifitm1 mRNA expression increased from late pro-oestrus to metoestrus, and decreased during dioestrus and early pro-oestrus. During pregnancy, Ifitm1 gene expression was minimal until parturition, but increased markedly 2 days after parturition. This significant elevation in Ifitm1 gene expression at post partum stage was identical to Ifitm1 expression after the induction of abortion by injection of prostaglandin F2α. Interestingly, pregnant mare serum gonadotropin (PMSG) and oestrogen are also facilitates changes in Ifitm1 gene expression in an ovariectomised (OVX) mouse model. Expression of Ifitm1 mRNA was higher in response to PMSG than other hormones investigated. These results suggest that Ifitm1 may be involved in uteri physiology, although the mechanisms involved in the regulation of this gene expression and function in the uterus remain unknown. In the present study, differential expression patterns of the Ifitm1 gene were identified in the uteri of mice and the correlation between the patterns of Ifitm1 gene expression and Wnt/β-catenin signalling discussed.

110 Temporal Changes in Endometrial Gene Expression Between Ipsi- and Contralateral Uterine Horns in Cattle

2018 ◽  
Vol 30 (1) ◽  
pp. 194
Author(s):  
J. M. Sánchez ◽  
C. Passaro ◽  
N. Forde ◽  
S. Behura ◽  
J. A. Browne ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Luteal Phase ◽  
Expression Patterns ◽  
Uterine Horn ◽  
Oestrous Cycle ◽  
Signalling Pathway ◽  
Signalling Pathways ◽  
Robust Analysis ◽  
The Impact

The transfer of an embryo into the uterine horn contralateral to the ovary bearing the corpus luteum has been associated with a decreased pregnancy rate in cattle compared with transfer into the ipsilateral horn. These findings suggest that the environment in the contralateral horn is less conducive to supporting conceptus development than that of the ipsilateral horn. Therefore, this study compared the endometrial transcriptome of the ipsi- and contralateral uterine horns during the luteal phase. Endometrial samples from the ipsi- (IPSI) and contralateral (CONTRA) horns were collected from synchronized nonpregnant beef heifers on Days 5, 7, 13 or 16 post-oestrus (n = 5 heifers per time point). Total RNA was isolated and sequenced. Differences in the transcriptome were determined by edgeR-robust analysis. Principal component analysis found that IPSI and CONTRA have distinct patterns of gene expression on each day, with Day 5 exhibiting the most variation and Day 16 being least variable. Further, the 2 uterine horns had distinct expression patterns on Day 5, with IPSI exhibiting significantly higher variation in gene expression compared twitho CONTRA. EdgeR-robust analysis found 217 (201 up- and 16 down-regulated), 54 (44 up- and 10 down-regulated), 14 (13 up- and 1 down-regulated), and 18 (14 up- and 4 down-regulated) differentially expressed genes (DEG; >2-fold change, false discovery rate P < 0.05) between IPSI and CONTRA endometria on Days 5, 7, 13, and 16 of the oestrous cycle, respectively. The top 5 canonical pathways associated with DEG between IPSI and CONTRA during the luteal phase of the oestrous cycle were involved in signalling pathways regulating pluripotency of stem cells (73/138), progesterone-mediated oocyte maturation (55/89), endometrial cancer (31/51), ErbB signalling pathway (50/87), and mTOR signalling pathway (36/61). The impact of DEG on signalling pathways was assessed using a pathway perturbation algorithm called Signalling Pathway Impact Analysis (SPIA). This topology-based pathway analysis was conducted using the Bioconductor ToPAseq package (https://bioconductor.org/packages/release/bioc/html/ToPASeq.html) and revealed that signalling pathways regulating pluripotency of stem cells showed the highest perturbation score when IPSI was compared with CONTRA irrespective of day. Discovering and cataloguing which pathways are perturbed in each uterine horn throughout the oestrous cycle may contribute to our understanding of the mechanisms underlying early embryonic loss. Ths study was supported by Science Foundation Ireland (13/IA/1983) and the Irish Department of Agriculture, Food and The Marine (13S528).

Gene expression analysis of the pro-oestrous-stage rat uterus reveals neuroligin 2 as a novel steroid-regulated gene

2004 ◽  
Vol 16 (8) ◽  
pp. 763 ◽  
Author(s):  
Han-Seung Kang ◽  
Chae-Kwan Lee ◽  
Ju-Ran Kim ◽  
Seong-Jin Yu ◽  
Sung-Goo Kang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Northern Blot ◽  
Blot Analysis ◽  
Northern Blot Analysis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Oestrous Cycle ◽  
Mrna Levels ◽  
Rat Uterus ◽  
Ovx Rats

In the present study, differential gene expression in the uteri of ovariectomised (OVX) and pro-oestrous rats (OVX v. pro-oestrus pair) was investigated using cDNA expression array analysis. Differential uterine gene expression in OVX rats and progesterone (P4)-injected OVX rats (OVX v. OVX + P4 pair) was also examined. The uterine gene expression profiles of these two sets of animals were also compared for the effects of P4 treatment. RNA samples were extracted from uterine tissues and reverse transcribed in the presence of [α32P]-dATP. Membrane sets of rat arrays were hybridised with cDNA probe sets. Northern blot analysis was used to validate the relative gene expression patterns obtained from the cDNA array. Of the 1176 cDNAs examined, 23 genes showed significant (>two-fold) changes in expression in the OVX v. pro-oestrus pair. Twenty of these genes were upregulated during pro-oestrus compared with their expression in the OVX rat uterus. In the OVX v. OVX + P4 pair, 22 genes showed significant (>two-fold) changes in gene expression. Twenty of these genes were upregulated in the OVX + P4 animals. The genes for nuclear factor I–XI, afadin, neuroligin 2, semaphorin Z, calpain 4, cyclase-associated protein homologue, thymosin β-4X and p8 were significantly upregulated in the uteri of the pro-oestrus and OVX + P4 rats of both experimental pairs compared with the OVX rat uteri. These genes appear to be under the control of P4. One of the most interesting findings of the present study is the unexpected and marked expression of the neuroligin 2 gene in the rat uterus. This gene is expressed at high levels in the central nervous system and acts as a nerve cell adhesion factor. According to Northern blot analysis, neuroligin 2 gene expression was higher during the pro-oestrus and metoestrus stages than during the oestrus and dioestrus stages of the oestrous cycle. In addition, neuroligin 2 mRNA levels were increased by both 17β-oestradiol (E2) and P4, although P4 administration upregulated gene expression to a greater extent than injection of E2. These results indicate that neuroligin 2 gene expression in the rat uterus is under the control of both E2 and P4, which are secreted periodically during the oestrous cycle.

scholarly journals RankerGUI: A Computational Framework to Compare Differential Gene Expression Profiles Using Rank Based Statistics

2019 ◽  
Vol 20 (23) ◽  
pp. 6098 ◽  
Author(s):  
Amarinder Singh Thind ◽  
Kumar Parijat Tripathi ◽  
Mario Rosario Guarracino
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Differential Gene Expression ◽  
Web Application ◽  
Cellular Response ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Experimental Conditions ◽  
Differential Gene

The comparison of high throughput gene expression datasets obtained from different experimental conditions is a challenging task. It provides an opportunity to explore the cellular response to various biological events such as disease, environmental conditions, and drugs. There is a need for tools that allow the integration and analysis of such data. We developed the “RankerGUI pipeline”, a user-friendly web application for the biological community. It allows users to use various rank based statistical approaches for the comparison of full differential gene expression profiles between the same or different biological states obtained from different sources. The pipeline modules are an integration of various open-source packages, a few of which are modified for extended functionality. The main modules include rank rank hypergeometric overlap, enriched rank rank hypergeometric overlap and distance calculations. Additionally, preprocessing steps such as merging differential expression profiles of multiple independent studies can be added before running the main modules. Output plots show the strength, pattern, and trends among complete differential expression profiles. In this paper, we describe the various modules and functionalities of the developed pipeline. We also present a case study that demonstrates how the pipeline can be used for the comparison of differential expression profiles obtained from multiple platforms’ data of the Gene Expression Omnibus. Using these comparisons, we investigate gene expression patterns in kidney and lung cancers.

scholarly journals Linked genetic variation and not genome structure causes widespread differential expression associated with chromosomal inversions

2018 ◽  
Vol 115 (21) ◽  
pp. 5492-5497 ◽  
Author(s):  
Iskander Said ◽  
Ashley Byrne ◽  
Victoria Serrano ◽  
Charis Cardeno ◽  
Christopher Vollmers ◽  
...  
Keyword(s):  
Gene Expression ◽  
Natural Selection ◽  
Differential Expression ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Genome Structure ◽  
Regulatory Domains ◽  
Chromosomal Inversions ◽  
Important Variation ◽  
Genome Wide

Chromosomal inversions are widely thought to be favored by natural selection because they suppress recombination between alleles that have higher fitness on the same genetic background or in similar environments. Nonetheless, few selected alleles have been characterized at the molecular level. Gene expression profiling provides a powerful way to identify functionally important variation associated with inversions and suggests candidate phenotypes. However, altered genome structure itself might also impact gene expression by influencing expression profiles of the genes proximal to inversion breakpoint regions or by modifying expression patterns genome-wide due to rearranging large regulatory domains. In natural inversions, genetic differentiation and genome structure are inextricably linked. Here, we characterize differential expression patterns associated with two chromosomal inversions found in natural Drosophila melanogaster populations. To isolate the impacts of genome structure, we engineered synthetic chromosomal inversions on controlled genetic backgrounds with breakpoints that closely match each natural inversion. We find that synthetic inversions have negligible effects on gene expression. Nonetheless, natural inversions have broad-reaching regulatory impacts in cis and trans. Furthermore, we find that differentially expressed genes associated with both natural inversions are enriched for loci associated with immune response to bacterial pathogens. Our results support the idea that inversions in D. melanogaster experience natural selection to maintain associations between functionally related alleles to produce complex phenotypic outcomes.

Evolution of gene expression patterns in a model of branching morphogenesis

1999 ◽  
Vol 277 (4) ◽  
pp. F650-F663 ◽  
Author(s):  
Anna Pavlova ◽  
Robert O. Stuart ◽  
Martin Pohl ◽  
Sanjay K. Nigam
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Expression Patterns ◽  
Branching Morphogenesis ◽  
Computational Method ◽  
Metanephric Mesenchyme ◽  
Ureteric Bud ◽  
Cdna Arrays ◽  
Apoptotic Genes ◽  
Collecting System

Branching morphogenesis of the ureteric bud in response to unknown signals from the metanephric mesenchyme gives rise to the urinary collecting system and, via inductive signals from the ureteric bud, to recruitment of nephrons from undifferentiated mesenchyme. An established cell culture model for this process employs cells of ureteric bud origin (UB) cultured in extracellular matrix and stimulated with conditioned media (BSN-CM) from a metanephric mesenchymal cell line (H. Sakurai, E. J. Barros, T. Tsukamoto, J. Barasch, and S. K. Nigam. Proc. Natl. Acad. Sci. USA 94: 6279–6284, 1997.). In the presence of BSN-CM, the UB cells form branching tubular structures reminiscent of the branching ureteric bud. The pattern of gene regulation in this model of branching morphogenesis of the kidney collecting system was investigated using high-density cDNA arrays. Software and analytical methods were developed for the quantification and clustering of genes. With the use of a computational method termed “vector analysis,” genes were clustered according to the direction and magnitude of differential expression in n-dimensional log-space. Changes in gene expression in response to the BSN-CM consisted primarily of differential expression of transcription factors with previously described roles in morphogenesis, downregulation of pro-apoptotic genes accompanied by upregulation of anti-apoptotic genes, and upregulation of a small group of secreted products including growth factors, cytokines, and extracellular proteinases. Changes in expression are discussed in the context of a general model for epithelial branching morphogenesis. In addition, the cDNA arrays were used to survey expression of epithelial markers and secreted factors in UB and BSN cells, confirming the largely epithelial character of the former and largely mesenchymal character of the later. Specific morphologies (cellular processes, branching multicellular cords, etc.) were shown to correlate with the expression of different, but overlapping, genomic subsets, suggesting differences in morphogenetic mechanisms at these various steps in the evolution of branching tubules.

scholarly journals Integrative analysis of gene expression patterns predicts specific modulations of defined cell functions by estrogen and tamoxifen in MCF7 breast cancer cells

2005 ◽  
Vol 34 (1) ◽  
pp. 61-75 ◽  
Author(s):  
F Gadal ◽  
A Starzec ◽  
C Bozic ◽  
C Pillot-Brochet ◽  
S Malinge ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Cell Cycle ◽  
Data Analysis ◽  
Differential Expression ◽  
Breast Cancer Cells ◽  
Cell Cycle Progression ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Cycle Progression

To explore the mechanisms whereby estrogen and antiestrogen (tamoxifen (TAM)) can regulate breast cancer cell growth, we investigated gene expression changes in MCF7 cells treated with 17β-estradiol (E2) and/or with 4-OH-TAM. The patterns of differential expression were determined by the ValiGen Gene IDentification (VGID) process, a subtractive hybridization approach combined with microarray validation screening. Their possible biologic consequences were evaluated by integrative data analysis. Over 1000 cDNA inserts were isolated and subsequently cloned, sequenced and analyzed against nucleotide and protein databases (NT/NR/EST) with BLAST software. We revealed that E2 induced differential expression of 279 known and 28 unknown sequences, whereas TAM affected the expression of 286 known and 14 unknown sequences. Integrative data analysis singled out a set of 32 differentially expressed genes apparently involved in broad cellular mechanisms. The presence of E2 modulated the expression patterns of 23 genes involved in anchors and junction remodeling; extracellular matrix (ECM) degradation; cell cycle progression, including G1/S check point and S-phase regulation; and synthesis of genotoxic metabolites. In tumor cells, these four mechanisms are associated with the acquisition of a motile and invasive phenotype. TAM partly reversed the E2-induced differential expression patterns and consequently restored most of the biologic functions deregulated by E2, except the mechanisms associated with cell cycle progression. Furthermore, we found that TAM affects the expression of nine additional genes associated with cytoskeletal remodeling, DNA repair, active estrogen receptor formation and growth factor synthesis, and mitogenic pathways. These modulatory effects of E2 and TAM upon the gene expression patterns identified here could explain some of the mechanisms associated with the acquisition of a more aggressive phenotype by breast cancer cells, such as E2-independent growth and TAM resistance.

scholarly journals Effect of the oestrous cycle, pregnancy and uterine region on the responsiveness of the isolated mouse uterus to prostaglandin F2α and the thromboxane mimetic U46619

2006 ◽  
Vol 188 (3) ◽  
pp. 569-577 ◽  
Author(s):  
A L Griffiths ◽  
K M Marshall ◽  
J Senior ◽  
C Fleming ◽  
D F Woodward
Keyword(s):  
Regional Variation ◽  
Area Under The Curve ◽  
Prostaglandin F2α ◽  
Uterine Horn ◽  
Oestrous Cycle ◽  
Late Gestation ◽  
Human Myometrium ◽  
Mouse Uterus ◽  
Prostaglandin F ◽  
Myogenic Activity

Previous studies in this laboratory have suggested that the isolated uterus from non-pregnant mice has a prostaglandin F and a thromboxane receptor population similar to that found in human myometrium. The aim of this study was to investigate any regional variation in myogenic activity ) and the and responsiveness to prostaglandin F2α (PGF2α thromboxane mimetic U46619 in the mouse uterus taken during different stages of the oestrous cycle and during pregnancy. Uterine samples from BKW mice were taken from different anatomical segments along the length of each uterine horn and set up for superfusion at 2 ml/min with Krebs solution (containing 1 μM indometacin) at 37 °C, and gassed with 95%O2/5%CO2. Responses (area under the curve) are expressed as a percentage of the final contraction induced by hypotonic shock. Data are expressed as the means ± s.e.m. of n=5–12 and were analysed using Student’s paired t-test or two-way ANOVA with a Bonferroni post hoc test. Regional variation in myogenic activity was observed in all tissues studied except those taken during labour. These tissues displayed significantly greater myogenic activity than tissues taken at late gestation and at all stages of the oestrous cycle. Tissues from pregnant animals were generally more responsive to U46619 and PGF2α than tissues taken from non-pregnant animals. Tissues taken from the upper segment of the uterine horn were more responsive to both agonists during the oestrous cycle. The findings demonstrated that the hormonal milieu and site of excision are important for myogenic activity and responsiveness.

scholarly journals Coding RNA Sequencing of Equine Endometrium during Maternal Recognition of Pregnancy

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 749 ◽  
Author(s):  
Kristin M. Klohonatz ◽  
Stephen J. Coleman ◽  
Alma D. Islas-Trejo ◽  
Juan F. Medrano ◽  
Ann M. Hess ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sample Preparation ◽  
Rna Sequencing ◽  
Splice Variants ◽  
Expression Patterns ◽  
Prostaglandin F2α ◽  
Endometrial Biopsy ◽  
Pregnancy Status ◽  
Maternal Recognition Of Pregnancy ◽  
Uterine Lavage

Equine maternal recognition of pregnancy (MRP) is a process whose signal remains unknown. During MRP the conceptus and endometrium communicate to attenuate prostaglandin F2α (PGF) secretion, sparing the corpus luteum and maintaining progesterone production. Recognition of a mobile conceptus by the endometrium is critical by days 14–16 post-ovulation (PO), when endometrium produces PGF, initiating luteolysis. The objective of this study was to evaluate endometrial gene expression changes based upon pregnancy status via RNA sequencing. This experiment utilized a cross-over design with each mare serving as both a pregnant and non-mated control on days nine, 11, and 13 PO (n = 3/status/day). Mares were randomly assigned to collection day and pregnancy confirmed by terminal uterine lavage at the time of endometrial biopsy. Total RNA was isolated and libraries prepared using Illumina TruSeq RNA sample preparation kit. Reads were mapped and annotated using HISAT2 and Stringtie. Expression values were evaluated with DESEQ2 (P ≤ 0.05 indicated significance). On day nine, 11, and 13 there were 1435, 1435 and 916 significant transcripts, respectively. Multiple genes with splice variants had different expression patterns within the same day. These are the first data to evaluate the endometrial transcriptome during MRP on days nine, 11, and 13.

scholarly journals Evidence of the Complexity of Gene Expression Analysis in Fish Wild Populations

2017 ◽  
Vol 2017 ◽  
pp. 1-14 ◽  
Author(s):  
Mbaye Tine
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Expression Patterns ◽  
Cell Volume Regulation ◽  
Mitogen Activated Protein Kinase ◽  
Wild Populations ◽  
Natural Habitats ◽  
Evolutionary Forces

The present work examines the induction of theband 3 anion transport protein,mitogen-activated protein kinase, andlactate dehydrogenase, respectively related to osmolyte transport, cell volume regulation, and energy production in the gills of two tilapia strains exposed to either freshwater or hypersaline water. Overall, genes showed similar expression patterns between strains. However, a wild population survey across a range of natural habitats and salinities did not reveal the expected patterns. Although significant, the correlations between gene expression and salinity were slightly ambiguous and did not show any link with phenotypic differences in life history traits previously reported between the same populations. The differential expression was also not associated with the population genetic structure inferred from neutral markers. The results suggest that the differential expression observed is not the result of evolutionary forces such as genetic drift or adaptation by natural selection. Instead, it can be speculated that genes responded to various abiotic and biotic stressors, including factors intrinsic to animals. This study provides clear evidence of the complexity of gene expression analysis in wild populations and shows that more attention needs to be paid when selecting candidates as potential biomarkers for monitoring adaptive responses to a specific environmental perturbation.

Regulation of expression of the retinoic acid-synthesising enzymes retinaldehyde dehydrogenases in the uteri of ovariectomised mice after treatment with oestrogen, gestagen and their combination

2006 ◽  
Vol 18 (3) ◽  
pp. 339 ◽  
Author(s):  
Ralph Rühl ◽  
Britta Fritzsche ◽  
Julien Vermot ◽  
Karen Niederreither ◽  
Ulrike Neumann ◽  
...  
Keyword(s):  
Retinoic Acid ◽  
Early Pregnancy ◽  
Expression Patterns ◽  
In Situ Hybridisation ◽  
Oestrous Cycle ◽  
Regulation Of Expression ◽  
Mouse Uterus ◽  
Blastocyst Implantation ◽  
Polymerase Chain

The active metabolite of vitamin A, retinoic acid (RA), plays an important role in the female reproductive system. The synthesis of RA is tightly regulated by the activity of retinaldehyde dehydrogenases (Raldh). Among these, Raldh1 and Raldh2 exhibit specific temporal and spatial expression patterns in the mouse uterus, both during the oestrous cycle and early pregnancy. In the present study, we have assessed whether oestradiol and progesterone directly influence the uterine expression of Raldh1 and Raldh2 in ovariectomised mice. We investigated the effect of gestagen (promegestone 0.3 mg kg−1 bodyweight), oestrogen (oestradiol 3 µg kg−1 bodyweight) and their combination on the uterine expression of Raldh2. Expression was analysed using in situ hybridisation and quantified using real-time detection reverse transcription–polymerase chain reaction. The results show that the expression of Raldh2 is rapidly (within 1–4 h) induced in stromal cells by oestrogen, but not by gestagen, treatment, whereas combined oestrogen + gestagen treatment leads to a more prolonged (48 h) response. In contrast, oestrogen, but not progesterone, treatment downregulates (within 4–24 h) Raldh1 expression in the uterine glandular epithelium. We conclude that the uterine RA concentrations are regulated by oestrogens via an effect on the expression of the Raldh synthesising enzymes. Such a regulation is consistent with the natural fluctuations of Raldh expression during the oestrous cycle, early pregnancy and blastocyst implantation.

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