Similarities and differences in uterine gene expression patterns caused by treatment with physiological and non-physiological estrogens

Administration of physiological and non-physiological estrogens during pregnancy or after birth is known to have adverse effects on the development of the reproductive tract and other organs. Although it is believed that both estrogens have similar effects on gene expression, this view has not been tested systematically. To compare the effects of physiological (estradiol; E2) and non-physiological (diethylstilbestrol; DES) estrogens, we used DNA microarray analysis to examine the uterine gene expression patterns induced by the two estrogens. Although E2 and DES induced many genes to respond in the same way, different groups of genes showed varying levels of maximal activities to each estrogen, resulting in different dose-response patterns. Thus, each estrogen has a distinct effect on uterine gene expression. The genes were classified into clusters according to their dose-responses to the two estrogens. Of the eight clusters, only two correlated well with the uterotropic effect of different doses of E2. One of these clusters contained genes that were upregulated by E2, which included genes encoding several stress proteins and transcription factors. The other cluster contained genes that were downregulated by E2, including genes related to metabolism, transcription and detoxification processes. The expression of these genes in estrogen receptor-deficient mice was not affected by E2 treatment, indicating that these genes are affected by the E2-bound estrogen receptor. Thus, of the many genes that are affected by estrogen, it was suggested that only a small number are directly involved in the uterotropic effects of estrogen treatment.

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The environmental estrogen, 4-nonylphenol modulates brain estrogen-receptor- and aromatase (CYP19) isoforms gene expression patterns in Atlantic salmon (Salmo salar)

Marine Environmental Research ◽

10.1016/j.marenvres.2006.04.005 ◽

2006 ◽

Vol 62 ◽

pp. S195-S199 ◽

Cited By ~ 18

Author(s):

Valentina Meucci ◽

Augustine Arukwe

Keyword(s):

Gene Expression ◽

Estrogen Receptor ◽

Atlantic Salmon ◽

Salmo Salar ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Environmental Estrogen ◽

Atlantic Salmon Salmo Salar

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Gene Expression Patterns in Ovarian Carcinomas

Molecular Biology of the Cell ◽

10.1091/mbc.e03-05-0279 ◽

2003 ◽

Vol 14 (11) ◽

pp. 4376-4386 ◽

Cited By ~ 227

Author(s):

Marci E. Schaner ◽

Douglas T. Ross ◽

Giuseppe Ciaravino ◽

Therese Sørlie ◽

Olga Troyanskaya ◽

...

Keyword(s):

Gene Expression ◽

Estrogen Receptor ◽

Dna Microarrays ◽

Clear Cell ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Published Data ◽

Breast Cancers ◽

Ovarian Carcinomas ◽

Ovarian Cancers

We used DNA microarrays to characterize the global gene expression patterns in surface epithelial cancers of the ovary. We identified groups of genes that distinguished the clear cell subtype from other ovarian carcinomas, grade I and II from grade III serous papillary carcinomas, and ovarian from breast carcinomas. Six clear cell carcinomas were distinguished from 36 other ovarian carcinomas (predominantly serous papillary) based on their gene expression patterns. The differences may yield insights into the worse prognosis and therapeutic resistance associated with clear cell carcinomas. A comparison of the gene expression patterns in the ovarian cancers to published data of gene expression in breast cancers revealed a large number of differentially expressed genes. We identified a group of 62 genes that correctly classified all 125 breast and ovarian cancer specimens. Among the best discriminators more highly expressed in the ovarian carcinomas were PAX8 (paired box gene 8), mesothelin, and ephrin-B1 (EFNB1). Although estrogen receptor was expressed in both the ovarian and breast cancers, genes that are coregulated with the estrogen receptor in breast cancers, including GATA-3, LIV-1, and X-box binding protein 1, did not show a similar pattern of coexpression in the ovarian cancers.

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Defining a relationship between dietary fatty acids and the cytochrome P450 system in a mouse model of fatty liver disease

Physiological Genomics ◽

10.1152/physiolgenomics.00209.2010 ◽

2011 ◽

Vol 43 (3) ◽

pp. 121-135 ◽

Cited By ~ 13

Author(s):

Monika Gonzalez ◽

Whitney Sealls ◽

Elliot D. Jesch ◽

M. Julia Brosnan ◽

Istvan Ladunga ◽

...

Keyword(s):

Gene Expression ◽

Fatty Acids ◽

Cytochrome P450 ◽

Fatty Liver ◽

Saturated Fatty Acids ◽

Expression Patterns ◽

Dietary Fatty Acids ◽

Gene Expression Patterns ◽

Expression Of Genes ◽

Genes Encoding

Liver-specific ablation of cytochrome P450 reductase in mice (LCN) results in hepatic steatosis that can progress to steatohepatitis characterized by inflammation and fibrosis. The specific cause of the fatty liver phenotype is poorly understood but is hypothesized to result from elevated expression of genes encoding fatty acid synthetic genes. Since expression of these genes is known to be suppressed by polyunsaturated fatty acids, we performed physiological and genomics studies to evaluate the effects of dietary linoleic and linolenic fatty acids (PUFA) or arachidonic and decosahexaenoic acids (HUFA) on the hepatic phenotypes of control and LCN mice by comparison with a diet enriched in saturated fatty acids. The dietary interventions with HUFA reduced the fatty liver phenotype in livers of LCN mice and altered the gene expression patterns in these livers to more closely resemble those of control mice. Importantly, the expression of genes encoding lipid pathway enzymes were not different between controls and LCN livers, indicating a strong influence of diet over POR genotype. These analyses highlighted the impact of POR ablation on expression of genes encoding P450 enzymes and proteins involved in stress and inflammation. We also found that livers from animals of both genotypes fed diets enriched in PUFA had gene expression patterns more closely resembling those fed diets enriched in saturated fatty acids. These results strongly suggest only HUFA supplied from an exogenous source can suppress hepatic lipogenesis.

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Spatial transcriptomics of C. elegans males and hermaphrodites identifies novel fertility genes

10.1101/348201 ◽

2018 ◽

Author(s):

Annabel Ebbing ◽

Abel Vertesy ◽

Marco Betist ◽

Bastiaan Spanjaard ◽

Jan Philipp Junker ◽

...

Keyword(s):

Gene Expression ◽

Reproductive Tract ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Specific Gene ◽

Comprehensive Overview ◽

Tissue Specific ◽

C Elegans ◽

Differential Gene ◽

Fertility Genes

SummaryTo advance our understanding of the genetic programs that drive cell and tissue specialization, it is necessary to obtain a comprehensive overview of gene expression patterns. Here, we have used RNA tomography to generate the first high-resolution, anteroposterior gene expression maps of C. elegans males and hermaphrodites. To explore these maps, we have developed computational methods for discovering region and tissue-specific genes. Moreover, by combining pattern-based analysis with differential gene expression analysis, we have found extensive sex-specific gene expression differences in the germline and sperm. We have also identified genes that are specifically expressed in the male reproductive tract, including a group of uncharacterized genes that encode small secreted proteins that are required for male fertility. We conclude that spatial gene expression maps provide a powerful resource for identifying novel tissue-specific gene functions in C. elegans. Importantly, we found that expression maps from different animals can be precisely aligned, which opens up new possibilities for transcriptome-wide comparisons of gene expression patterns.

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Homogenization of sub-genome secretome gene expression patterns in the allodiploid fungus Verticillium longisporum

10.1101/341636 ◽

2018 ◽

Cited By ~ 4

Author(s):

Jasper R.L. Depotter ◽

Fabian van Beveren ◽

Luis Rodriguez-Moreno ◽

Grardy C.M. van den Berg ◽

Thomas A. Wood ◽

...

Keyword(s):

Gene Expression ◽

Plant Pathogens ◽

Genome Duplication ◽

Expression Patterns ◽

Secreted Proteins ◽

Plant Colonization ◽

Gene Expression Patterns ◽

Adaptive Potential ◽

Verticillium Longisporum ◽

Genes Encoding

AbstractAllopolyploidization, genome duplication through interspecific hybridization, is an important evolutionary mechanism that can enable organisms to adapt to environmental changes or stresses. The increased adaptive potential of allopolyploids can be particularly relevant for plant pathogens in their ongoing quest for host immune response evasion. To this end, plant pathogens secrete a plethora of molecules that enable host colonization. Allodiploidization has resulted in the new plant pathogen Verticillium longisporum that infects different hosts than haploid Verticillium species. To reveal the impact of allodiploidization on plant pathogen evolution, we studied the genome and transcriptome dynamics of V. longisporum using next-generation sequencing. V. longisporum genome evolution is characterized by extensive chromosomal rearrangements, between as well as within parental chromosome sets, leading to a mosaic genome structure. In comparison to haploid Verticillium species, V. longisporum genes display stronger signs of positive selection. The expression patterns of the two sub-genomes show remarkable resemblance, suggesting that the parental gene expression patterns homogenized upon hybridization. Moreover, whereas V. longisporum genes encoding secreted proteins frequently display differential expression between the parental sub-genomes in culture medium, expression patterns homogenize upon plant colonization. Collectively, our results illustrate of the adaptive potential of allodiploidy mediated by the interplay of two sub-genomes.Author summaryHybridization followed by whole-genome duplication, so-called allopolyploidization, provides genomic flexibility that is beneficial for survival under stressful conditions or invasiveness into new habitats. Allopolyploidization has mainly been studied in plants, but also occurs in other organisms, including fungi. Verticillium longisporum, an emerging fungal pathogen on brassicaceous plants, arose by allodiploidization between two Verticillium spp. We used comparative genomics to reveal the plastic nature of the V. longisporum genomes, showing that parental chromosome sets recombined extensively, resulting in a mosaic genome pattern. Furthermore, we show that non-synonymous substitutions frequently occurred in V. longisporum. Moreover, we reveal that expression patterns of genes encoding secreted proteins homogenized between the V. longisporum sub-genomes upon plant colonization. In conclusion, our results illustrate the large adaptive potential upon genome hybridization for fungi mediated by genomic plasticity and interaction between sub-genomes.

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