Version: 8.0.0Date: Tue Jan 28 2025
HTP Dataset Index Species: Mus musculus
Effects of estradiol and growth hormone on liver transcriptome in hypothyroid-orquiectomized rats
(Rattus norvegicus)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by RGD
ID: GEO:GSE50014
Tags: unclassified
Summary: E2 and GH are critical regulators of growth and intermediate metabolism in mammals. Hypothyroidism causes endocrine and metabolic disturbances in the liver with features that mimic deficiencies of E2 or GH signalling. In this work, we used the hypothyroid-orchiectomized (TXOX) adult rat model to evaluate the influence of E2 and GH on the liver in terms of global changes in gene expression. This study shows the changes in hepatic transcriptome that were provoked by E2 benzoate (50 ug/kg; sc; 5 days per week x 27 days), intermittent GH administration (0.3 mg/kg/day;sc injection divided into two daily injections x 7 days) or the combination of E2 plus GH in TXOX rats. E2 influenced the liver transcriptome, particularly genes involved in metabolism of lipids and endo-xenobiotics, and the GH-regulated endocrine, metabolic, gender, and immune responses. E2 did not prevent the inhibitory effects of GH on urea and amino acid metabolism-related genes. Notably, the combination of E2 and GH caused deleterious effects on transcriptional immune response. These results highlight the role of E2 as a critical regulator of liver metabolism in mammals and provide insights into the functional interplay between E2 and GH in the liver.
Estrogen receptor-dependent attenuation of hypoxia-induced changes in the lung genome of pulmonary hypertension rats
(Rattus norvegicus)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by RGD
ID: GEO:GSE85618
Tags: unclassified
Summary: 17β-estradiol (E2) exerts complex and context-dependent effects in pulmonary hypertension. In hypoxia-induced pulmonary hypertension (HPH), E2 attenuates lung vascular remodeling through estrogen receptor (ER)-dependent effects; however, ER target genes in the hypoxic lung remain unknown. In order to identify the genome regulated by the E2-ER axis in the hypoxic lung, we performed a microarray analysis in lungs from HPH rats treated with E2 (75 mcg/kg/d) ± ER-antagonist ICI182,780 (3 mg/kg/d). Untreated HPH rats and normoxic rats served as controls. Using a false discovery rate of 10%, we identified a significantly differentially regulated genome in E2-treated vs. untreated hypoxia rats. Genes most up-regulated by E2 encoded matrix metalloproteinase 8, S100 calcium binding protein A8, and IgA Fc receptor; genes most down-regulated by E2 encoded olfactory receptor 63, secreted frizzled-related protein 2, and thrombospondin 2. Several genes affected by E2 changed in the opposite direction after ICI182,780 co-treatment, indicating an ER-regulated genome in HPH lungs. The bone morphogenetic protein antagonist Grem1 (gremlin 1) was up-regulated by hypoxia, but found to be among the most down-regulated genes after E2 treatment. Gremlin 1 protein was reduced in E2-treated vs. untreated hypoxic animals, and ER-blockade abolished the inhibitory effect of E2 on Grem1 mRNA and protein. In conclusion, E2 ER-dependently regulates several genes involved in proliferative and inflammatory processes during hypoxia. Gremlin 1 is a novel target of the E2-ER axis in HPH. Understanding the mechanisms of E2 gene regulation in HPH may allow for selectively harnessing beneficial transcriptional activities of E2 for therapeutic purposes.
To elucidate the role of estradiol- 17ß (E2) in the regulation of corpus luteum function
(Rattus norvegicus)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by RGD
ID: GEO:GSE41735
Tags: unclassified
Summary: Corpus luteum (CL) is a transient endocrine tissue formed from the remnants of the ovarian follicle after ovulation. In response to gonadotropin surge, the ovulating follicle undergoes dramatic changes in expression of genes and differentiation of follicular cells into luteal cells. In several species, of the several genes that are down- regulated post ovulation, Cyp19A1 that codes for aromatase, essential for biosynthesis of estradiol- 17ß (E2), also get down- regulated but appears to get up- regulated at later time points in the estrous cycle to have critical role in E2 secretion. In primates and rodents, higher expression and higher E2 levels has been observed in CL. Surprisingly, in the recently carried out gene expression profiling of PGF2a- induced luteolysis studies in the bovine species [GSE27961], it was observed that expression of one of the earliest genes that was down- regulated was Cyp19A1 in the CL. However, the specific role of E2 in the regulation of CL function remains poorly defined. Thus, in the present study, efforts were made to examine the temporal changes in the global gene expression profile in the CL of pregnant rats after treatment with aromatase inhibitor (AI), Anastrozole, and E2 supplementation. The results obtained will further expand our knowledge on E2 target/responsive genes and the basic mechanism(s) that regulates the CL function. Key words: CL, E2, AI, Gene expression
Expression data from the mammary gland of ovariectomized (ovx) rats treated for three days with E2, 3-MC, E2+3-MC
(Rattus norvegicus)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by RGD
ID: GEO:GSE64636
Tags: unclassified
Summary: The study was designed to see the overall gene-expression change in the mammary gland induced by AHR ligand 3-MC alone and in combination with E2.
Symbol: Expression data from the mammary gland of ovariectomized (ovx) rats treated for three days with E2, 3...-MC, E2+3-MC
Expression data from the uterus of ovariectomized young adult rats treated for three days with E2, 3-MC, E2+3-MC
(Rattus norvegicus)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by RGD
ID: GEO:GSE95783
Tags: unclassified
Summary: The study was designed to see the overall gene-expression change in the uterus induced by E2, the AHR ligand 3-MC alone and in combination with E2.
Symbol: Expression data from the uterus of ovariectomized young adult rats treated for three days with E2, 3-...MC, E2+3-MC
Expression data from yeast strain containing CDC34tm allele compared to WT
(Saccharomyces cerevisiae)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by SGD
ID: GEO:GSE8453
Tags: protein modification
Summary: Cdc34 is an essential E2 ubiquitin conjugating enzyme found in nearly all eukaryotes
Transcriptomic analysis of the estrogenic effect of soy protein isolate in rat uterus
(Rattus norvegicus)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by RGD
ID: GEO:GSE69819
Tags: unclassified
Summary: There are concerns regarding possible reproductive toxicity from consumption of soy including an increased risk of endometriosis and endometrial cancer. We used global uterine gene expression profiles in adult ovariectomized (OVX) female rats assessed by RNAseq to examine the estrogenicity of soy protein isolate (SPI) and the potential for feeding SPI to alter estrogen signaling in the uterus. Rats were fed AIN93G diets made with casein (CAS) or SPI from postnatal day (PND) 30. Rats were OVX on PND 50 and infused with 17 beta-estradiol (E2) or vehicle. E2 increased uterine wet weight (P<0.05) and significantly altered expression of 2084 uterine genes. In contrast, SPI feeding had no effect on uterine weight and only altered expression of 177 genes. Overlap between E2 and SPI genes was limited to 69 genes (3%). GO analysis indicated significant differences in uterine biological processes affected by E2 and SPI and little evidence for recruitment of ER alpha to the promoters of ER-responsive genes after SPI feeding. The major E2 up-regulated uterine pathways were cancer pathways and extracellular organization. SPI feeding up-regulated uterine PPAR signaling and fatty acid metabolism. The combination of E2 and SPI feeding resulted in significant regulation of 715 fewer genes relative to E2 alone. In a separate experiment, the combination of E2 and SPI reversed the ability of E2 to induce uterine proliferation in response to the carcinogen dimethybenz(a)anthracene (DMBA). These data suggest SPI does not act as a weak estrogen in the uterus but appears to be a selective estrogen receptor modulator (SERM) interacting with a small sub-set of E2-regulated genes and to be anti-estrogenic in the presence of endogenous estrogens.
Different effects of 17 beta estrodial and soy protein isolate on bone gene expression in the pre-pubertal female rats
(Rattus norvegicus)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by RGD
ID: GEO:GSE30862
Tags: unclassified
Summary: Beneficial effects of a soy diet on bone quality have been assumed to be due to the putative estrogenic actions of isoflavones. We studied the effects of soy protein isolate (SPI) on bone quality and compared these effects to 17ß-estradiol (E2) in pre-pubertal rats. Female rats were weaned to a control diet with or without E2 (0.1, 1, 10 µg/kg/d), or SPI-containing diet with or without E2 (10 µg/kg/d) for 14 days beginning on postnatal day 20. In long bones from SPI-fed rats, only cancellous bone mineral density (BMD) was increased (p<0.05), while cortical BMD was decreased accompanied by lower bone strength compared to control casein-fed rats (p<0.05). In sharp contrast, 10 µg/kg/d E2 not only increased trabecular BMD, but also cortical BMD compared to controls. Rats treated with the combination of SPI and E2 had an intermediate bone effect. SPI increased while E2 decreased bone turnover, and increased trabecular BMD by both E2 and SPI was associated with decreased serum sclerostin levels. Microarray analysis revealed 652 genes regulated by SPI diet, 491 genes regulated by E2, and 266 genes regulated in common by both SPI diet and E2 compared to rats fed casein. The expression of caveolin-1, a protein localized in cell membrane, was down-regulated (p<0.05) in rats fed SPI, but not by E2 compared to rats fed casein. Down-regulated caveolin-1 by SPI was associated with increased BMP2, Smad and Runx2 expression in bone and osteoblasts (p<0.05). These results suggest SPI consumption results in significant non-classical estrogenic stimulation of cancellous bone formation prior to puberty, but may have adverse effects on overall bone quality and strength at this developmental stage as a result of reduced cortical bone formation.
High-Throughput (HTP) Dataset Index metadata provided by SGD
ID: GEO:GSE253055
Tags: cell aging, evolution
Summary: Yeast has proven to be a useful model system for aging studies, including CR effects. We report here that yeast adapted through in vitro evolution to the severe cellular stress caused by loss of the Ulp2 SUMO-specific protease exhibit both enhanced growth rates and replicative lifespan, and they have altered gene expression profiles similar to those observed in CR. Notably, in certain evolved ulp2Δ lines, a dramatic increase in the auto-sumoylation of Ubc9 E2 SUMO-conjugating enzyme results in altered regulation of multiple targets involved in energy metabolism and translation at both transcriptional and post-translational levels. This increase is essential for the survival of aged cells and CR-mediated lifespan extension
Symbol: Auto-sumoylation of the Ubc9 E2 SUMO-conjugating Enzyme Extends Cellular Lifespan
Name: Auto-sumoylation of the Ubc9 E2 SUMO-conjugating Enzyme Extends Cellular Lifespan
miRNA Expression data from the uterus of ovariectomized young adult rats treated for three days with E2
(Rattus norvegicus)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by RGD
ID: GEO:GSE95790
Tags: unclassified
Summary: The study was designed to see the overall ncRNA-expression change in the uterus induced by E2
Symbol: miRNA Expression data from the uterus of ovariectomized young adult rats treated for three days with E2
Name: miRNA Expression data from the uterus of ovariectomized young adult rats treated for three days with E2
HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by SGD
ID: GEO:GSE254981
Tags: cell aging, evolution
Summary: Yeast has proven to be a useful model system for aging studies, including CR effects. We report here that yeast adapted through in vitro evolution to the severe cellular stress caused by loss of the Ulp2 SUMO-specific protease exhibit both enhanced growth rates and replicative lifespan, and they have altered gene expression profiles similar to those observed in CR. Notably, in certain evolved ulp2Δ lines, a dramatic increase in the auto-sumoylation of Ubc9 E2 SUMO-conjugating enzyme results in altered regulation of multiple targets involved in energy metabolism and translation at both transcriptional and post-translational levels. This increase is essential for the survival of aged cells and CR-mediated lifespan extension
Symbol: Auto-sumoylation of the Ubc9 E2 SUMO-conjugating Enzyme Extends Cellular Lifespan (RNA-Seq)
Name: Auto-sumoylation of the Ubc9 E2 SUMO-conjugating Enzyme Extends Cellular Lifespan (RNA-Seq)
An E2F1-Dependent Gene Expression Program That Determines the Balance Between Proliferation and Cell Death
(Rattus norvegicus)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by RGD
ID: GEO:GSE9496
Tags: unclassified
Summary: Keywords: PI3K dependent modulation of E2F1 gene expression measured by Affymetrix gene expression analysis
Symbol: An E2F1-Dependent Gene Expression Program That Determines the Balance Between Proliferation and Cell
Aqp1 overexpression may enhance glioma tumorigenesis by interacting with the transcriptional regulation networks of Foxo4, Maz, and E2F families
(Rattus norvegicus)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by RGD
ID: GEO:GSE137733
Tags: unclassified
Summary: Gliomas is the most common and aggressive primary brain tumor. The C6 glioma cell line has been widely used for decades as experimental model system for the study of glioblastoma growth and invasion. Recently, aquaporin-1 (Aqp1) is reported to facilitate cell migration and potentially involved in tumor progression. Here we overexpressed Aqp1 in C6 cells to examine its potential role in glioblastoma. We found overexpression of Aqp1 in C6 cells significantly increased cell viability and cell migration. The upregulated genes were enriched for cell mobility and glioblastoma. Transcriptional factor binding analysis indicates the upregulated genes were regulated by FOXO4, MAZ, and E2F TF families, which are known factors involved in cell cycle control and cancer progression. Our study suggests Aqp1 is potentially involved in gliomas formation by interacting with the transcriptional regulation networks of FOXO4, MAZ, and E2F TF families.
Symbol: glioma tumorigenesis by interacting with the transcriptional regulation networks of Foxo4, Maz, and E2F
Examination of CA1 hippocampal DNA methylation as a mechanism for closing of estrogen’s critical window
(Rattus norvegicus)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by RGD
ID: GEO:GSE167038
Tags: unclassified
Summary: The study presents several novel findings that relate to the idea that alterations in DNA methylation occurs during aging and may be linked to senescent physiology, including a decline in circulating E2. In addition, the evidence has been provided that DNA methylation contributes to the closing of the critical window for E2 effects on synaptic function.
High-Throughput (HTP) Dataset Index metadata provided by SGD
ID: GEO:GSE22271
Tags: chemical stimulus
Summary: The target of rapamycin (TOR) plays a central role in eukaryotic cell growth control
Symbol: Saccharomyces cerevisiae temperature-sensitive strains specific for SCF core components (Skp1, Cullin (Cdc53), E2
Name: Saccharomyces cerevisiae temperature-sensitive strains specific for SCF core components (Skp1, Cullin (Cdc53), E2
Association of Cellular and Molecular Responses in the Rat Mammary Gland to 17beta-Estradiol with Susceptibility to Mammary Cancer
(Rattus norvegicus)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by RGD
ID: GEO:GSE49548
Tags: unclassified
Summary: We are using ACI and BN rats, which differ markedly in their susceptibility to 17beta-Estradiol (E2)-induced mammary cancer, to identify genetic variants and environmental factors that determine mammary cancer susceptibility. The objective of this study was to characterize the cellular and molecular responses to E2 in the mammary glands of ACI and BN rats to identify qualitative and quantitative phenotypes that associate with and/or may confer differences in susceptibility to mammary cancer. Female ACI and BN rats were treated with E2 for 1, 3 or 12 weeks and cell proliferation, apoptosis, differentiation and gene expression were evaluated. The luminal epithelium of ACI rats exhibited a rapid and sustained proliferative response to E2. By contrast, the proliferative response exhibited by the mammary epithelium of BN rats was restrained and transitory. Moreover, the epithelium of BN rats appeared to undergo differentiation in response to E2, as evidenced by production of milk proteins as well as luminal ectasia and associated changes in the extracellular matrix (ECM). Marked differences in expression of genes that encode proteins with well-defined roles in mammary gland development (Pgr, Wnt4, Tnfsf11, Prlr, Stat5a, Areg, Gata3), differentiation and milk production (Lcn2, Spp1), regulation of extracellular environment (Mmp7, Mmp9), and cell-cell or cell-ECM interactions (Cd44, Cd24, Cd52) were observed. We propose that these cellular and molecular phenotypes are heritable and may underlie, at least in part, the differences in mammary cancer susceptibility exhibited by ACI and BN rats.
Estrogen regulated genes in rat testes and their relationship to recovery of spermatogenesis after irradiation
(Rattus norvegicus)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by RGD
ID: GEO:GSE24672
Tags: unclassified
Summary: Despite numerous observations of effects of estrogens on spermatogenesis, identification of estrogen-regulated genes in the testis is limited. We previously showed in rats, in which irradiation had completely blocked spermatogonial differentiation, that testosterone (T) suppression with GnRH-antagonist and antiandrogen stimulated spermatogenic recovery and addition of estradiol (E2) to this regimen accelerated this recovery. We report here the global changes in testicular cell gene expression induced by the E2 treatment. By minimizing the changes in other hormones and also having concurrent data on the regulation of the genes by those hormones, we were able to dissect the effects of estrogen on gene expression, independent of gonadotropin or T changes. Expression of 20 genes, largely in somatic cells, was up- or down-regulated between 2- and 5-fold by E2. There were also early germ cell genes whose expression increased but this was a result of a small increase in spermatogonial numbers. The striking enrichment of transcripts not corresponding to known genes among the E2-downregulated probes led to the identification of one as micro-RNA miR-34a. We propose that genes whose expression levels are altered in one direction by irradiation and in the opposite direction by both T suppression and E2 treatment are candidates for controlling the block in differentiation. Several genes, including insulin-like 3 (Insl3), satisfied those criteria. If they are indeed involved in the inhibition of spermatogonial differentiation, they may be candidate targets for clinical treatments to enhance recovery of spermatogenesis following gonadotoxic exposures, such as those resulting from cancer therapy.
Effects of Follicle Stimulating Hormone on Adipose Tissue Metabolic Health After Loss of Ovarian Function
(Rattus norvegicus)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by RGD
ID: GEO:GSE247952
Tags: unclassified
Summary: Loss of ovarian function imparts increased susceptibility to obesity and metabolic disease. These effects are largely attributed to decreased estradiol (E2), but the role of increased follicle stimulating hormone (FSH) in modulating energy balance has not been fully investigated. Previous work that inhibited FSH activity in mice suggested this hormone may play a part in modulating body weight and energy expenditure after ovariectomy. We used an alternate approach to experimentally isolate the individual and combined contributions of FSH and E2 in mediating energy imbalance and changes in tissue-level metabolic health. Female Wistar rats were ovariectomized and given the GnRH antagonist degarelix to suppress FSH production. E2 and FSH were then added back individually and in combination for a period of 3 weeks. Energy balance, body mass composition, and transcriptomic profiles of individual tissues were obtained. In contrast to previous studies, ablation and replacement of FSH in our paradigm had no effect on body weight, body composition, food intake, or energy expenditure. We did, however, observe organ-specific effects of FSH that produced unique transcriptomic signatures of FSH in retroperitoneal white adipose tissue. These included reductions in biological processes related to lipogenesis and carbohydrate transport. Additionally, rats administered FSH had reduced liver triglyceride concentration (p<0.001), which correlated with FSH-induced changes at the transcriptomic level. While not appearing to modulate energy balance after loss of ovarian function in rats, FSH may still impart tissue-specific effects in the liver and white adipose tissue that might affect the metabolic health of those organs.
Effects of Follicle Stimulating Hormone on Liver Metabolic Health After Loss of Ovarian Function
(Rattus norvegicus)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by RGD
ID: GEO:GSE248104
Tags: unclassified
Summary: Loss of ovarian function imparts increased susceptibility to obesity and metabolic disease. These effects are largely attributed to decreased estradiol (E2), but the role of increased follicle stimulating hormone (FSH) in modulating energy balance has not been fully investigated. Previous work that inhibited FSH activity in mice suggested this hormone may play a part in modulating body weight and energy expenditure after ovariectomy. We used an alternate approach to experimentally isolate the individual and combined contributions of FSH and E2 in mediating energy imbalance and changes in tissue-level metabolic health. Female Wistar rats were ovariectomized and given the GnRH antagonist degarelix to suppress FSH production. E2 and FSH were then added back individually and in combination for a period of 3 weeks. Energy balance, body mass composition, and transcriptomic profiles of individual tissues were obtained. In contrast to previous studies, ablation and replacement of FSH in our paradigm had no effect on body weight, body composition, food intake, or energy expenditure. We did, however, observe organ-specific effects of FSH that produced unique transcriptomic signatures of FSH in retroperitoneal white adipose tissue. These included reductions in biological processes related to lipogenesis and carbohydrate transport. Additionally, rats administered FSH had reduced liver triglyceride concentration (p<0.001), which correlated with FSH-induced changes at the transcriptomic level. While not appearing to modulate energy balance after loss of ovarian function in rats, FSH may still impart tissue-specific effects in the liver and white adipose tissue that might affect the metabolic health of those organs.
Expression data from the hearts of aged Norway Brown rats (18-22 months-old)
(Rattus norvegicus)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by RGD
ID: GEO:GSE30851
Tags: unclassified
Summary: Despite an abundance of evidence to the contrary from animal studies, large clinical trials on humans have shown that estrogen administered to post-menopausal women increases the risk of cardiovascular disease. However, timing may be everything, as estrogen is often administered immediately after ovariectomy (ovx) in animal studies, while estrogen administration in human studies occurred many years post-menopause. This study investigates the discrepancy by administering 17ß-estradiol (E2) in a slow-release capsule to Norway Brown rats both immediately following ovx and 9 weeks post-ovx (Late), and studying differences in gene expression between these 2 groups as compared to age-matched ovx and sham operated animals. Two different types of microarray were used to analyze the left ventricles from these groups: an Affymetrix array (2 samples/group, each sample contained total RNAs pooled from 3 rats) and an Inflammatory Cytokines and Receptors PCR array (N=4 /group). Key genes were analyzed by western blotting. Ovx without replacement led to an increase in caspase 3, caspase 9, calpain 2, MMP9, and TNFa. Caspase 6, STAT3, and CD11b increased in the Late group, while TIMP2, MMP14, and collagen I a1 were decreased. MADD and fibronectin were increased in both Ovx and Late. TNFa protein levels increased with Late replacement. Many of these changes were prevented by early E2 replacement. These findings suggest that increased TNFa may be involved in some of the deleterious effects of delayed E2 administration seen in human studies.
HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by SGD
ID: GEO:GSE139633
Tags: chromatin organization
Summary: Rad6 E2 ubiquitin-conjugating enzyme and Bre1 E3 ubiquitin ligase catalyze histone H2B Lysine-123 monoubiquitination (H2Bub1), which stabilizes nucleosomes and regulates the trans-histone H3K4 and K79 methylation during gene transcription and other nuclear processes. The interaction interfaces within the Rad6-Bre1-containing H2B ubiquitin-conjugating complex has remained unknown. By solving the crystal structure of Rad6 along with a non-RING domain N-terminal region of Bre1, we report a beta-turn in Rad6's so-called backside region away from catalytic pocket as a binding site for a homodimer of Bre1 E3 ligase. Using quantitative ChIP-seq or ChIP-Rx, we further demonstrate that Rad6's backside beta-turn residues also govern the chromatin binding dynamics of the Rad6-Bre1 complex.
HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by SGD
ID: GEO:GSE131639
Tags: chromatin organization, disease
Summary: The conserved yeast E3 ligase Bre1 and its partner E2 Rad6 monoubiquitinate histone H2B across gene bodies during the transcription cycle. While processive ubiquitination might in principle arise from Bre1/Rad6 traveling with RNA polymerase II, we provide a different explanation. Here we implicate liquid-liquid phase separation as the underlying mechanism. Biochemical reconstitution shows that Bre1 binds the scaffold protein Lge1, whose intrinsically disordered region phase separates via dynamic, multivalent interactions. The resulting condensates comprise a core of Lge1 encapsulated by an outer catalytic shell of Bre1. This layered liquid recruits Rad6 and the nucleosomal substrate, accelerating H2B ubiquitination. In vivo, the condensate-forming region of Lge1 is required to ubiquitinate H2B in gene bodies beyond the +1 nucleosome. Our data suggest that layered condensates of histone modifying enzymes generate chromatin-associated reaction chambers with augmented catalytic activity along gene bodies. Equivalent processes may occur in human cells, causing neurological disease when impaired.
Gene modulation in acetic acid-induced oral ulcerative mucositis
(Rattus norvegicus)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by RGD
ID: GEO:GSE83349
Tags: unclassified
Summary: To reveal the molecular mechanisms underlying oral ulcerative mucositis-induced pain, we investigated putative pain-associated mediators, pain-related behaviors and gene modulation in a rat oral mucositis model. On day 1 after acetic acid treatment, the mucosal area showed slight redness and swelling but no evidence of ulceration or pain induction. On day 2, oral ulcers were obvious, as was the induction of spontaneous and mechanical pain. In the treated mucosal area, bacterial loading and prostaglandin E2 increased beginning on day 2; no significant changes were observed on day 1. DNA microarray analysis of trigeminal ganglion tissue collected on day 2 identified 32 significantly regulated genes (>1.5-fold change in expression). The up-regulation of the top 3 genes, Hamp (hepcidin antimicrobial peptide), Reg3b (regenerating islet-derived 3ß) and Serpina3n (serine peptidase inhibitor A3N), was validated through quantitative RT-PCR. Systemic antibiotic pre-treatment did not increase the mRNA levels. Therefore, we conclude that the oral ulcerative mucositis-induced pain is caused by infectious inflammation of the ulcerative area and stimulates anti-bacterial and anti-peptidase gene expressions in sensory neurons.
High-Throughput (HTP) Dataset Index metadata provided by SGD
ID: GEO:GSE146296
Tags: transcriptional regulation
Summary: Project abstract : The trimethylation of histone H3 lysine 4 (H3K4me3) is a crucial factor in defining the promoter regions of active genes in all eukaryotes ranging from Saccharomyces cerevisiae (yeast) to humans. In budding yeast, this trimethylation process facilitated by the Set1 complex results in H3K4me3 requiring a prior mono-ubiquitination at the histone H2BK123 residue (H2Bub) by E2 enzyme Rad6 and E3 enzyme Bre1. A previous in vitro study suggested that ubiquitinated H2B directly facilitates H3K4me3. However, even low levels of global H2Bub is sufficient for the required H3K4me3 in yeast cells, thereby indicating that other factors resulting in the H2Bub-dependent H3K4me3 remain unknown. This study revealed the high level of correlation of H3K4me3 with chromatin recruitment of Rad6 at the genome-wide level. Rad6 is confirmd to interact and co-localize with Swd2/Cps35, a key factor for the H2Bub-dependent H3K4me3 in genes with high levels of H3K4me3 and intronic genes rather than non-intronic genes. This study therefore provides a mechanistic insight of the H2Bub-Rad6- Swd2/Cps35-H3K4me3 axis and its potential role in RNA biogenesis.
Effect of Rad6 backside beta-turn mutations on gene expression
(Saccharomyces cerevisiae)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by SGD
ID: GEO:GSE139632
Tags: chromatin organization
Summary: Rad6 E2 ubiquitin-conjugating enzyme and Bre1 E3 ubiquitin ligase catalyze histone H2B Lysine-123 monoubiquitination (H2Bub1), which stabilizes nucleosomes and regulates the trans-histone H3K4 and K79 methylation during gene transcription and other nuclear processes. The interaction interfaces within the Rad6-Bre1-containing H2B ubiquitin-conjugating complex have remained unknown. By solving the crystal structure of Rad6 along with a non-RING domain N-terminal region of Bre1, we report a beta-turn in Rad6's so-called backside region away from catalytic pocket as a binding site for a homodimer of Bre1 E3 ligase. Using quantitative ChIP-seq or ChIP-Rx, we further demonstrate that Rad6's backside beta-turn residues also govern the chromatin binding dynamics and transcriptional regulatory functions of the Rad6-Bre1 complex.
The ubiquitin conjugase Rad6 mediates ribosome pausing during oxidative stress
(Saccharomyces cerevisiae)HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by SGD
ID: GEO:GSE226082
Tags: oxidative stress
Summary: Oxidative stress causes K63-linked ubiquitination of ribosomes by the E2 ubiquitin conjugase, Rad6. How Rad6-mediated ubiquitination of ribosomes affects translation, however, is unclear. We therefore performed Ribo-seq and Disome-seq in Saccharomyces cerevisiae, and found that oxidative stress caused ribosome pausing at specific amino acid motifs, and this also led to ribosome collisions. However, these redox pausing signatures were lost in the absence of Rad6 but did not depend on the ribosome-associated quality control (RQC) pathway. We also found that Rad6 is needed to inhibit overall translation in response to oxidative stress and its deletion leads to increased expression of antioxidant genes. Finally, we observed that the lack of Rad6 leads to changes during translation initiation that affect activation of the integrated stress response (ISR) pathway. Our results provide a high-resolution picture of the gene expression changes during oxidative stress and unravel an additional stress response pathway affecting translation elongation.