Effect of egr3 knockout on gene expression of dissected zebrafish hearts
Ontology highlight
ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE241935 | GEO | 2024/04/05
REPOSITORIES: GEO
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Project description:The goal of this study is to compare the relative expression genes in hearts of foxc1a-null mutants and WT siblings. 96hpf hearts of foxc1anju18 and WT siblings were dissected for total RNA extraction. RNA profiles were generated using Illumina deep sequencing. Our study represents the reduced expression of several trabeculation related signaling pathways and cell processes.
2021-12-05 | GSE174156 | GEO
Project description:Muscle spindles are skeletal muscle stretch receptors that mediate axial and limb position sensation (proprioception) to the central nervous system. Defective proprioception, often characterized by gait ataxia and poor coordination, is present in a variety of human sensory and motor neuropathies having diverse etiologies. Spindles contain specialized intrafusal muscle fibers that are induced during development by sensory innervation. The molecular events mediating the morphogenetic induction process are poorly characterized but depend upon neuregulins and their cognate ErbB receptor signaling. Recently, we demonstrated that the transcription factor Egr3 is induced and regulated by intrafusal muscle fiber sensory innervation during spindle induction. Moreover, Egr3-deficient mice have impaired spindle morphogenesis and profound gait ataxia. Thus, Egr3 mediated transcription is critical for muscle stretch receptor development and potentially for myotube fate specification.,Egr3 may mediate spindle morphogenesis induced by Neuregulin/ErbB signaling after myotubes are contacted by sensory axons during development. As a starting point for understanding the specific role for Egr3 in this process, we will use a genome wide expression analysis to identify genes regulated (either directly or indirectly) by Egr3 in primary myotubes. It is not practical to examine Egr3 mediated gene expression directly within spindles since they comprise less than 0.1% of the muscle mass. Therefore, gene expression analysis will be examined in primary myotubes grown in vitro. Primary myoblasts isolated from mice and differentiated in vitro are biochemically most similar to extrafusal muscle fibers which do not express Egr3. To identify genes regulated by Egr3 in myotubes, gene expression in myotubes enforced to express full length Egr3 will be compared to gene expression in myotubes enforced to express truncated (transcriptionally inactive) Egr3.,Egr3-deficient mice lack muscle spindles and have profound proprioceptive deficits. Egr3 is specifically expressed in a subset of developing primary myotubes after innervation by sensory axons. Spindle induction is dependent upon sensory/myotube contact which involves sensory axon produced neuregulin and ErbB receptor signaling in the myotube. Shortly after or during induction, Egr3 expression is upregulated and maintained in the nascent myotube/spindle as one of the earliest molecular events know to occur during spindle morphogenesis. We hypothesize that Egr3 mediated transcription is critical for engaging gene programs specific to and essential for, muscle spindle formation. Moreover, Egr3 may be involved in fate specification of myotubes that develop into biochemically and physiologically distinct intrafusal muscle fibers within spindles. To date, the target genes regulated by Egr3 during spindle morphogenesis have not been characterized.,Myoblasts from wild type newborn mice will be isolated and purified. Myoblasts will be plated on collagen coated plates and differentiated in vitro for 7 days. During in vitro differentiation, myoblasts fuse to form multinucleated myotubes that exhibit contractile properties. Egr3 is not expressed in myotubes in vitro, which is consistent with their similarity to extrafusal muscle fibers that also do not express Egr3 in vivo. Only intrafusal fibers of muscle spindles express high levels of Egr3 in this muscle fiber context. Adenoviruses that express full length Egr3 (Egr3wt; transcriptionally active) and truncated Egr3 (Egr3tr; transcriptionally inactive) have been generated and characterized in our laboratory. After 7 days of in vitro differentiation, primary myotubes will be infected with either Egr3wt or Egr3tr adenoviruses. 100% infection is routinely obtained which is confirmed by coexpression of enhanced green fluorescent protein (EGFP). Care will be taken to minimize viral induced toxicity of the myotubes after infection. Myotubes are maintained after infection for 24 hours, after which total RNA is extracted from the cell lysates. The two RNA samples will be used for microarray analysis to identify genes that are upregulated and downregulated by Egr3 in the myotube cellular context. We will repeat the infection, RNA isolation and microarray analysis three times to minimize identifying false positive differentially expressed genes. Differentially expressed genes will be confirmed using real-time PCR. Interesting differentially expressed genes will be examined by in situ hybridization to determine if they are specifically expressed in wild type spindles. Since the identified differentially expressed genes will represent both indirect and direct target genes, we will perform Chromatin Immunoprecipitation (ChIP) from Egr3wt infected myotubes and screen the ChIP DNA library by PCR to determine which gene promoters are directly bound by Egr3.
2007-07-07 | E-GEOD-1998 | biostudies-arrayexpress
Project description:The transcription factor Egr3 has been shown to have a cell autonomous role in sympathetic nervous system (SNS) development. We utilized microarray analysis to identify potential downstream target genes deregulated with loss of Egr3. Both conditions were in the null Bax background to prevent apoptosis and therefore mitigate identification of apoptosis related genes. Our analysis identified genes involved in biological processes that were expected such as SNS development and axonogenesis as well as those that were unexpected such as dendritogenesis and axon guidance. This led us to investigate whether Egr3 is important in these unexpected biological processes within sympathetic neurons. Total RNA was obtained from superior cervical ganglion (SCG) dissected from P0 mice with the genotype of Egr3+/+; Bax-/- or Egr3-/-; Bax-/-. Each genotype had 3 samples each.
2013-03-22 | E-GEOD-41290 | biostudies-arrayexpress
Project description:Muscle spindles are skeletal muscle stretch receptors that mediate axial and limb position sensation (proprioception) to the central nervous system. Defective proprioception, often characterized by gait ataxia and poor coordination, is present in a variety of human sensory and motor neuropathies having diverse etiologies. Spindles contain specialized intrafusal muscle fibers that are induced during development by sensory innervation. The molecular events mediating the morphogenetic induction process are poorly characterized but depend upon neuregulins and their cognate ErbB receptor signaling. Recently, we demonstrated that the transcription factor Egr3 is induced and regulated by intrafusal muscle fiber sensory innervation during spindle induction. Moreover, Egr3-deficient mice have impaired spindle morphogenesis and profound gait ataxia. Thus, Egr3 mediated transcription is critical for muscle stretch receptor development and potentially for myotube fate specification. Egr3 may mediate spindle morphogenesis induced by Neuregulin/ErbB signaling after myotubes are contacted by sensory axons during development. As a starting point for understanding the specific role for Egr3 in this process, we will use a genome wide expression analysis to identify genes regulated (either directly or indirectly) by Egr3 in primary myotubes. It is not practical to examine Egr3 mediated gene expression directly within spindles since they comprise less than 0.1% of the muscle mass. Therefore, gene expression analysis will be examined in primary myotubes grown in vitro. Primary myoblasts isolated from mice and differentiated in vitro are biochemically most similar to extrafusal muscle fibers which do not express Egr3. To identify genes regulated by Egr3 in myotubes, gene expression in myotubes enforced to express full length Egr3 will be compared to gene expression in myotubes enforced to express truncated (transcriptionally inactive) Egr3. Egr3-deficient mice lack muscle spindles and have profound proprioceptive deficits. Egr3 is specifically expressed in a subset of developing primary myotubes after innervation by sensory axons. Spindle induction is dependent upon sensory/myotube contact which involves sensory axon produced neuregulin and ErbB receptor signaling in the myotube. Shortly after or during induction, Egr3 expression is upregulated and maintained in the nascent myotube/spindle as one of the earliest molecular events know to occur during spindle morphogenesis. We hypothesize that Egr3 mediated transcription is critical for engaging gene programs specific to and essential for, muscle spindle formation. Moreover, Egr3 may be involved in fate specification of myotubes that develop into biochemically and physiologically distinct intrafusal muscle fibers within spindles. To date, the target genes regulated by Egr3 during spindle morphogenesis have not been characterized. Myoblasts from wild type newborn mice will be isolated and purified. Myoblasts will be plated on collagen coated plates and differentiated in vitro for 7 days. During in vitro differentiation, myoblasts fuse to form multinucleated myotubes that exhibit contractile properties. Egr3 is not expressed in myotubes in vitro, which is consistent with their similarity to extrafusal muscle fibers that also do not express Egr3 in vivo. Only intrafusal fibers of muscle spindles express high levels of Egr3 in this muscle fiber context. Adenoviruses that express full length Egr3 (Egr3wt; transcriptionally active) and truncated Egr3 (Egr3tr; transcriptionally inactive) have been generated and characterized in our laboratory. After 7 days of in vitro differentiation, primary myotubes will be infected with either Egr3wt or Egr3tr adenoviruses. 100% infection is routinely obtained which is confirmed by coexpression of enhanced green fluorescent protein (EGFP). Care will be taken to minimize viral induced toxicity of the myotubes after infection. Myotubes are maintained after infection for 24 hours, after which total RNA is extracted from the cell lysates. The two RNA samples will be used for microarray analysis to identify genes that are upregulated and downregulated by Egr3 in the myotube cellular context. We will repeat the infection, RNA isolation and microarray analysis three times to minimize identifying false positive differentially expressed genes. Differentially expressed genes will be confirmed using real-time PCR. Interesting differentially expressed genes will be examined by in situ hybridization to determine if they are specifically expressed in wild type spindles. Since the identified differentially expressed genes will represent both indirect and direct target genes, we will perform Chromatin Immunoprecipitation (ChIP) from Egr3wt infected myotubes and screen the ChIP DNA library by PCR to determine which gene promoters are directly bound by Egr3. Keywords: other
2004-11-24 | GSE1998 | GEO
Project description:FLAG-tagged EGR3 was overexpressed in the cell line SEM to investigate promotor binding of EGR3 in the t(4;11) cellular context.
2022-06-09 | GSE205652 | GEO
Project description:EGR3 expression is upregulated in human prostate cancer compared to normal prostate tissue and is associated with absence of relapse, while low EGR3 expression in tumors is predicitive of disease relapse (Pio et al., PLOS One 2013; 8(1):e54096). However the function of EGR3 in prostate cancer is unknown. Human prostate cancer cells M12 containing high levels of EGR3 were used for shRNA-mediated silencing of EGR3. Gene expression analysis of EGR3 knockdown cells reveals a role in inflammation and the existence of a crosstalk with the NFkB pathway.
2013-11-06 | GSE52108 | GEO
Project description:Chronic pain can be a debilitating condition, leading to profound changes in nearly every aspect of life. However, the reliance on opioids such as oxycodone for pain management is thought to initiate dependence and addiction liability. The neurobiological intersection at which opioids relieve pain and possibly transition to addiction is poorly understood. Using RNA sequencing pathway analysis in rats with complete Freund's adjuvant (CFA)-induced chronic inflammation, we found that the transcriptional signatures in the medial prefrontal cortex (mPFC; a brain region where pain and reward signals integrate) elicited by CFA in combination with oxycodone differed from those elicited by CFA or oxycodone alone. However, the expression of Egr3 was augmented in all animals receiving oxycodone. Furthermore, virus-mediated overexpression of EGR3 in the mPFC increased mechanical pain relief but not the affective aspect of pain in animals receiving oxycodone, whereas pharmacological inhibition of EGR3 via NFAT attenuated mechanical pain relief. Egr3 overexpression also increased the motivation to obtain oxycodone infusions in a progressive ratio test without altering the acquisition or maintenance of oxycodone self-administration. Taken together, these data suggest that EGR3 in the mPFC is at the intersection of nociceptive and addictive-like behaviors.
2023-05-18 | GSE232804 | GEO
Project description:Seeking to identify additional transcription factors required for cardiac valve formation, we determined and explored the transcriptional landscape of endocardial cells at the time when key morphogenetic events underlying valve development take place.
2024-02-13 | GSE242483 | GEO
Project description:The transcription factor Egr3 has been shown to have a cell autonomous role in sympathetic nervous system (SNS) development. We utilized microarray analysis to identify potential downstream target genes deregulated with loss of Egr3. Both conditions were in the null Bax background to prevent apoptosis and therefore mitigate identification of apoptosis related genes. Our analysis identified genes involved in biological processes that were expected such as SNS development and axonogenesis as well as those that were unexpected such as dendritogenesis and axon guidance. This led us to investigate whether Egr3 is important in these unexpected biological processes within sympathetic neurons.
2013-03-22 | GSE41290 | GEO
Project description:EGR3 expression is upregulated in human prostate cancer compared to normal prostate tissue and is associated with absence of relapse, while low EGR3 expression in tumors is predicitive of disease relapse (Pio et al., PLOS One 2013; 8(1):e54096). However the function of EGR3 in prostate cancer is unknown. Human prostate cancer cells M12 containing high levels of EGR3 were used for shRNA-mediated silencing of EGR3. Gene expression analysis of EGR3 knockdown cells reveals a role in inflammation and the existence of a crosstalk with the NFkB pathway. The M12 prostate cancer cell line is a tumorigenic derivative of the P69 SV40-T immortalized epithelial cells obtained through serial passages of P69 tumor xenografts in mice (Bae et al., Prostate 1998; 34:275-82). M12 cells were transfected with shRNA scramble plasmid (shSCR) or shEGR3 plasmid and selected with puromycin (1 μg/ml). Single-cell clones were isolated using standard methods. Stably transfected cells (shSCR-M12 and shEGR3-M12) were then maintained in growth medium supplemented with puromycin. Two separate clones (termed cl 2 and cl 3) were studied. Knockdown of EGR3 (50% efficacy on average) was stable over many cell culture passages. Biological duplicates of control cells (scramble shRNA) and of two separate clones of shEGR3 cells (clone 2 and clone 3) were used for the gene expression arrays (i.e. 6 samples).
2013-11-06 | E-GEOD-52108 | biostudies-arrayexpress