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Changes in nascent transcripts upon glucocorticoid stimulation in macrophages

ABSTRACT: Changes in nascent transcripts upon glucocorticoid stimulation in macrophages

PROVIDER: PRJNA774825 | ENA |

REPOSITORIES: ENA

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Changes in nascent transcripts upon glucocorticoid stimulation in macrophages

Project description:Glucocorticoids are widely prescribed anti-inflammatory drugs with tissue-specific effects. Beneficial anti-inflammatory effects are caused in cells of the immune system whereas metabolic adverse effects of glucocorticoid therapy are seen in metabolic tissues such as liver. The glucocorticoid receptor (GR), a nuclear receptor targeted by glucocorticoids, bind its DNA response elements upon ligand exposure in a tissue-specific manner. Tissue-specific GR binding patterns depend on the access of its binding sites, which determines the tissue-specific glucocorticoid response. Here, we investigated this response by nascent RNAseq in murine bone marrow-derived macrophages (BMDMs) after stimulation with lipopolysaccharide (LPS) and dexamethasone (Dex). After labelling newly synthesized transcripts with 4-thiouracile (4sU), we identified macrophage-specific non-coding transcripts expressed at intergenic GR binding sites. Those transcripts are regulated by the GR and correlate with its anti-inflammatory function in macrophages. Those findings add another layer to the mechanisms underpinning GR's tissue-specific gene regulation and represent potential drug targets in anti-inflammatory therapy and/or management of adverse effects in glucocorticoid therapy.

2021-12-31 | GSE186629 | GEO

Nascent transcription upon interferon-α2 stimulation on human and rhesus macaque lymphoblastoid cell lines

Project description:Nascent transcription upon interferon-α2 stimulation on human and rhesus macaque lymphoblastoid cell lines

| PRJNA884834 | ENA

Nascent transcription upon interferon-α2 stimulation on human and rhesus macaque lymphoblastoid cell lines

Project description:Changes in gene transcription regulation are necessary for species to respond to changes in their environment. In particular, host-pathogen dynamics have been observed to entail rapid evolution of genes involved in the host innate immune system. Cytokines such as type I interferon alpha and beta trigger an antiviral cellular state controlled by members of the transcription factor families STAT and IRF. However, it remains poorly understood how gene transcription regulation has been rewired through evolutionary time to achieve species-specific interferon-controlled changes in gene expression. We generated nascent transcription (PRO-seq) datasets to determine the initial transcriptional response on lymphoblastoid cell lines derived from homo sapiens and macaca mulatta upon stimulation with interferon alpha2 to assess species-specific changes in gene regulation.

2022-10-02 | GSE214304 | GEO

Nascent HIV reverse transcripts

Project description:3' end mapping of nascent HIV-1 reverse transcripts during infection of CEM-SS T cells in the presence of APOBEC3G

| PRJEB22170 | ENA

Widespread targeting of nascent transcripts by RsmA in Pseudomonas aeruginosa

Project description:In the opportunistic pathogen Pseudomonas aeruginosa RsmA is an RNA-binding protein that plays critical roles in the control of virulence, interbacterial interactions and biofilm formation. Although RsmA is thought to exert its regulatory effects by binding full-length transcripts, the extent to which RsmA binds nascent transcripts has not been addressed. Moreover, which transcripts are direct targets of this key post-transcriptional regulator is largely unknown. Using chromatin immunoprecipitation coupled with high-throughput DNA sequencing, with cells grown in the presence and absence of the RNA polymerase inhibitor rifampicin, we identify hundreds of nascent transcripts that RsmA associates with in P. aeruginosa. We also find that the RNA chaperone Hfq targets a subset of the RsmA-associated nascent transcripts and that the two RNA-binding proteins can exert regulatory effects on common targets. Our findings establish that RsmA associates with many transcripts as they are being synthesized in P. aeruginosa, identify the direct targets of RsmA, and suggest that RsmA and Hfq may act in a combinatorial fashion on certain target transcripts. More broadly, our data suggest that the binding of post-transcriptional regulators to nascent transcripts may be commonplace in bacteria where distinct regulators can function alone or in concert to achieve control over the translation of transcripts as soon as they emerge from RNA polymerase.

2020-04-20 | GSE138338 | GEO

Widespread targeting of nascent transcripts by RsmA in Pseudomonas aeruginosa

Project description:Widespread targeting of nascent transcripts by RsmA in Pseudomonas aeruginosa

| PRJNA575528 | ENA

Chronic Restraint Stress Upregulates Erythropoiesis Through Glucocorticoid Stimulation

Project description:In response to elevated glucocorticoid levels, erythroid progenitors rapidly expand to produce large numbers of young erythrocytes. Previous work demonstrates hematopoietic changes in rodents exposed to various physical and psychological stressors, however, the effects of chronic psychological stress on erythropoiesis has not be delineated. We employed laboratory, clinical and genomic analyses of a murine model of chronic restraint stress (RST) to examine the influence of psychological stress on erythropoiesis. Mice exposed to RST demonstrated markers of early erythroid expansion involving the glucocorticoid receptor. In addition, these RST-exposed mice had increased numbers of circulating reticulocytes and increased erythropoiesis in primary and secondary erythroid tissues. Mice also showed increases in erythroid progenitor populations and elevated expression of the erythroid transcription factor KLF1 in these cells. Together this work describes some of the first evidence of psychological stress affecting erythroid homeostasis through glucocorticoid stimulation and begins to define the transcription factor pathway involved.

2016-06-07 | GSE47725 | GEO

POINT technology illuminates the processing of polymerase-associated intact nascent transcripts

Project description:POINT technology illuminates the processing of polymerase-associated intact nascent transcripts

| PRJNA668366 | ENA

Glucocorticoid stimulation induces regionalized gene responses within topologically associating domains

Project description:Glucocorticoid stimulation induces regionalized gene responses within topologically associating domains

| PRJNA940425 | ENA

Act1 modulates mRNA metabolism upon IL-17 stimulation

Project description:Act1 modulates mRNA metabolism upon IL-17 stimulation

| PRJNA1099569 | ENA