Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nascent RNA sequencing defines dynamic aryl hydrocarbon receptor signaling responses to wood smoke particles [ATAC-seq]

ABSTRACT: Nascent RNA sequencing defines dynamic aryl hydrocarbon receptor signaling responses to wood smoke particles [ATAC-seq]

PROVIDER: PRJNA704406 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13772342_1.fastq.gz	Fastqsanger.gz
	SRR13772342_2.fastq.gz	Fastqsanger.gz
	SRR13772343_1.fastq.gz	Fastqsanger.gz
	SRR13772343_2.fastq.gz	Fastqsanger.gz
	SRR13772344_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Nascent RNA sequencing defines dynamic aryl hydrocarbon receptor signaling responses to wood smoke particles

Project description:Nascent RNA sequencing defines dynamic aryl hydrocarbon receptor signaling responses to wood smoke particles

| PRJNA704405 | ENA

Nascent RNA sequencing defines dynamic aryl hydrocarbon receptor signaling responses to wood smoke particles [PRO-seq]

Project description:Transcriptional responses to wildfire smoke, an increasingly important cause of human morbidity, are poorly understood. Here, using a combination of precision nuclear run-on sequencing (PRO-seq) and the assay for transposase-accessible chromatin using sequencing (ATAC-seq), we identify rapid and dynamic changes in transcription and chromatin structure in Beas-2B airway epithelial cells after exposure to wood smoke particles (WSP). By comparing 30 and 120 minutes of WSP exposure, we defined three distinct temporal patterns of transcriptional induction and chromatin responses to WSP. Whereas transcription of canonical targets of the aryl hydrocarbon receptor (AHR), such as CYP1A1 and AHRR, was robustly increased after 30 minutes of WSP exposure, transcription of these genes and associated enhancers returned to near baseline at 120 minutes. ChIP-qPCR assays and AHR knockdown confirmed a role for AHR in regulating these transcriptional responses, and we applied bioinformatics approaches to identify novel AHR-regulated pathways and targets including the DNA methyltransferase, DNMT3L, and its interacting factor, SPOCD1. Our analysis also defined a role for NFkB as a primary transcriptional effector of WSP-induced changes in gene expression. The kinetics of AHR- and NFkB-regulated responses to WSP were distinguishable based on the timing of both transcriptional responses and chromatin remodeling, with induction of several cytokines implicated in maintaining the NFkB response. In aggregate, our data establish a direct and primary role for AHR in mediating airway epithelial responses to WSP and identify crosstalk between AHR and NFkB signaling in controlling pro-inflammatory gene expression.

2021-02-24 | GSE167371 | GEO

Nascent RNA sequencing defines dynamic aryl hydrocarbon receptor signaling responses to wood smoke particles [ATAC-seq]

2021-02-24 | GSE167370 | GEO

Nascent RNA sequencing defines dynamic aryl hydrocarbon receptor signaling responses to wood smoke particles [PRO-seq]

Project description:Nascent RNA sequencing defines dynamic aryl hydrocarbon receptor signaling responses to wood smoke particles [PRO-seq]

| PRJNA704407 | ENA

Nascent RNA sequencing defines dynamic aryl hydrocarbon receptor signaling responses to wood smoke particles

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-02-24 | GSE167372 | GEO

Deconvolution of multiplexed transcriptional responses to wood smoke particles defines rapid aryl hydrocarbon receptor signaling dynamics.

Project description: Not available

| S-EPMC8517214 | biostudies-literature

Functional Variant Discovery Identifies SPRY2 as a Genetic Mechanism Linking Wood Smoke with Asthma

Project description:Climate change is impacting human health through a historic rise in wildfire smoke across the United States and the world. Whereas the deleterious effects of wildfire smoke and associated air pollution on asthma outcomes are well-established epidemiologically, genetic risks and molecular mechanisms of how wildfire smoke affects asthma are unknown. This knowledge gap hinders the identification of high-risk individuals and the creation of targeted therapies or recommendations to protect these individuals. Here, we employ a genetic approach to identify common variant (minor allele frequency > 0.05) exposure-conditional genetic risk variants that localize with genomic responses to wood smoke particles (WSP), a model of wildfire smoke exposure, and associate with asthma in the Genetic Epidemiology Research on Aging (GERA) cohort. Our novel approach used nascent transcriptional signatures derived from WSP-exposed Beas-2B airway epithelial cells to reduce the genome sequence for discovery and allow a permutation-based statistical approach to identify 52 candidate SNPs. We applied biologic and bioinformatic filters to prioritize variants for direct testing of allele-dependent transcriptional regulatory function in plasmid reporters. The rs3861144 variant identified by this approach controls WSP responses of airway epithelial cells to SPRY2, which we showed is involved in mechanical injury repair in cell culture. Our results demonstrate that wildfire particulates contribute to asthma risk at the molecular level, and we have identified mechanistic targets and genetic variant candidates to apply for clinical risk prediction and development of targeted therapies for high-risk individuals.

2024-12-02 | GSE283113 | GEO

Wildfire smoke particulate matter induces ovarian hyperandrogenism via aryl hydrocarbon receptor activation III

Project description:Wildfire smoke particulate matter induces ovarian hyperandrogenism via aryl hydrocarbon receptor activation III

| PRJNA1405778 | ENA

Wildfire smoke particulate matter induces ovarian hyperandrogenism via aryl hydrocarbon receptor activation I

Project description:Wildfire smoke particulate matter induces ovarian hyperandrogenism via aryl hydrocarbon receptor activation I

| PRJNA1405765 | ENA

Wildfire smoke particulate matter induces ovarian hyperandrogenism via aryl hydrocarbon receptor activation II

Project description:Wildfire smoke particulate matter induces ovarian hyperandrogenism via aryl hydrocarbon receptor activation II

| PRJNA1405768 | ENA