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Series GSE167371 Query DataSets for GSE167371
Status Public on Feb 24, 2021
Title Nascent RNA sequencing defines dynamic aryl hydrocarbon receptor signaling responses to wood smoke particles [PRO-seq]
Organism Homo sapiens
Experiment type Other
Expression profiling by high throughput sequencing
Summary 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.
 
Overall design Deep sequencing of nascent transcripts was performed using Precision Run-on sequencing (PRO-seq) in BEAS-2B cells airway epithelial cells following exposure to WSP. All samples were sequenced in duplicate.
 
Contributor(s) Gupta A, Sasse SK, Gruca MA, Sanford L, Dowell RD, Gerber AN
Citation(s)
  • Gupta A, Sasse SK, Gruca MA, Sanford L et al. Deconvolution of multiplexed transcriptional responses to wood smoke particles defines rapid aryl hydrocarbon receptor signaling dynamics. J Biol Chem 2021 Oct;297(4):101147. PMID: 34520756
Submission date Feb 23, 2021
Last update date Oct 27, 2021
Contact name Arnav Gupta
E-mail(s) arnav.gupta@cuanschutz.edu, arnavgupta06@gmail.com
Organization name National Jewish Health
Department Pulmonary and Critical Care
Street address 1400 Jackson St. K720
City Denver
State/province CO
ZIP/Postal code 80206
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (6)
GSM5103029 Beas-2B_veh-1_PRO-seq
GSM5103030 Beas-2B_veh-2_PRO-seq
GSM5103031 Beas-2B_30WSP-1_PRO-seq
This SubSeries is part of SuperSeries:
GSE167372 Nascent RNA sequencing defines dynamic aryl hydrocarbon receptor signaling responses to wood smoke particles
Relations
BioProject PRJNA704407
SRA SRP307784

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE167371_RAW.tar 2.8 Gb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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