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Series GSE266345 Query DataSets for GSE266345
Status Public on Sep 27, 2024
Title Remodeling of Il4-Il13-Il5 locus underlies selective gene expression (fHiC)
Organism Mus musculus
Experiment type Other
Summary The type 2 cytokines, interleukin (IL)-4, IL-5 and IL-13 reside within a multi-gene cluster in mammals. These cytokines represent the hallmark of type 2 immune responses controlling parasites and promoting tissue repair, as well as causing allergic diseases. Both innate and adaptive lymphocytes secrete type 2 cytokines with discordant production spectra. We took a holistic structural and functional view of the type 2 cytokine locus before and after activation, comparing innate (ILC2) and adaptive (Th2) lymphocytes to understand mechanisms underlying their distinctive programs. Rapid induction of IL-5 dominates in ILC2, whereas IL-4 does so in Th2 cells. Using high-resolution chromatin conformation capture we found that global cellular chromatin architecture remained constant, whereas the type 2 cytokine locus rapidly remodeled. In ILC2, Il13 and Il5 loci were aligned in proximity whereas Il4 locus was insulated. In Th2 cells, Il4 and Il13 positioned in proximity while the Il5 locus remained distal. Select REs were individually deleted in mice to confirm cell-type specific and activation-dependent roles in type 2 responses in vivo. Thus, contrary to the premise that chromatin architecture plays a minimal role in steady-state gene induction, signal-dependent remodeling of 3D configuration underlies the discordant cytokine outputs in ILC2s versus Th2 cells.
 
Overall design Focused HiC for mouse ILC2s
 
Contributor(s) Nagashima H, Jiang K
Citation(s) 39567762
Submission date May 01, 2024
Last update date Dec 06, 2024
Contact name Hiroyuki Nagashima
E-mail(s) hiroyuki.nagashima@nih.gov
Phone 3013383729
Organization name NIH
Street address 10 Center Dr, Room 13C120
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (20)
GSM8245385 HN_fHiC_001_Nostim_1h_WT_ILC2_rep1
GSM8245386 HN_fHiC_002_Nostim_1h_WT_ILC2_rep2
GSM8245387 HN_fHiC_003_Nostim_1h_5HSII_ILC2_rep1
This SubSeries is part of SuperSeries:
GSE266349 Remodeling of Il4-Il13-Il5 locus underlies selective gene expression
Relations
BioProject PRJNA1106802

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
GSE266345_RAW.tar 6.3 Gb (http)(custom) TAR (of HIC)
SRA Run SelectorHelp
Raw data are available in SRA

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