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Series GSE211023 Query DataSets for GSE211023
Status Public on Aug 08, 2023
Title Multi-scale epigenomic priming of inflammatory genes enables rapid recall in human memory T helper cells [ChIP-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Memory T cells provide long-lasting defense responses through their ability to rapidly reactivate. How memory T cells efficiently ‘recall’ an inflammatory transcriptional program remains unclear. Here, we show that primary human CD4+ memory T helper (Th) cells carry three distinct activation-inducible recall gene modules that drive metabolic adaptation, T cell activation and inflammatory cytokine production. Enhancer elements controlling recall genes were epigenetically primed through the local maintenance of transcription-permissive chromatin in resting memory Th cells. At the three-dimensional level, recall genes clustered in transcriptionally permissive subnuclear compartments and resided in topologically associating domains (‘memory TADs’), in which activation-associated promoter-enhancer interactions were pre-formed. This primed epigenomic landscape was exploited by AP-1 transcription factors - including MAF - to promote rapid transcriptional activation. Finally, recall genes and their enhancers were linked to memory Th cell dysfunction in chronic inflammatory disease. Together, our results implicate multi-scale epigenomic priming - comprising a specialized three-dimensional chromatin organization - as a key mechanism underlying immunological memory.
 
Overall design ChIP-Seq (n=2-3 biological replicates, independent donors) was performed on primary human naive or memory T helper cells.
 
Contributor(s) van Schoonhoven A, Stadhouders R
Citation(s) 37418545
Submission date Aug 11, 2022
Last update date Aug 09, 2023
Contact name Ralph Stadhouders
E-mail(s) stadhoudersralph@gmail.com
Organization name Erasmus Medical Center
Department Pulmonary Medicine
Street address Dr. Molewaterplein 50
City Rotterdam
ZIP/Postal code 3015 GE
Country Netherlands
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (11)
GSM6447499 H3K4me2 naive CD4+ T cell, resting (rep1)
GSM6447500 H3K4me2 naive CD4+ T cell, resting (rep2)
GSM6447501 H3K4me2 naive CD4+ T cell, resting (rep3)
This SubSeries is part of SuperSeries:
GSE211389 Multi-scale epigenomic priming of inflammatory genes enables rapid recall in human memory T helper cells
Relations
BioProject PRJNA868704

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
GSE211023_RAW.tar 855.6 Mb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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