Postnatal expansion of the lymph node stromal cell pool towards reticular and CD34+ stromal cell subsets [ATAC-seq]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA721376 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17799616_1.fastq.gz | Fastqsanger.gz | |||
| SRR17799616_2.fastq.gz | Fastqsanger.gz | |||
| SRR17799617_1.fastq.gz | Fastqsanger.gz | |||
| SRR17799617_2.fastq.gz | Fastqsanger.gz | |||
| SRR17799618_1.fastq.gz | Fastqsanger.gz |
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Project description:Postnatal expansion of the lymph node stromal cell pool towards reticular and CD34+ stromal cell subsets
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Project description:Gut-draining mesenteric lymph nodes (mLN) provide the framework and microenvironment to shape intestinal adaptive immune responses. We previously delineated transcriptional signatures in LN stromal cells (SC), pointing to tissue-specific variability in composition and immuno-modulatory function of SCs. Here, we dissect the tissue-specific epigenomic DNA accessibility and CpG methylation landscape of LN non-endothelial SCs and identify a microbiota-independent core epigenomic signature of LN SCs. By combined analysis of transcription factor (TF) binding sites together with the gene expression profiles of non-endothelial SCs, we delineated TFs poising skin-draining peripheral LN (pLN) SCs for pro-inflammatory responses. Furthermore, using scRNA-seq, we dissected the developmental trajectory of mLN SCs derived from postnatal to aged mice, identifying two distinct putative progenitors, namely CD34+ SC and fibroblastic reticular stromal cell (FRC) progenitors, which both feed the rapid postnatal LN expansion. Finally, we identified Irf3 as a key differentiation TF inferred from the epigenomic signature of mLN SCs that is dynamically expressed along the differentiation trajectories of FRCs, and validated Irf3 as a regulator of Cxcl9+ FRC differentiation. Together, our data constitute a comprehensive transcriptional and epigenomic map of mLN development and dissect location-specific, microbiota-independent properties of mLN non-endothelial SCs. As such, our findings represent a valuable resource to identify core transcriptional regulators that impinge on the developing mLN early in life, thereby shaping long-lasting intestinal adaptive immune responses.
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