The long non-coding RNA Dreg1 is required for optimal ILC2 development
- The Walter and Eliza Hall Institute of Medical Research, Australia
- Department of Medical Biology, The University of Melbourne, Australia
- Olivia Newton-John Cancer Research Institute, Australia
- La Trobe University, Australia
- Peter MacCallum Cancer Centre, Australia
Figures
Figure 1 with 1 supplement
Dreg1 deletion results in a specific reduction in peripheral ILC2 cells.
(A) Deletion of Dreg1 in mice using CRISPR-Cas9. (B–E) Representative FACS plots and % of CD45+, TCRβ-, CD19-, CD11c- NK, and ILC populations from the visceral adipose tissue (VAT), small intestinal lamina propria (SI LP), and lung from wild type (WT) or Dreg1-/- mice. Shown is one representative experiment of two with n=4 mice/group. (F) SI LP from mixed bone marrow chimeras were examined for the proportion of ILC2 from the wildtype (CD45.1) or Dreg1-deficient (CD45.2) compartment. Data is pooled from three independent experiments. Mean and SEM together with individual data points are shown. Data were statistically analysed by Student’s t-test.
Figure 1—figure supplement 1
Dreg1 deletion does not affect T or NK cells.
(A–C) Representative FACS plots with quantification (right) showing expression of (A) CD8α and CD4 in splenic T cells. (B) CD44 and CD62L in splenic CD8+ T cells (C) CD44 and CD62L in splenic CD4+ T cells. (D) Quantification of splenic γδ T cells and NK cells. Shown is one representative experiment of two with n=3 mice/group. Mixed bone marrow chimeras were examined for the proportion of SI LP B cells (E), VAT ILC2 or B cells (F) or Lung ILC2 or B cells (G) from the wildtype (CD45.1) or Dreg1-deficient (CD45.2) compartment. Data is pooled from three independent experiments. Mean and SEM together with individual data points are shown. Data were statistically analysed by Student’s t-test.
Figure 2 with 1 supplement
Dreg1 deletion results in a bottleneck in ILC development and a reduction in ILC2P in the bone marrow.
(A) Boxplots showing expression of Gata3 and Dreg1 from RNA-Seq (GSE77695). (B–G) Quantification of ILC progenitor subsets in the bone marrow with percentages (upper) and total numbers (below). (H) Mean fluorescence intensity (MFI) of Gata3 measured on CHILP, ILCP, and ILC2P. Shown is one representative experiment of two with n=3–4 mice/group. Mean and SEM together with individual data points are shown. Data were statistically analysed by Student’s t-test.
Figure 2—figure supplement 1
Gating of ILC progenitors in bone marrow.
(A) Flow cytometric analysis of bone marrow cells was used to quantify the changes between wild type and Dreg1-deficient haematopoietic and ILC progenitors in Figure 2. Viable, lineage negative, CD45.2+ bone marrow cells were gated by the expression of cell surface markers into the delineated progenitor populations, and this was used to quantify their proportions and numbers.
Figure 3
Dreg1 locus is dynamically regulated in a Tcf1-dependent manner during ILC2 development.
(A) Chromatin accessibility around Dreg1 in ILC progenitors (GSE169542). (B) Motifs enriched in accessible regions around Dreg1. (C) Tcf1 binding around Dreg1 locus in EILP (GSE128483). (D) Histone marks around Dreg1 at different stages of ILC development and in Tcf7-/- EILP (GSE142468). (E) Gata3 and Dreg1 expression quantified from RNA-Seq data in ILC progenitors and Tcf7-/- EILP (GSE113767).
Figure 4
A syntenic region in humans represents a GATA3 enhancer element with a transcriptional profile akin to murine Dreg1.
(A) GATA3 and DREG1.1 and DREG1.2 expression quantified from RNA-Seq data in ILC and T helper populations isolated from healthy human blood (PRJEB35186). (B) Alignment of Functional Sequence 23 (FS23) that overlaps the syntenic region revealed as regulating GATA3 expression in a CRISPR deletion screen of human TH2 cells (Chen et al., 2023). (C) Chromatin accessibility around FS23 guides from the CRISPR deletion screen (Chen et al., 2023) (GSE231999).
Additional files
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MDAR checklist
- https://cdn.elifesciences.org/articles/109408/elife-109408-mdarchecklist1-v1.docx
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Source data 1
Source data associated with flow cytometry analyses in Figures 1 and 2.
- https://cdn.elifesciences.org/articles/109408/elife-109408-data1-v1.xlsx
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The long non-coding RNA Dreg1 is required for optimal ILC2 development
eLife 15:RP109408.
https://doi.org/10.7554/eLife.109408.3
