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Status |
Public on Jun 04, 2020 |
Title |
E proteins orchestrate dynamic transcriptional cascades implicated in the suppression of the differentiation of group 2 innate lymphoid cells [ATAC-Seq] |
Organism |
Mus musculus |
Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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Summary |
Group 2 innate lymphoid cells (ILC2s) represent a subset of newly discovered immune cells that are involved in immune reactions against microbial pathogens, host allergic reactions as well as tissue repair. The basic helix-loop-helix transcription factors collectively called E proteins powerfully suppress the differentiation of ILC2s from bone marrow and thymic progenitors while promoting the development of B and T lymphocytes. How E proteins exert the suppression is not well understood. Here we investigated the underlying molecular mechanisms using inducible gain and loss of function approaches in ILC2s and their precursors, respectively. Cross-examination of RNA sequencing and ATAC sequencing data obtained at different time points reveals a set of genes which are likely direct targets of E proteins. Consequently, a widespread down-regulation of chromatin accessibility occurs at a later time point, possibly due to the activation of transcriptional repressor genes such as Cbfa2t3 and Jdp2. The large number of genes repressed by gain of E protein function leads to the down-regulation of a transcriptional network important for ILC2 differentiation.
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Overall design |
ATAC-seq was performed on thymic ILC2 cells isolated from Id1 transgenic mice, which were transduced with retroviruses expressing either GFP alone or together with an E47-ER fusion protein after stimulation with ILC2, IL-7, IL-25 and IL-33. Transduced cells were sorted for GFP and expanded in ILC2, IL-7, IL-25 and IL-33. The cells were then treated with 4-hydroxy-Tamoxifen for 4 or 16 hours before harvesting for DNA isolation.
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Contributor(s) |
Sun X, Peng V |
Citation(s) |
32817168 |
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Submission date |
Jun 03, 2020 |
Last update date |
Sep 04, 2020 |
Contact name |
Jonathan Wren |
E-mail(s) |
Jonathan-Wren@omrf.org
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Phone |
(405) 271-6989
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Organization name |
OMRF
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Department |
Genes & Human Disease Research Program
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Street address |
825 N.E. 13th Street
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City |
Oklahoma City |
State/province |
OK |
ZIP/Postal code |
73104 |
Country |
USA |
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Platforms (1) |
GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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Samples (8)
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This SubSeries is part of SuperSeries: |
GSE151739 |
E proteins orchestrate dynamic transcriptional cascades implicated in the suppression of the differentiation of group 2 innate lymphoid cells |
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Relations |
BioProject |
PRJNA637071 |
SRA |
SRP265834 |
Supplementary file |
Size |
Download |
File type/resource |
GSE151737_E47-3_16h_S1_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval.signal.bigwig |
674.9 Mb |
(ftp)(http) |
BIGWIG |
GSE151737_E47-3_4h_S5_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval.signal.bigwig |
790.5 Mb |
(ftp)(http) |
BIGWIG |
GSE151737_E47_16h_idr.conservative_peak.narrowPeak.gz |
2.3 Mb |
(ftp)(http) |
NARROWPEAK |
GSE151737_E47_4h_idr.conservative_peak.narrowPeak.gz |
2.8 Mb |
(ftp)(http) |
NARROWPEAK |
GSE151737_GFP-3_16h_S2_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval.signal.bigwig |
858.9 Mb |
(ftp)(http) |
BIGWIG |
GSE151737_GFP-3_4h_S6_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval.signal.bigwig |
875.7 Mb |
(ftp)(http) |
BIGWIG |
GSE151737_GFP_16h_idr.conservative_peak.narrowPeak.gz |
2.8 Mb |
(ftp)(http) |
NARROWPEAK |
GSE151737_GFP_4h_idr.conservative_peak.narrowPeak.gz |
2.4 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |