GSE157259
GSE GEODDX5 RNA interactome in cultured T cells
Relations
Summary
RAR-related orphan receptor gamma (ROR t)-expressing regulatory T (ROR t+ Treg) cells play pivotal roles in preventing T cell hyperactivation and maintaining tissue homeostasis, in part, by secreting the anti-inflammation cytokine interleukin 10 (IL-10). Here, we report that Hypoxia Induced Factor 1a (HIF1alpha) is the master transcription factor for *Il10* in ROR t+ Tregs. Interestingly, this critical anti-inflammatory pathway is negatively regulated by an RNA-binding protein DEAD box helicase 5 (DDX5). As a transcriptional corepressor, DDX5 restricts the expression of HIF1 and its downstream target gene *Il10* in ROR t+ Tregs. T cell specific *Ddx5* knockout (DDX5 T) mice have augmented ROR t+ Treg suppressor activities and are better protected from intestinal inflammation. Genetic ablation or pharmacologic inhibition of HIF1a restores enteropathy susceptibility in DDX5 T mice. The DDX5-HIF1 -IL-10 pathway is conserved in mice and humans. These findings reveal potential therapeutic targets for intestinal inflammatory diseases.
Overall Design
Primary cultured Th17 from two 8-10 weeks old wild-type (C57BL/6) female mice were subjected to UV- mediated crosslinking, lysis, and treatment with RNases, followed by immunoprecipitation (IP) of the DDX5-containing RNA complexes.
Analysis (22 steps)
View Data Processing- Sequenced reads were removed of inline barcodes and reformatted to include randomers in read headers with eclipdemux (v0.0.1).
- Args: --length 10
- Reads were then trimmed with cutadapt (1.9.1).
- Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -g g_adapters.fasta -A A_adapters.fasta -a a_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
- Reads were then trimmed once more with cutadapt (1.9.1) to remove double-ligation events.
- Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -A A_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
- Trimmed reads were then mapped with STAR (2.4.0i) against a mouse-specific repeat element database (RepBase 18.05).
- Args: --runThreadN 16 \ --genomeDir mouse_repbase \ --readFilesIn path/to/read1 path/to/read2 \ --outFileNamePrefix out_prefix \ --outReadsUnmapped Fastx \ --outSAMtype BAM Unsorted \ --outSAMattributes All \ --outSAMunmapped Within \ --outSAMattrRGline ID:foo \ --outFilterType BySJout \ --outFilterMultimapNmax 30 \ --outFilterMultimapScoreRange 1 \ --outFilterScoreMin 10 \ --alignEndsType EndToEnd
Supplementary Files (3)
GEO Samples (4)
Dataset Citations (1)
SRA Experiments (4) and Runs (4)
Total: 3788 MBSample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR12563740 | 32544916 | 3254491600 | 1183.17 | COLLAB18_DDX5-R1-IP_S117_L008_R1_001.fastq.gz, COLLAB18_DDX5-R1-IP_S1… | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR12563741 | 24535532 | 2453553200 | 901.68 | COLLAB16_DDX5-R1-input_S115_L008_R1_001.fastq.gz, COLLAB16_DDX5-R1-in… | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR12563742 | 24736443 | 2473644300 | 912.68 | COLLAB19_DDX5-R2-IP_S118_L008_R1_001.fastq.gz, COLLAB19_DDX5-R2-IP_S1… | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR12563743 | 21598952 | 2159895200 | 790.69 | COLLAB17_DDX5-R2-input_S116_L008_R1_001.fastq.gz, COLLAB17_DDX5-R2-in… | SRA |
Linked Publications (2)
Data Files (4)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | COLLAB16_DDX5-R1-input_S115_L008_R1_001.fastq.gz | RIP-Seq | 901.7 MB | link | |||
| — | COLLAB17_DDX5-R2-input_S116_L008_R1_001.fastq.gz | RIP-Seq | 790.7 MB | link | |||
| — | COLLAB18_DDX5-R1-IP_S117_L008_R1_001.fastq.gz | RIP-Seq | 1.2 GB | link | |||
| — | COLLAB19_DDX5-R2-IP_S118_L008_R1_001.fastq.gz | RIP-Seq | 912.7 MB | link |