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Series GSE65796 Query DataSets for GSE65796
Status Public on Feb 11, 2015
Title Multiple Arkadia/RNF111 structures coordinate its Polycomb body association and transcriptional control
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The RING domain protein Arkadia/RNF111 is a ubiquitin ligase in the transforming growth factor beta (TGFβ) pathway. We previously identified Arkadia as a small ubiquitin-like modifier (SUMO)-binding protein with clustered SUMO-interacting motifs (SIMs) that together form a SUMO-binding domain (SBD). However, precisely how SUMO interaction contributes to the function of Arkadia was not resolved. Through analytical molecular and cell biology, we found that the SIMs share redundant function with Arkadia's M domain, a region distinguishing Arkadia from its paralogs ARKL1/ARKL2 and the prototypical SUMO-targeted ubiquitin ligase (STUbL) RNF4. The SIMs and M domain together promote both Arkadia's colocalization with CBX4/Pc2, a component of Polycomb bodies, and the activation of a TGFbeta pathway transcription reporter. Transcriptome profiling through RNA sequencing showed that Arkadia can both promote and inhibit gene expression, indicating that Arkadia's activity in transcriptional control may depend on the epigenetic context, defined by Polycomb repressive complexes and DNA methylation [Sun, Liu, and Hunter (2014) Mol Cell Biol 34(16):2981-2995].
Overall design To determine the role of Arkadia in TGFβ signaling at the transcriptome level, the profiles of TGFβ-stimulated gene expression were examined in Ark+/+ (Ark_WT), Ark-/- (Ark_null), and Arkadia (WT and sim mutant)-reconstituted Ark-/- MEFs. RNA sequencing was carried out using poly(A)-enriched RNA samples from unstimulated cells and cells treated with TGFβ for 1h, 4h, or 16h as indicated. Two batches of sequencing data for a total of 16 independent samples were submitted.
Contributor(s) Sun H, Hunter T
Citation(s) 24912682
Submission date Feb 10, 2015
Last update date May 15, 2019
Contact name Huaiyu Sun
Organization name Salk Institute for Biological Studies
Department Molecular and Cell Biology Laboratory
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (16)
GSM1606458 Ark_WT_0hr [HS_A1]
GSM1606459 Ark_WT_TGFb_1hr [HS_A2]
GSM1606460 Ark_WT_TGFb_ 4hr [HS_A3]
BioProject PRJNA275102
SRA SRP053423

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Supplementary file Size Download File type/resource
GSE65796_HS_RNAseq_FPKM_merged.txt.gz 1.0 Mb (ftp)(http) TXT
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