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Series GSE180071 Query DataSets for GSE180071
Status Public on Jul 12, 2022
Title seRNA PAM-1 interacts with Ddx5 to regulate skeletal muscle satellite cell activation and aging through trans regulation of Timp2 expression [PAM-1 ChIRP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary There is an absolute requirement of Pax7 for the normal function of MuSCs during regenerative myogenesis in skeletal muscle at any stage of life. Here using RNA-seq, H3K27ac and Pax7 ChIP-seq, we discover PAM-1 (Pax7 Associated Muscle lncRNA) that is enriched in activated skeletal muscle satellite cells (ASCs) 24 and 48 hours after activation. Knockdown of PAM-1 reduces proliferating Pax7+Myod+ ASCs number, while overexpression of PAM-1 increases ASCs number. Mechanistically, PAM-1 is located on ASCs and myoblast specific super-enhancer (SE), and we categorize it as seRNA. Through a series of multiomics analysis of PAM-1 interactome in myoblast including PAM-1-DNA interaction by ChIRP-seq, PAM-1 SE-DNA interaction by 4C-seq, PAM-1-protein interaction by mass spectrometry and ChIP-seq, we identify a novel class of transcriptional regulation that seRNA PAM-1 interacts with RNA binding protein Ddx5 and tethers PAM-1 SE to regulate inter-chromosomal targets Timp2. Altogether, our findings identify PAM-1 is driven by Pax7 in ASC and myoblast to regulate myogenic activation through binding with Ddx5 and targeting Timp2.
Overall design ChIRP-seq on PAM-1 seRNA
Contributor(s) So KK, Huang Y, Sun H, Wang H
Citation(s) 35851988
Submission date Jul 14, 2021
Last update date Aug 24, 2022
Contact name Yile Huang
Phone 56289467
Organization name The Chinese University of HongKong
Department Chemical Pathology
Street address Room 503, Li Ka Shing Health and Science Buiding, Prince of Wales Hospital, Sha Tin
City Sha Tin
State/province Hong Kong
ZIP/Postal code 999077
Country China
Platforms (1)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (3)
GSM5452258 PAM-1 ChIRP-seq odd
GSM5452259 PAM-1 ChIRP-seq even
GSM5452260 PAM-1 ChIRP-seq input
This SubSeries is part of SuperSeries:
GSE180073 seRNA PAM-1 interacts with Ddx5 to regulate skeletal muscle satellite cell activation and aging through trans regulation of Timp2 expression
BioProject PRJNA746467
SRA SRP328286

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Supplementary file Size Download File type/resource
GSE180071_RAW.tar 30.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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