Dataset Information

Phosphoproteomics of C2C12 differentiation

ABSTRACT: Phosphoproteomic analysis of myogenesis in C2C12 myoblasts differentiating into myotubes. Four time points were analysed (0min, 30min, 24h and 5d) with four biological replicates.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Skeletal Muscle Myoblast

SUBMITTER: Benjamin Parker

LAB HEAD: Benjamin Parker

PROVIDER: PXD023413 | Pride | 2024-01-26

REPOSITORIES: Pride

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Publications

SnapKin: a snapshot deep learning ensemble for kinase-substrate prediction from phosphoproteomics data.

Xiao Di D Lin Michael M Liu Chunlei C Geddes Thomas A TA Burchfield James G JG Parker Benjamin L BL Humphrey Sean J SJ Yang Pengyi P

NAR genomics and bioinformatics 20231106 4

A major challenge in mass spectrometry-based phosphoproteomics lies in identifying the substrates of kinases, as currently only a small fraction of substrates identified can be confidently linked with a known kinase. Machine learning techniques are promising approaches for leveraging large-scale phosphoproteomics data to computationally predict substrates of kinases. However, the small number of experimentally validated kinase substrates (true positive) and the high data noise in many phosphopro ...[more]

PMID: 37954574

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Project description:In skeletal muscle differentiation, muscle-specific genes are regulated by two groups of transcription factors, the MyoD and MEF2 families, which work together to drive the differentiation process. Here we show that ERK5 regulates muscle cell fusion through Klf transcription factors. The inhibition of ERK5 activity suppresses muscle cell fusion with minimal effects on the expression of MyoD, MEF2, and their target genes. Promoter analysis coupled to microarray assay reveals that Klf-binding motifs are highly enriched in the promoter regions of ERK5-dependent upregulated genes. Remarkably, Klf2 and Klf4 expression are also upregulated during differentiation in an ERK5-dependent manner, and knockdown of Klf2 or Klf4 specifically suppresses muscle cell fusion. Moreover, we show that the Sp1 transcription factor links ERK5 to Klf2/4, and that nephronectin, a Klf transcriptional target, is involved in muscle cell fusion. Therefore, an ERK5/Sp1/Klf module plays a key role in the fusion process during skeletal muscle differentiation. To identify those genes whose expression levels are regulated by the ERK5 pathway in differentiating C2C12 cells, we performed genome-wide analysis by using Affymetrix GeneChip oligonucleotide microarrays. We performed two independent experiments. For each experiment, we used five samples: cells in growth medium (0 day), lacZ-infected cells at two time points (2.5 days and 4.5 days of differentiation) and dnMEK5-infected cells at two time points (2.5 days and 4.5 days of differentiation). Each virus was infected at 1 day of differentiation. Total RNA was prepared using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. The total RNA of each condition was obtained from two independent experiments. Synthesis of cDNA in vitro transcription and biotin labeling cRNA, and hybridization to the Mouse Genome 430 2.0 array (Affymetrix) were performed according to Affymetrix protocols. Hybridized arrays were scanned using an Affymetrix GeneChip Scanner. Scanned Chip images were analyzed with GeneChip operating Software v.1.4 (GCOS) and GeneSpring GX 11.0.2. (Agilent technologies).

Dataset Information

Phosphoproteomics of C2C12 differentiation

Publications

SnapKin: a snapshot deep learning ensemble for kinase-substrate prediction from phosphoproteomics data.

Similar Datasets

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