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A novel ERK substrate regulates wide varieries of IEGs

ABSTRACT: A novel ERK substrate regulates wide varieries of IEGs

PROVIDER: PRJNA703962 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13763155.fastq.gz	Fastqsanger.gz
	SRR13763156.fastq.gz	Fastqsanger.gz
	SRR13763157.fastq.gz	Fastqsanger.gz
	SRR13763158.fastq.gz	Fastqsanger.gz
	SRR13763159.fastq.gz	Fastqsanger.gz

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A novel ERK substrate regulates wide varieries of IEGs

Project description:The ERK pathway induces cell proliferation in response to growth factor stimulation. Although ERK controls various transcription factors in the nucleus, gene regulation mechanisms underlying the rapid IEG inductions were not fully elucidated. Here we report that ERK phosphorylates an unique novel substrate. We found that ERK facilitates rapid transcription of IEGs through the phosphorylation of the substrate.

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Nono, a novel bivalent domain factor, regulates Erk signaling and mouse embryonic stem cell pluripotency [ChIP-Seq]

Project description:Here we report that NONO, a nuclear para-speckle component, instead functions as a chromatin regulator in mESCs acting in the ERK signaling pathway to regulate the balance between ground state versus mESCs primed for differentiation. NONO loss increases a \u201cground-like\u201d population of mESCs favoring self-renewal and more resist to differentiation, partially mimicking the effects of 2i. Mechanistically, NONO and ERK mainly co-binds a subset of development related, bivalent genes. Importantly, NONO and ERK reciprocally regulate one another, i.e. NONO regulates ERK activation while ERK controls NONO chromatin association, forming a self-reinforcing feedback loop. Our findings thus reveal a cell intrinsic mechanism involving NONO and ERK, which impact the balance between self-renewal and differentiation, respectively.

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Nono, a novel bivalent domain factor, regulates Erk signaling and mouse embryonic stem cell pluripotency

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Project description:Dcp1a, a novel Mek substrate, regulates the self-renewal and differentiation of mouse embryonic stem cells

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The ERK-dependent proteome in KRAS mutant pancreatic cancer

Project description:Mutational activation of the KRAS oncogene is a major genetic driver of pancreatic ductal adenocarcinoma (PDAC) growth. KRAS-dependent PDAC growth is mediated primarily through persistent activation of the RAF-MEK-ERK mitogen-activated protein kinase (MAPK) cascade, one of the most extensively studied cancer signaling networks. While substrates of RAF and MEK kinases are highly restricted, ERK1/2 has been attributed to over 1,000 substrates. In this study, we used the highly selective ERK1/2 inhibitor, SCH772984, and proteomic and phosphoproteomic analyses to extend the repertoire of ERK-dependent phosphosites and phosphoproteins in PDAC. We validated the specificity of SCH772984 in our cell lines using multiplexed inhibitor beads coupled with mass spectrometry (MIB/MS). We then performed phosphoproteomics and global proteomics in a panel of PDAC cell lines and identified 5,117 ERK-dependent phosphosites on 2,252 proteins, of which 88% and 67%, respectively, were not previously associated with ERK. We then utilized our recently annotated serine/threonine kinome motif database to dissect the phosphoproteome and reveal an expansive ERK-regulated kinase network. We found that ERK- and immediate downstream kinase RSK-substrate motifs predominated after one hour of ERK inhibition, whereas cell cycle regulatory cyclin-dependent kinase motifs predominated by 24 h, reflecting a highly dynamic ERK-dependent phosphoproteome. We find compensatory activation of HIPK, CLK, PKN, PAK, and DYRK family kinases. Finally, using the genome-wide CRISPR-Cas9 dataset in the Cancer Dependency Map portal (DepMap), we determined that approximately 18% of ERK dependent phosphoproteins are essential for pancreatic cancer growth, and these are enriched in nuclear proteins. Together, our findings provide a system-wide profile of the mechanistic basis for ERK-driven pancreatic cancer growth.

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The ERK-dependent phosphoproteome in KRAS mutant pancreatic cancer

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Project description:Dcp1a, a novel Mek substrate, regulates the self-renewal and differentiation of mouse embryonic stem cells [RNA-seq]

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Dcp1a, a novel Mek substrate, regulates the self-renewal and differentiation of mouse embryonic stem cells [Ribo-seq]

Project description:Dcp1a, a novel Mek substrate, regulates the self-renewal and differentiation of mouse embryonic stem cells [Ribo-seq]

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Dcp1a, a novel Mek substrate, regulates the self-renewal and differentiation of mouse embryonic stem cells

Project description:Mek inhibitor is widely applied to maintain pluripotency, while prolonged Mek inhibition compromises the developmental potential of mouse embryonic stem cells (ESCs). To better understand the mechanism of Mek in pluripotency maintenance, we first demonstrated that Mek regulates gene expression at post-transcriptional steps. Consistently, many of the 66 Mek substrates identified by quantitative phosphoproteomic analysis are involved in RNA processing. We further confirmed that S563 of Dcp1a, a mRNA decapping cofactor and P-body component, is phosphorylated by Mek1. Dcp1a, as well as two other P-body components Edc4 and Dcp2, are required for the proper self-renewal and differentiation of ESCs, indicating the role of P-bodies in ESCs. Dephosphorylation of Dcp1a S563 facilitates both self-renewal and differentiation of ESCs, through promoting P-body formation and RNA storage. In summary, our study identified 66 Mek substrates supporting the Erk-independent function of Mek, and revealed that Dcp1a, phosphorylated by Mek, regulates ESC self-renewal and differentiation, through modulating P-body formation.

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Nono, a novel bivalent domain factor, regulates Erk signaling and mouse embryonic stem cell pluripotency [RNA-Seq]

Project description:Here we report that Nono instead functions as a chromatin regulator cooperating with Erk to regulate mESC pluripotency. We demonstrate that Nono loss leads to robust self-renewing mESCs with enhanced expression of Nanog and Klf4, epigenome and transcriptome re-patterning to a “ground-like state” with global reduction of H3K27me3 and DNA methylation resembling the Erk inhibitor PD03 treated mESCs and 2i (both GSK and Erk kinase inhibitors)-induced “ground state”. Mechanistically, Nono and Erk co-bind at a subset of development-related, bivalent genes. Ablation of Nono compromises Erk activation and RNA polymerase II C-terminal Domain serine 5 phosphorylation, and while inactivation of Erk evicts Nono from chromatin, revealing reciprocal regulation. Furthermore, Nono loss results in a compromised activation of its target bivalent genes upon differentiation and the differentiation itself. These findings reveal an unanticipated role of Nono in collaborating with Erk signaling to regulate the integrity of bivalent domain and mESC pluripotency.

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