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ER-Localized Deadenylase PNLDC1 Suppresses Colorectal Cancer Progression by Targeting the mRNA decay of TUBB4B

ABSTRACT: ER-Localized Deadenylase PNLDC1 Suppresses Colorectal Cancer Progression by Targeting the mRNA decay of TUBB4B

PROVIDER: PRJNA1211634 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR32028088_1.fastq.gz	Fastqsanger.gz
	SRR32028088_2.fastq.gz	Fastqsanger.gz
	SRR32028089_1.fastq.gz	Fastqsanger.gz
	SRR32028089_2.fastq.gz	Fastqsanger.gz
	SRR32028090_1.fastq.gz	Fastqsanger.gz

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ER-Localized Deadenylase PNLDC1 Suppresses Colorectal Cancer Progression by Targeting the mRNA decay of TUBB4B

Project description:Colorectal cancer (CRC) remains a leading cause of cancer-related mortality, highlighting the urgent need for novel therapeutic strategies. In this study, we find that PNLDC1, an endoplasmic reticulum (ER)-localized deadenylase, lower expresses in 91 clinical CRC tissues. Using both in vitro and in vivo models, we identify PNLDC1 as a key tumor suppressor by modulating cell cycle progression in CRC. RNA-immunoprecipitation and sequencing analyses reveal that PNLDC1 binds cell cycle-associated mRNAs, with TUBB4B emerging as a critical target. PNLDC1 downregulates TUBB4B mRNA, whose regulated degradation is essential for PNLDC1’s tumor-suppressive function. Restoration of TUBB4B expression counteracts PNLDC1-mediated suppression of CRC cell proliferation, underscoring its pivotal role in CRC pathogenesis. Importantly, we demonstrate that the TUBB4B inhibitor, mebendazole, effectively suppresses the enhanced proliferation in lower-expression PNLDC1 models, including cell, mouse xenografts, and patient-derived tumor-like cell clusters, positioning it as a promising therapeutic agent. These findings establish PNLDC1 as a valuable biomarker and therapeutic target, paving the way for developing novel CRC treatments.

2025-01-20 | GSE287213 | GEO

Roles of mRNA decay in liver development

Project description:mRNA decay machineries play important roles in various biological events. Among them, Cnot deadenylase complex has a critical function to trigger mRNA decay. To understand roles of the complex in liver development, we compare RNA expression between control and Cnot complex-deficient liver.

2019-02-01 | E-MTAB-7182 | biostudies-arrayexpress

Examination of mRNA decay rate in mature adipocytes

Project description:The CCR4-NOT deadenylase complex has a critical function to trigger mRNA decay and various biological events. To understand roles of the complex in adipocyte function, we compare mRNA half-lives between control and Cnot complex-deficient mature adipocytes from iWAT and BAT.

2019-10-24 | E-MTAB-8371 | biostudies-arrayexpress

RNA-seq to identify the role of mRNA decay in mouse adipose tissues

Project description:The CCR4-NOT deadenylase complex has a critical function to trigger mRNA decay and various biological events. To understand roles of the complex in adipocyte function, we compare RNA expression between control and Cnot complex-deficient brown and white adipose tissues.

2019-10-24 | E-MTAB-8366 | biostudies-arrayexpress

Identification of subcellular gene expression changes due to a Nonsense-Mediated Decay pathway at the Endoplasmic Reticulum

Project description:Nonsense-mediated decay (NMD) is a translation-dependent RNA quality control mechanism that occurs in the cytoplasm. However, it is unknown how NMD regulates the stability of RNAs translated at the Endoplasmic Reticulum (ER). Here, we identify a localized NMD pathway dedicated to ER-translated mRNAs. We previously identified NBAS, a component of the Syntaxin 18 complex involved in Golgi-to-ER trafficking, as a novel NMD factor. Here, we show that NBAS fulfils an independent function in NMD. This ER-NMD pathway requires the interaction of NBAS with the core NMD factor UPF1, which is partially localized at the ER in the proximity of the translocon. NBAS and UPF1 co-regulate the stability of ER-associated transcripts, in particular those associated with the cellular stress response. We propose a model where NBAS recruits UPF1 to the membrane of the ER and activates an ER-dedicated NMD pathway, thus providing an ER protective function by ensuring quality control of ER-translated mRNAs.

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Identification of total gene expression changes due to a Nonsense-Mediated Decay pathway at the Endoplasmic Reticulum

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LncRNA LINC00525 suppresses p21 expression via mRNA decay and triplex-mediated changes in chromatin structure in lung adenocarcinoma

Project description:LncRNA LINC00525 suppresses p21 expression via mRNA decay and triplex-mediated changes in chromatin structure in lung adenocarcinoma Our findings demonstrate that LINC00525 promote lung adenocarcinoma progression by reducing the transcription and stability of p21 mRNA in concert with EZH2 and RBMS2, which highlights the importance of LINC00525 acting as a potential therapeutic target of LUAD.

2021-04-06 | GSE171460 | GEO

Genome-wide mapping of decay factor-mRNA interactions in yeast identifies nutrient responsive transcripts as targets of the deadenylase Ccr4

Project description:The Ccr4-Not complex is a major regulator of stress responses that controls gene expression at multiple levels, from transcription to mRNA decay. Ccr4, a core subunit of the complex, is the main cytoplasmic deadenylase in Saccharomyces cerevisiae, however its mRNA targets have not been mapped on a genome-wide scale. Here we describe a genome-wide approach, RNA immunoprecipitation-high throughput sequencing (RIP-seq), to identify the RNAs bound to Ccr4, and two proteins that associate with it, Dhh1 and Puf5. All three proteins were preferentially bound to lowly abundant mRNAs, most often at the 3’ end of the transcript. Furthermore, Ccr4, Dhh1 and Puf5 are recruited to mRNAs that are targeted by other RNA-binding proteins that promote decay, mRNA transport and inhibit translation. Although Ccr4-Not regulates mRNA transcription and decay, Ccr4 recruitment to mRNAs correlates better with decay rates, suggesting it imparts greater control over transcript abundance through decay. Ccr4-enriched mRNAs are refractory to control by the other deadenylase complex in yeast, Pan2/3, suggesting a division of labor between these deadenylation complexes. Finally, Ccr4 and Dhh1 associate with mRNAs whose abundance increases during nutrient starvation and those that fluctuate during metabolic and oxygen consumption cycles, which explains the known genetic connections between these factors and nutrient utilization and stress pathways.

2017-12-04 | GSE72366 | GEO

Comparison of infloresence transcriptome of bp er vs. bp er fil

Project description:BP and ER encode proteins that act synergistically to regulate Arabidopsis inflorescence architecture. To search for genes/proteins that influence the BP/ER signaling pathways, we conducted mutagenesis of the bp er double mutant and found that a mutation in FILAMENTOUS FLOWER (FIL) suppresses many of the morphological/developmental defects in bp er. Given that FIL encodes a Zn-finger containing transcription factor, microarray analysis was conducted on bp er vs. the bp er fil line to identify genes that are misregulated and which might implicate specific genes/proteins/pathways that are involved in regulating inflorescence development.

2016-09-10 | GSE86643 | GEO

ADAR1 controls apoptosis of stressed cells by inhibiting Staufen-mediated mRNA decay

Project description:Both p150 and p110 isoforms of ADAR1 convert adenosine to inosine in double-stranded RNA (dsRNA). The p150 isoform suppresses the dsRNA sensing mechanism that activates the interferon induction mediated by the MDA5-MAVS signaling. In contrast, the biological function of the p110 isoform localized in the nucleus remains largely unknown. Here we show that stress-activated phosphorylation of ADAR1p110 by MKK6/p38 MAP kinases promotes its binding to Exportin-5 and nuclear export to the cytoplasm. Once translocated to the cytoplasmic, ADAR1p110 suppresses apoptosis of stressed cells by protecting many anti-apoptotic gene transcripts that contain 3’UTR dsRNA structures such as those consisting of inverted Alu repeats. ADAR1p110 competitively inhibits binding of Staufen1 to the 3’UTR dsRNAs and antagonizes the Staufen1-mediated mRNA decay mechanism. Our studies revealed a new stress response mechanism regulated by MAP kinases, in which ADAR1p110 translocates to the cytoplasm and regulates a class of mRNAs required for survival of stressed cells.

2017-03-21 | GSE85455 | GEO

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