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ALKBH5 promotes tumor progression by decreasing RIG-I expression mediated by N6-methyladenosine-dependent HNRNPC binding in HNSCC [MeRIP-seq]

ABSTRACT: ALKBH5 promotes tumor progression by decreasing RIG-I expression mediated by N6-methyladenosine-dependent HNRNPC binding in HNSCC [MeRIP-seq]

PROVIDER: PRJNA771104 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16323943_1.fastq.gz	Fastqsanger.gz
	SRR16323943_2.fastq.gz	Fastqsanger.gz
	SRR16323944_1.fastq.gz	Fastqsanger.gz
	SRR16323944_2.fastq.gz	Fastqsanger.gz
	SRR16323945_1.fastq.gz	Fastqsanger.gz

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ALKBH5 promotes tumor progression by decreasing RIG-I expression mediated by N6-methyladenosine-dependent HNRNPC binding in HNSCC

Project description:ALKBH5 promotes tumor progression by decreasing RIG-I expression mediated by N6-methyladenosine-dependent HNRNPC binding in HNSCC

| PRJNA771102 | ENA

ALKBH5 promotes tumor progression by decreasing RIG-I expression mediated by N6-methyladenosine-dependent HNRNPC binding in HNSCC [RNA-seq]

Project description:ALKBH5 promotes tumor progression by decreasing RIG-I expression mediated by N6-methyladenosine-dependent HNRNPC binding in HNSCC [RNA-seq]

| PRJNA771103 | ENA

ALKBH5 promotes tumor progression by decreasing RIG-I expression mediated by N6-methyladenosine-dependent HNRNPC binding in HNSCC [MeRIP-seq]

Project description:To determine the targets underlying ALKBH5 during head and neck squamouse cell carcinoma progression, Methylated RNA immunoprecipitation (MeRIP) with an m6A specific antibody followed by RNA sequencing (MeRIP-seq) and next generation sequencing were combined to screen the potential targets haboring m6A modificatios and mRNA level alteration after ALKBH5 knockdown in a HNSCC cell line.

2022-04-13 | GSE185885 | GEO

ALKBH5 promotes tumor progression by decreasing RIG-I expression mediated by N6-methyladenosine-dependent HNRNPC binding in HNSCC [RNA-seq]

2022-04-13 | GSE185886 | GEO

ALKBH5 promotes tumor progression by decreasing RIG-I expression mediated by N6-methyladenosine-dependent HNRNPC binding in HNSCC

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-04-13 | GSE185888 | GEO

Function of HNRNPC in breast cancer cells by controlling the dsRNA-induced interferon response

Project description:Elevated expression of RNA binding protein HNRNPC has been reported in cancer cells, while the essentialness and functions of HNRNPC in tumors were not clear. We showed that repression of HNRNPC in the breast cancer cells MCF7 and T47D inhibited cell proliferation and tumor growth. Our computational inference of the key pathways and extensive experimental investigations revealed that the cascade of interferon responses mediated by RIG-I was responsible for such tumor-inhibitory effect. Interestingly, repression of HNRNPC resulted in accumulation of endogenous double-stranded RNA (dsRNA), the binding ligand of RIG-I. These up-regulated dsRNA species were highly enriched by Alu sequences and mostly originated from pre-mRNA introns that harbor the known HNRNPC binding sites. Such source of dsRNA is different than the recently well-characterized endogenous retroviruses that encode dsRNA. In summary, essentialness of HNRNPC in the breast cancer cells was attributed to its function in controlling the endogenous dsRNA and the down-stream interferon response. This is a novel extension from the previous understandings about HNRNPC in binding with introns and regulating RNA splicing.

2018-08-23 | GSE100451 | GEO

ALKBH5 is a New Mammalian RNA Demethylase

Project description:N6-methyladenosine (m6A) is the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Here we report ALKBH5 as a new mammalian demethylase that oxidatively removes the m6A modification in mRNA in vitro and inside cells. This demethylation activity of ALKBH5 significantly affects mRNA export and RNA metabolism as well as the assembly of mRNA processing factors in nuclear speckles. Alkbh5-deficient male mice are characterized by impaired fertility resulting from apoptosis that affects meiotic metaphase-stage spermatocytes. In accordance with this defect, we have identified in mouse testes 1552 differentially expressed genes which cover broad functional categories and include spermatogenesis-related mRNAs involved in the p53 functional interaction network. We show that Alkbh5-deficiency impacts the expression levels of some of these mRNAs, supporting the observed phenotype. The discovery of this new RNA demethylase strongly suggests that the reversible m6A modification plays fundamental and broad functions in mammalian cells. RNA-seq in two cell types

2013-02-15 | E-GEOD-40132 | biostudies-arrayexpress

Identification of splicing factors signature predicting prognosis risk and the mechanistic roles of novel oncogenes in HNSCC

Project description:Head and neck squamous cell carcinoma (HNSCC) is the most frequent subtype of head and neck cancer generally with a poor prognosis and limited treatment options due to its highly heterogeneous malignancy. In this study, we screened functional splicing regulatory RNA binding proteins (RBPs) that are closely related with prognosis of patients with HNSCC and showed significant expression difference between HNSCC tumors and normal tissues. Based on this finding, we have selected six candidate genes (HNRNPC, ZCRB1, RBM12B, SF3A2, SF3B3, and SRSF11) to construct a prognostic prediction model and validated the prognostic model for predicting patient survival. We found that the risk score predicted by our model can serve as an independent prognostic predictor, notably, HNSCC tumors showed enhanced expression of SF3B3, HNRNPC, and ZCRB1, which increases a patient's risk score in the discovered prediction model. The investigation of underlying mechanism validated that knockdown of SF3B3, HNRNPC, and ZCRB1 separately induced a substantial impairment of HNSCC cell survival. Conversely, single overexpression of one of the three genes promoted tumor cellular proliferation. High throughput RNA sequencing analysis and identification revealed that changes in the expression of SF3B3 and HNRNPC remarkably affected the splicing isoforms of genes related to cell cycle regulation, whereas the depletion of ZCRB1 contributed to notable DNA damage. Additionally, the prognostic prediction model's risk score was suggested to be related with immune infiltration score, particularly, SF3B3 has a negative correlation with CD8A expression. Therefore, our findings provide promising prognosis predictors and potential therapeutic targets for better treatment efficacy of HNSCC.

2025-06-21 | GSE243085 | GEO

hNRNPC iCLIP

Project description:hNRNPC iCLIP

| PRJEB2253 | ENA

Transcriptome profiling of cells depleted of hnRNPC, Upf1, or co-depleted of hnRNPC and Upf1.

Project description:The purpose of this experiment was to compare differences in Alu-exon inclusion in cells depleted of hnRNPC, Upf1, or both.

2016-04-01 | E-MTAB-4008 | biostudies-arrayexpress