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Research on the effect of PRMT5 on the genomic binding sites of ΔNp63α and its impact on the global transcriptomic regulation in the human tongue squamous cell carcinoma cell line UM1.

ABSTRACT: Research on the effect of PRMT5 on the genomic binding sites of ΔNp63α and its impact on the global transcriptomic regulation in the human tongue squamous cell carcinoma cell line UM1.

PROVIDER: PRJNA1250473 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR33130978_1.fastq.gz	Fastqsanger.gz
	SRR33130978_2.fastq.gz	Fastqsanger.gz
	SRR33130979_1.fastq.gz	Fastqsanger.gz
	SRR33130979_2.fastq.gz	Fastqsanger.gz
	SRR33130980_1.fastq.gz	Fastqsanger.gz

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Research on the effect of PRMT5 on the genomic binding sites of ΔNp63α and its impact on the global transcriptomic regulation in the human tongue squamous cell carcinoma cell line UM1.

Project description:By performing PRMT5 knockdown in the human tongue squamous cell carcinoma cell line UM1, we analyzed the effects of this treatment on the global gene transcription level and its impact on the genomic binding capacity of the transcription factor ΔNp63α. Using genomic binding data supplemented with the histone activation marker H3K27ac, we identified a significant impact of PRMT5 on the transcriptional regulatory capability of ΔNp63α.

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Project description:Of the multiple anatomical sites represented in oral cancer, squamous cell carcinoma of the tongue (TSCC) shows the highest incidence among younger age group. Chewing betel leaf, areca nut & slaked lime and smoking tobacco are common practises in India which have direct clinical implication in TSCC carcinogenesis. Here, for the first time we define the landscape of genomic alterations in TSCC from the Indian diaspora which would help to identify novel therapeutic targets for clinical intervention and define the genetic basis for TSCC. We performed high throughput sequencing of fifty four tongue samples using whole exome sequencing (n=47, 23 paired normal tumor and 1 unpaired) and transcriptome sequencing (n=17, 10 tumor and 5 normal). Mutation, copy number analysis were carried out using exome sequencing data and transcriptome analysis provided expressed genes and transcript fusions in tongue cancer patients. Further, integrated analysis were performed to identify biologically relevant alterations. Our preliminary analysis revealed presence of most frequently altered mutations in TSCC which includes mutations in TP53, NOTCH1, CDKN2A, USP6, KMT2D etc, consistent with literature. We observed high frequency of CG/T(GC/A) transversions in non-CpG islands, a signature associated with tobacco exposure. Somatic copy number analysis revealed copy number gain in known hallmarks such as CCND1, MYC, ORAOV1 genes along with copy number alteration in novel genes. Significant positive correlation was observed in the genes harbouring copy number gains and showing increased expression.

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Identification of PRMT5 phosphorylation sites in Hey cells LC-MS

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