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Deep RNA sequencing analysis after Malat1 silencing in mouse HL1 cells

ABSTRACT: Deep RNA sequencing analysis after Malat1 silencing in mouse HL1 cells

PROVIDER: PRJNA826457 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18742781.fastq.gz	Fastqsanger.gz
	SRR18742782.fastq.gz	Fastqsanger.gz
	SRR18742783.fastq.gz	Fastqsanger.gz
	SRR18742784.fastq.gz	Fastqsanger.gz
	SRR18742785.fastq.gz	Fastqsanger.gz

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Deep RNA sequencing analysis after Malat1 silencing in mouse HL1 cells

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Project description:Cutaneous squamous cell carcinoma (CSCC) is the most common metastatic skin cancer, and its incidence is increasing globally. In this study, metastasis-associated in lung adenocarcinoma transcript 1 (MALAT1), a long non-coding RNA, was identified to be significantly up-regulated in CSCC tumors and cell lines. We conducted RNA sequencing to characterize gene expression changes in MALAT1-silenced cutaneous squamous cell carcinoma cells (A431).

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Project description:Malat1 is an abundant long noncoding RNA that localizes to nuclear bodies known as nuclear speckles, which contain a distinct set of pre-mRNA processing factors. Previous in vitro studies have demonstrated that Malat1 interacts with pre-mRNA splicing factors, including the serine- and arginine-rich (SR) family of proteins, and regulates a variety of biological processes, including cancer cell migration, synapse formation, cell cycle progression, and responses to serum stimulation. To address the physiological function of Malat1 in a living organism, we generated Malat1-KO (KO) mice using homologous recombination. Unexpectedly, the Malat1-KO mice were viable and fertile, showing no apparent phenotypes. Nuclear speckle markers were also correctly localized in cells that lacked Malat1. However, the cellular levels of another long noncoding RNA, Neat1, which is an architectural component of nuclear bodies known as paraspeckles, were downregulated in a particular set of tissues and cells lacking Malat1. To address if the the absence of Malat1 affects the expression of other genes, including other long noncoding RNA, microarrays were used to study the impact of knocking-out Malat1 on global gene expression in mouse embryonic fibroblasts (MEFs). MEFs were prepared from E13.5 mouse embryos from wildtype and Malat1 knock-out mice. RNA harvested from these cells were hybridized to Affymetirx mouse gene expression array.

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