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Effect of Akirin2 knockdown on the mRNA profile of human HL60 cells

ABSTRACT: Effect of Akirin2 knockdown on the mRNA profile of human HL60 cells

PROVIDER: PRJNA666895 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12759747_1.fastq.gz	Fastqsanger.gz
	SRR12759747_2.fastq.gz	Fastqsanger.gz
	SRR12759748_1.fastq.gz	Fastqsanger.gz
	SRR12759748_2.fastq.gz	Fastqsanger.gz
	SRR12759749_1.fastq.gz	Fastqsanger.gz

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Effect of Akirin2 knockdown on the mRNA profile of human HL60 cells

Project description:The Akirin (AKR) family are transcription cofactors without catalytic or DNA-binding capability with a conserved function in the regulation of multiple biological processes (BPs) throughout the metazoan. Human akirin2 (AKR2) is involved in various BPs in cell type and stimulus-dependent manner by acting as a link between NF-κB and chromatin remodeling complexes (remodelers) for transcriptional regulation. The regulome (transcription factors/cofactors-target genes interactions) plays an important role in the regulation of these BPs and the application of transcriptomics studies can be critical to better understanding the role of this transcription factors/cofactors as AKR2. In this study, we focused in AKR2 regulome to clarify its function as conserved regulatory cofactor. To assess this, RNA-seq analysis were conducted in wild type (WT) and AKR2-knock down (KO) human Caucasian promyelocytic leukemia HL60 cells. Results have shown a different gene expression profile that allowed us to identify immune response genes as putative AKR2 functional complements providing a better understanding of AKR2 regulome and its possible chromatin remodeling function.

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Project description:Cytarabine is the main drug for acute myeloid leukemia (AML) treatment; however, drug resistance hinders the treatment of AML. Although microRNA (miRNA) alteration is one of the well-recognized mechanisms underlying drug resistance in AML, few studies have investigated the role and function of miRNAs in the development of cytarabine resistance. In this study, total RNA was isolated from parental HL60 and cytarabine resistant HL60 (R-HL60) cells. Subsequently, miRNAs and mRNAs were detected using small RNA sequencing and gene expression array, respectively. The miRNAs and genes with ≥ 2-fold difference in expression between HL60 and R-HL60 cells were screened out. Negatively correlated miRNA–mRNA pairs were selected as candidate miRNA–mRNA target pairs by using the miRDB, Targetscan or miRTar databases. Functional enrichment analysis of differentially expressed genes (DEGs) included in the candidate miRNA–mRNA network was performed. The results revealed that CCL2, SOX9, SLC8A1, ICAM1, CXCL10, SIPR2, FGFR1, OVOL2, MITF, and CARD10 were simultaneously involved in seven GO pathways, namely the regulation of cell migration, regulation of locomotion, regulation of cellular component movement, cell migration, locomotion, cell motility, localization of cell. These genes were negatively correlated with the altered miRNAs (miR-1-3p, miR-155-5p, miR-1255b-5p, miR-200c-5p, miR-3609, miR-1285-3p, miR-124-3p, miR-146a-5p, miR-497a-5p, and miR-3150a-5p), suggesting that they are the potential targets of the miRNAs to regulate cell migration behavior or ability. Therefore, our results advance our understanding of the regulatory mechanism underlying cytarabine resistance development, specifically related to miRNAs.

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Identification of potential miRNA–mRNA regulatory network contributing to cytarabine resistance HL60 cells [miRNA-seq]

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Transcription profiling by array of human HL60 cells treated with eicosapantaenoic acid (EPA) to investigate the effect on the signalling pathways involved in growth arrest/apoptosis

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The effect of KIF11 knockdown on gene expression profile in HepG2 cells

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Genome-Wide profile of c-Myc binding in HL60 cells

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The effect of Dicer knockdown on the transcriptional expression profile of 3.10 mTEC cell line.

Project description:Dicer, also known as endoribonuclease Dicer or helicase with RNase motif, cleaves double-stranded RNA (dsRNA) and pre-microRNA (pre-miRNA) into short mature double-stranded RNA fragments called small interfering RNA and microRNA, respectively. Medullary thymic epithelial cells (mTECs) express close to 90% of the protein-coding genome, besides they play an important role to self-tolerance through the ectopic expression of peripheral tissue antigens (PTAs) in the thymus. MicroRNAs are potent post-transcriptional regulators in developmental switches, lineage commitment and gene expression regulation, but their role in representation of the immunological self in mature mTECs is not fully understood. So we used a Mus musculus mTEC cell line (mTEC 3.10) to knockdown Dicer transcript by means of siRNA transfection and then observe the effect of Dicer knockdown in the transcriptional profile of messenger RNAs (mRNAs) by means of oligo microarray hybridization. The Agilent oligo microarrays were used to determine the large scale mRNA transcriptional profiles of control or Dicer-knockdown 3.10 mTECs.

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