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Genome-wide maps of factors and gene expression in pre-B leukemic 697 line

ABSTRACT: Genome-wide maps of factors and gene expression in pre-B leukemic 697 line

PROVIDER: PRJNA574266 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10189270.fastq.gz	Fastqsanger.gz
	SRR10189271.fastq.gz	Fastqsanger.gz
	SRR10189272.fastq.gz	Fastqsanger.gz
	SRR10189273.fastq.gz	Fastqsanger.gz
	SRR10189274.fastq.gz	Fastqsanger.gz

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Genome-wide maps of chromatin state and gene expression in control and TPA-stimulated pre-B leukemic 697 line

Project description:Genome-wide maps of chromatin state and gene expression in control and TPA-stimulated pre-B leukemic 697 line

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Genome-wide maps of factors and gene expression in pre-B leukemic 697 line

Project description:E2A, a basic helix-loop-helix (bHLH) transcription factor, plays a crucial role in determining tissue-specific cell fate, including differentiation of B cell lineages. In 5% of childhood acute lymphoblastic leukemia (ALL), the t(1,19) chromosomal translocation specifically targets the E2A gene and produces an oncogenic E2A-PBX1 fusion protein. While previous studies have demonstrated oncogenic functions of E2A-PBX1 in cell and animal models, the E2A-PBX1-enforced cistrome, the E2A-PBX1 interactome, and related mechanisms underlying leukemogenesis remain unclear. Here, by unbiased genomic profiling approaches, we identify the direct target sites of E2A-PBX1 in t(1,19)-positive pre-B ALL cells and show that, compared to normal E2A, E2A-PBX1 preferentially binds to a subset of gene loci co-bound by RUNX1 and gene-activating machineries (p300, MED1, and H3K27 acetylation). Using biochemical analyses, we further document a direct interaction between E2A-PBX1 and RUNX1 and show that E2A-PBX1 binding to gene enhancers is dependent on RUNX1, but not the DNA-binding activity harbored within the PBX1 homeodomain of E2A-PBX1. Transcriptome analyses and cell transformation assays further establish a significant RUNX1 requirement for E2A-PBX1-mediated target gene activation and leukemogenesis. Notably, the RUNX1 locus itself is also directly activated by E2A-PBX1, indicating a multilayered interplay between E2A-PBX1 and RUNX1. Collectively, our study provides the first unbiased profiling of the E2A-PBX1 cistrome in pre-B ALL cells and reveals a previously unappreciated pathway in which E2A-PBX1 acts in concert with RUNX1 to enforce transcriptome alterations for the development of pre-B ALL.

2020-03-06 | GSE138031 | GEO

miRNA profiling of extracellular vesicled derived from acute lymphoblastic leukemic cell line 697 treated with ActivinA against untreated cells

Project description:Role of ActivinA in the modulation of EV-miRNA cargo in acute lymphoblastic leukemic cell line 697.

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Transcriptome profiling of MED1 wild-type and knockout human pre-B ALL cell line 697 (RNA-seq)

Project description:CRISPR/Cas9 system was used to generate mediator complex subunit 1 (MED1) knockout human pre-B ALL cell line 697. RNA-seq was performed to observe the effects of MED1 deletion on gene expression in 697.

2020-05-13 | E-MTAB-8178 | biostudies-arrayexpress

Transcriptomic effects of forced expression of FOXO3 and FOXO1 in pre-B ALL cell line 697 [exp2]

Project description:To investigate diferences in function between the related transcription factors FOXO1 and FOXO3 in pre-B acute lymphocytic leukaemia (ALL) cells we extracted RNA from triplicate 697 cultures four days after transduced with empty vector (SIN-SIEW) or constructs expressing FOXO1 or FOXO3. Approximately 30 million 70bp paired-end reads were generated per sample by illumina sequencing.

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Project description:CRISPR/Cas9 system was used to generate mediator complex subunit 1 (MED1) knockout human pre-B ALL cell line 697. ChIP-seq was performed to identify genomic regions responsible for recruitment of MED1 and RUNX1.

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Project description:RIBO-seq analysis of YTHDF2-deficient pre-leukemic cells and control pre-leukemic cells

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Transcriptomic effects of forced expression of FOXO3, PRDM1⍺ and PRDM1β in pre-B ALL cell line 697 [exp1]

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Project description:YTHDF2 is overexpressed in a broad spectrum of human acute myeloid leukemias (AML). To study the role of YTHDF2 in leukemia, c-Kit+ cells from foetal livers of Ythdf2fl/fl;Vav-iCre (Ythdf2CKO) and Ythdf2fl/fl (Ythdf2CTL) 14.5 dpc embryos were transduced with Meis1 and Hoxa9 oncogenes and serially re-plated to generate pre-leukemic cells. Total RNA from Ythdf2CKO (n=5) and Ythdf2CTL (n=5) pre-leukemic cells were used for Affymetrix global gene expression analysis.

2019-04-05 | E-MTAB-6783 | biostudies-arrayexpress

RIBO-seq analysis of YTHDF2-deficient pre-leukemic cells and control pre-leukemic cells

Project description:YTHDF2 is overexpressed in a broad spectrum of human acute myeloid leukemias (AML). To study the role of YTHDF2 on translation regulation in leukemia, c-Kit+ cells from foetal livers of Ythdf2fl/fl; Vav-iCre (Ythdf2CKO) and Ythdf2fl/fl (Ythdf2CTL) 14.5 dpc embryos were transduced with Meis1 and Hoxa9 oncogenes and serially re-plated to generate pre-leukemic cells. RIBO-seq libraries were then prepared from Ythdf2CKO (n=3) and Ythdf2CTL (n=3) pre-leukemic cells.

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