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Whole-genome mapping of ETV6-RUNX1 in pre-B lymphoblast models

ABSTRACT: Whole-genome mapping of ETV6-RUNX1 in pre-B lymphoblast models

PROVIDER: PRJNA734856 | ENA |

REPOSITORIES: ENA

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Whole-genome mapping of ETV6-RUNX1 in pre-B lymphoblast models

Project description:Genome binding/occupancy profiling of ETS Variant Transcription Factor 6- Runt Related Transcription Factor 1 fusion protein (ETV6-RUNX1) in REH cells by high throughput sequencing. ETV6-RUNX1 is expressed in pediatric t(12;21) ETV6-RUNX1 B cell precursor acute lymphoblastic leukemia.

2022-04-01 | GSE176084 | GEO

ChIP-seq for RUNX1 and ETV6-RUNX1 in an induced pluripotent stem cell model of ETV6-RUNX1 pre-leukaemia

Project description:ETV6-RUNX1 is a first-hit mutation in childhood B cell precursor acute lymphoblastic leukaemia. ETV6-RUNX1 is a fusion protein which inherits the DNA-binding runt domain from RUNX1. Here we performed chromatin precipitation for native RUNX1 and ETV6-RUNX1 using RUNX1 antibodies and specifically for the ETV6-RUNX1 fusion using a V5-tag pull down.

2022-10-31 | E-MTAB-12208 | biostudies-arrayexpress

Whole-genome mapping of RUNX1, CBFA2T3, H3K4me1, H3K4me3, H3k27me3 and H3K27ac in pre-B lymphoblast models

Project description:Genome binding/occupancy profiling of Runt Related Transcription Factor 1 (RUNX1), CBFA2T3 (ETO2, MRG16) and histone marks by high throughput sequencing. RUNX1 and CBFA2T3 are found overexpressed in pediatric t(12;21) ETV6-RUNX1 B cell precursor acute lymphoblastic leukemia. As CBFA2T3 is a transcription regulator, we hypothesized a potential collaboration between the transcription factor RUNX1 and CBFA2T3. Here, we investigated the molecular proximity between RUNX1 and CBFA2T3 proteins on chromatin and identified a regulatory loop between RUNX1 and CBFA2T3.

2020-12-19 | GSE117684 | GEO

Whole-genome mapping of RUNX1, CBFA2T3, H3K4me1, H3K4me3, H3k27me3 and H3K27ac in pre-B lymphoblast models

Project description:Whole-genome mapping of RUNX1, CBFA2T3, H3K4me1, H3K4me3, H3k27me3 and H3K27ac in pre-B lymphoblast models

| PRJNA482944 | ENA

Identification of ETV6/RUNX1 regulated lncRNAs

Project description:Overwhelming evidence indicates that long non-coding RNAs have essential roles in tumorigenesis. Nevertheless, their expression and role in pediatric B-cell precursor acute lymphoblastic leukemia has not been extensively explored. Here, we conducted a comprehensive analysis of the long non-coding RNA transcriptome in ETV6/RUNX1 positive BCP-ALL, one of the most frequent subtypes of pediatric leukemia. An ETV6/RUNX1 expression signature was established, consisting of 596 lncRNAs (434 up and 162 down) using expression analysis of a series of primary patient samples. Subsequently, RNA sequencing from BCP-ALL cell lines and shRNA-mediated silencing of ETV6/RUNX1, illustrated that lnc-NKX2-3-1, lnc-TIMM21-5, lnc-ASTN1-1 and lnc-RTN4R-1 are bona fide ETV6/RUNX1 targets and could serve as novel biomarkers of this prevalent subtype of human leukemia.

2016-09-26 | GSE79868 | GEO

Loss of BTG1 function promotes ETV6-RUNX1-mediated leukemic transformation by upregulation of BCL6

Project description:Analysis of gene signatures in WT+Ctrl vs WT+ETV6-RUNX1, Btg1-/- and Btg1-/-+ETV6-RUNX1 in cKit+Ter119- fetal liver-derived hematopoietic progenitor cells (FL-HPCs). The Btg1-/-+ETV6-RUNX1 FL-HPCs display a strong increase in proliferation compared to WT+ETV6-RUNX1. Total RNA otained from WT+Ctrl, WT+ETV6-RUNX1, Btg1-/-+Ctrl and Btg1-/-+ETV6-RUNX1 FL-HPCs cells that were cultured for 12 days in expansion medium.

2014-08-22 | E-GEOD-60589 | biostudies-arrayexpress

Loss of BTG1 function promotes ETV6-RUNX1-mediated leukemic transformation by upregulation of BCL6

2014-08-22 | GSE60589 | GEO

ChIP-seq for RUNX1 and ETV6-RUNX1 in B-ALL cell lines and patient samples

Project description:Identification of RUNX1 and ETV6-RUNX1 binding sites

2022-04-10 | E-MTAB-10312 | biostudies-arrayexpress

ChIP-seq in the cell line NALM-6 for RUNX1 and ETV6-RUNX1 to assess competition between the two proteins for DNA binding

Project description:RUNX1 and ETV6-RUNX1 possess the same DNA-binding runt domain and are therefore expected to bind to canonical RUNX motifs. As the ETV6-RUNX1 fusion arises in the context of native RUNX1 expression, and since RUNX1 is retained or amplified in B-ALL, the two proteins are likely to compete for the same target sites. To assess this, we performed RUNX1 ChIP-seq in the presence of exogenous ETV6-RUNX1 (or non DNA binding ETV6-RUNX1-R139G) and the reciprocal experiment: ETV6-RUNX1 ChIP (using a V5 tag) in the presence of exogenous RUNX1 or vector control.

2022-10-31 | E-MTAB-12209 | biostudies-arrayexpress

Histone H3, lysine 27 acetylation ChIP-seq in NALM6 expressing ETV6-RUNX1

Project description:ETV6-RUNX1 is a fusion protein bringing together almost the entire coding sequence of RUNX1, including the DNA binding runt domain, and the N-terminus of ETV6 which is known to include transcriptional repressors including histone deacetylation 3 (HDAC3). Here we perform ChIP-seq for the active chromatin mark H3K27ac in the NALM6 B-cell acute lymphoblastic leukaemia cell line expressing ETV6-RUNX1 or mutant derivatives of ETV6-RUNX1: Delta helix-loop-helix (dHLH) is a deletion of the pointed domain; R139G is a point mutation in the runt DNA-binding domain.

2022-10-31 | E-MTAB-12207 | biostudies-arrayexpress

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