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ABSTRACT: RNA Sequencing following ZNF384-AS Knockdown

PROVIDER: PRJNA1143963 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30141185_1.fastq.gz	Fastqsanger.gz
	SRR30141185_2.fastq.gz	Fastqsanger.gz
	SRR30141186_1.fastq.gz	Fastqsanger.gz
	SRR30141186_2.fastq.gz	Fastqsanger.gz
	SRR30141187_1.fastq.gz	Fastqsanger.gz

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Project description:RNA Sequencing following ZNF384 Knockdown

| PRJNA1143931 | ENA

RNA-sequencing to investigate transcriptional changes caused by ZNF384 fusion proteins in murine pre-B cells

Project description:RNA-sequencing was performed on Arf-/- pre-B cell expressing either wild-type ZNF384, TAF15-ZNF384, or TCF3-ZNF384. We found that pre-B cells that express ZNF384 fusion proteins have a gene expression profile similar to patients with ZNF384-rearranged leukemia.

2018-10-18 | GSE112558 | GEO

ChIP-sequencing to investigate occupancy of wild-type and fusion ZNF384 proteins in murine pre-B cells

Project description:We report the changes in chromatin occupancy between HA-tagged wild-type ZNF384 and the two leukemogenic fusion proteins, TAF15-ZNF384, and TCF3-ZNF384, in Arf-/- pre-B cells. Using ChIP-sequencing we found that 2298 peaks have new or increased binding while 495 peaks have decreased or lost binding of the fusion proteins compared to wild-type ZNF384.

2018-10-18 | GSE112560 | GEO

Epigenetic regulation of FLT3 by ZNF384-fusion protein

Project description:Profiling global gene expression in large ALL cohorts, we identified unique over-expression of FLT3 in ZNF384-rearranged ALL, consistently across cases harboring different fusion partners with ZNF384. Mechanistically, we discovered an intergenic enhancer element at the FLT3 locus that is exclusively activated in ZNF384-rearranged ALL, with the enhancer-promoter looping directly mediated by the fusion protein. There was also a striking global enrichment of active enhancers within ZNF384 binding sites across the genome in ZNF384-rearranged ALL cells.

2022-08-11 | GSE197890 | GEO

Expression data from B-cell precursor acute lymphoblastic leukemia

Project description:B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a heterogeneous disease that can be subdivided according to primary recurrent genetic abnormalities that are strongly associated with characteristic biological and clinical features. The detection of these abnormalities can facilitate diagnosis, risk stratification, and targeted therapy. We identified an unexpectedly high incidence of fusion genes involving ZNF384 genes, including TCF3-ZNF384, EP300-ZNF384, and CREBBP-ZNF384, in BCP-ALL of our cohort. We therefore used microarrays to evaluate the gene-expression characteristics of BCP-ALL harboring ZNF384-related fusion genes and compared with those of BCP-ALL with other types of conventional genetic abnormality.

2017-03-21 | GSE79533 | GEO

Project description:RNA sequencing following KLF12 knockdown in KYSE30 cells

| PRJNA1047887 | ENA

Project description:RNA sequencing following TRIM27 knockdown in KYSE30 cells

| PRJNA1049157 | ENA

ZNF384 fusion oncoproteins drive lineage aberrancy in acute leukemia [ChIP-seq]

Project description:We report changes in chromatin occupancy dependent on TCF3-ZNF384 splicing isoform usage. The isoform including exon 8, which encodes 2 zinc finger domains, has increased binding near genes important for nomal hematopoiesis. We report no global changes in H3K27Ac upon expression of ZNF384 fusions but 47 loci with increased H3K27Ac.

2022-08-31 | GSE181617 | GEO

ZNF384 fusion oncoproteins drive lineage aberrancy in acute leukemia

Project description:ZNF384-rearranged fusion oncoproteins (FO) define a subset of lineage ambiguous leukemias, but the mechanistic role of ZNF384 FO in leukemogenesis and lineage ambiguity is poorly understood. Here, using viral expression in mouse and human hematopoietic stem and progenitor cells (HSPCs) and a Ep300-Zfp384 mouse model we show that ZNF384 FO promote hematopoietic expansion, myeloid lineage skewing, and self-renewal. In mouse HSPCs, concomitant lesions such as NRASG12D, were required for fully penetrant leukemia, whereas expression of ZNF384 FO drove development of B/myeloid leukemia in human HSPCs, with sensitivity of human ZNF384r leukemia to FLT3 inhibition in vivo. Mechanistically, ZNF384 FO occupy a subset of predominantly intragenic/enhancer regions with increased histone 3 lysine acetylation suggesting enhancer function. These data define a paradigm for FO-driven lineage ambiguous leukemia, in which expression in HSPCs results in deregulation of lineage-specific genes and hematopoietic skewing, progressing to full leukemic transformation in the presence of proliferative stress.

2022-03-16 | PXD028481 | Pride

Zinc finger protein ZNF384 is an adaptor of KU to DNA during classical non-homologous end-joining

Project description:DNA double-strand breaks (DSBs) are among the most deleterious types of DNA damages as they can lead to mutations and chromosomal rearrangements, which underlie cancer development and progression. Non-homologous end-joining (NHEJ) is the dominant pathway for the repair of DSBs in human cells, which involves the DNA binding proteins Ku70/Ku80. Other DNA binding proteins such as Zinc Finger (ZnF) domain-containing proteins have also been implicated in DNA repair. However, their role in NHEJ has remained elusive. Here we show that ZNF384, which is a member of the C2H2 family of ZnF proteins that binds DNA in vitro, is recruited to DSBs in vivo. ZNF384 recruitment requires the PARP/PAR-dependent expansion of damaged chromatin followed by binding of ZNF384 to the exposed DNA via its unique C2H2 motifs. Mass-spectrometry-based experiments revealed that ZNF384 interacts with the Ku70/Ku80 NHEJ complex via its N-terminus. This interaction promotes the assembly of Ku70/Ku80 at DBSs as revealed by fluorescence recovery after photobleaching and fluorescence correlation spectroscopy. By regulating Ku70/80 dynamics, ZNF384 facilitates the assembly of several downstream NHEJ factors (e.g. APLF and XRCC4) and repair by cNHEJ at DSBs. Altogether, our data suggest that ZNF384 acts as a ‘Ku-adaptor’ that binds to DSBs and Ku70/80 to facilitate their binding and the subsequent build-up of a functional cNHEJ repairosome at these lesions, high-lighting a role for ZNF384 in DSB repair and genome maintenance.

2021-11-15 | PXD020417 | Pride

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