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Enhancer looping protein LDB1 affects T-ALL cell proliferation by cooperating with master transcription factors

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE253040 | GEO | 2024/10/15

REPOSITORIES: GEO

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Enhancer looping protein LDB1 affects T-ALL cell proliferation by cooperating with master transcription factors [RNA-Seq]

Project description:LIM domain-binding protein 1 (LDB1) is a highly conserved and widely expressed chromatin looping protein that connects enhancer-promoter genes through LIM and LIM homologous domains in various cell types. LDB1 has been confirmed to play a crucial role in various physiological and pathological processes. In our study, we aim to investigate the function and mechanisms of LDB1 in the context of T-cell acute lymphoblastic leukemia (T-ALL). RNA-seq was conducted and the differently expressed genes were revealed in the LDB1-knockdown 6T-CEM and J.gamma1 cells in comparison to control group. Cleavage Under Targets and Tagmentation (CUT&Tag) showed the co-localization of LDB1 with several master transcription factors on chromatin in 6T-CEM cells.

2024-10-15 | GSE253038 | GEO

Enhancer looping protein LDB1 affects T-ALL cell proliferation by cooperating with master transcription factors [CUT&Tag]

2024-10-15 | GSE252992 | GEO

Enhancer looping protein LDB1 regulates hepatocyte gene expression by cooperating with liver transcription factors.

Project description:Enhancers establish proximity with distant target genes to regulate temporospatial gene expression and specify cell identity. Lim domain binding protein 1 (LDB1) is a conserved and widely expressed protein that functions as an enhancer looping factor. Previous studies in erythroid cells and neuronal cells showed that LDB1 forms protein complexes with different transcription factors to regulate cell-specific gene expression. Here, we show that LDB1 regulates expression of liver genes by occupying enhancer elements and cooperating with hepatic transcription factors HNF4A, FOXA1, TCF7 and GATA4. Using the glucose transporter SLC2A2 gene, encoding GLUT2, as an example, we find that LDB1 regulates gene expression by mediating enhancer-promoter interactions. In vivo, we find that LDB1 deficiency in primary mouse hepatocytes dysregulates metabolic gene expression and changes the enhancer landscape. Conditional deletion of LDB1 in adult mouse liver induces glucose intolerance. However, Ldb1 knockout hepatocytes show improved liver pathology under high-fat diet conditions associated with increased expression of genes related to liver fatty acid metabolic processes. Thus, LDB1 is linked to liver metabolic functions under normal and obesogenic conditions.

| S-EPMC9458430 | biostudies-literature

Enhancer looping protein LDB1 affects T-ALL cell proliferation by cooperating with master transcription factors

Project description:Enhancer looping protein LDB1 affects T-ALL cell proliferation by cooperating with master transcription factors

| PRJNA1063684 | ENA

Enhancer looping protein LDB1 affects T-ALL cell proliferation by cooperating with master transcription factors [RNA-Seq]

Project description:Enhancer looping protein LDB1 affects T-ALL cell proliferation by cooperating with master transcription factors [RNA-Seq]

| PRJNA1063689 | ENA

Enhancer looping protein LDB1 affects T-ALL cell proliferation by cooperating with master transcription factors [CUT&Tag]

Project description:Enhancer looping protein LDB1 affects T-ALL cell proliferation by cooperating with master transcription factors [CUT&Tag]

| PRJNA1063599 | ENA

Enhancer looping protein LDB1 regulates hepatocyte gene expression by cooperating with liver transcription factors

Project description:To study LDB1 function in liver cell, gene expression changes and LDB1 binding and H3K27ac modification were detected by RNA-seq and ChIP-seq.

2022-08-22 | GSE179845 | GEO

IRF2BP2 affects T-ALL cell proliferation by cooperating with master transcription factors

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-10-26 | GSE267455 | GEO

IRF2BP2 affects T-ALL cell proliferation by cooperating with master transcription factors [RNA-Seq]

2024-10-26 | GSE267261 | GEO

IRF2BP2 affects T-ALL cell proliferation by cooperating with master transcription factors [Cut&Tag]

Project description:Knocking down IRF2BP2 led to decreased T-cell acute lymphoblastic leukemia (T-ALL) cell survival and growth both in vitro and in vivo. To explore IRF2BP2-dependent gene regulation, RNA-seq analysis was conducted and the differently expressed genes were revealed in the IRF2BP2-knockdown J.gamma1 cells in comparison to control group. Cleavage Under Targets and Tagmentation (CUT&Tag) showed the co-localization of IRF2BP2 with several master transcription factors on chromatin in J.gamma1 cells.

2024-10-26 | GSE267451 | GEO

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