AML displays increased CTCF occupancy associated with ...

MYELOID NEOPLASIA| JULY 16, 2020

AML displays increased CTCF occupancy associated with aberrant gene expression and transcription factor binding

Huthayfa Mujahed, Sophia Miliara, Anne Neddermeyer, Sofia Bengtzén, Christer Nilsson, Stefan Deneberg, Lina Cordeddu, Karl Ekwall, Andreas Lennartsson, Sören Lehmann

Blood (2020) 136 (3): 339–352.

https://doi.org/10.1182/blood.2019002326

Key Points

AML cells display aberrant CTCF occupancy, and patients with TET2 mutations show a particularly strong gain of CTCF binding in promoters.

Aberrant CTCF binding is enriched at CEBPA, PU.1, and RUNX1 motifs, and azacitidine exerts profound effects on CTCF occupancy.

Abstract

CCTC-binding factor (CTCF) is a key regulator of gene expression through organization of the chromatin structure. Still, it is unclear how CTCF binding is perturbed in leukemia or in cancer in general. We studied CTCF binding by chromatin immunoprecipitation sequencing in cells from patients with acute myeloid leukemia (AML) and in normal bone marrow (NBM) in the context of gene expression, DNA methylation, and azacitidine exposure. CTCF binding was increased in AML compared with NBM. Aberrant CTCF binding was enriched for motifs for key myeloid transcription factors such as CEBPA, PU.1, and RUNX1. AML with TET2 mutations was characterized by a particularly strong gain of CTCF binding, highly enriched for gain in promoter regions, while AML in general was enriched for changes at enhancers. There was a strong anticorrelation between CTCF binding and DNA methylation. Gain of CTCF occupancy was associated with increased gene expression; however, the genomic location (promoter vs distal regions) and enrichment of motifs (for repressing vs activating cofactors) were decisive for the gene expression pattern. Knockdown of CTCF in K562 cells caused loss of CTCF binding and transcriptional repression of genes with changed CTCF binding in AML, as well as loss of RUNX1 binding at RUNX1/CTCF-binding sites. In addition, CTCF knockdown caused increased differentiation. Azacitidine exposure caused major changes in CTCF occupancy in AML patient cells, partly by restoring a CTCF-binding pattern similar to NBM. We conclude that AML displays an aberrant increase in CTCF occupancy that targets key genes for AML development and impacts gene expression.

Subjects:

Hematopoiesis and Stem Cells, Myeloid Neoplasia

Topics:

azacitidine, chromatin, chromatin immunoprecipitation sequencing, dna methylation, gene expression, leukemia, myelocytic, acute, transcription factor, dna, kiaa1546 gene, genes

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