Contribution of CTCF binding to transcriptional activity at the HOXA locus in NPM1-mutant AML cells

Reza Ghasemi,Heidi Struthers,Elisabeth R Wilson,David H Spencer

doi:10.1038/s41375-020-0856-3

Reza Ghasemi, Heidi Struthers + Show 2 more

Open Access

https://doi.org/10.1038/s41375-020-0856-3

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Abstract

Transcriptional regulation of the HOXA genes is thought to involve CTCF-mediated chromatin loops and the opposing actions of the COMPASS and Polycomb epigenetic complexes. We investigated the role of these mechanisms at the HOXA cluster in AML cells with the common NPM1c mutation, which express both HOXA and HOXB genes. CTCF binding at the HOXA locus is conserved across primary AML samples, regardless of HOXA gene expression, and defines a continuous chromatin domain marked by COMPASS-associated histone H3 trimethylation in NPM1-mutant primary AML samples. Profiling of the three-dimensional chromatin architecture in primary AML samples with the NPM1c mutation identified chromatin loops between the HOXA cluster and loci in the SNX10 and SKAP2 genes, and an intergenic region located 1.4 Mbp upstream of the HOXA locus. Deletion of CTCF binding sites in the NPM1-mutant OCI-AML3 AML cell line reduced multiple long-range interactions, but resulted in CTCF-independent loops with sequences in SKAP2 that were marked by enhancer-associated histone modifications in primary AML samples. HOXA gene expression was maintained in CTCF binding site mutants, indicating that transcriptional activity at the HOXA locus in NPM1-mutant AML cells may be sustained through persistent interactions with SKAP2 enhancers, or by intrinsic factors within the HOXA gene cluster.

Highlights

The HOX genes encode developmentally regulated transcription factors that are highly expressed in acute myeloid leukemia (AML) and are important drivers of malignant self-renewal in this disease
We investigated histone modifications and chromatin interactions at the HOXA locus in NPM1-mutated AML samples vs. other AML subtypes, and used a NPM1-mutant AML cell line model to determine whether CTCF at the HOXA locus is required to maintain HOXA expression and chromatin structure
ChIP-seq for CTCF using OCI-AML3 cells identified the four conserved CTCF sites observed in primary AML samples (Figs. 3b and S3A), as well as two smaller peaks in the anterior HOXA cluster

Summary

Introduction

The HOX genes encode developmentally regulated transcription factors that are highly expressed in acute myeloid leukemia (AML) and are important drivers of malignant self-renewal in this disease. Previous studies have shown that expression of HOX family members in AML is nearly always restricted to specific genes in the HOXA and/or HOXB clusters (HOXC and HOXD genes are rarely expressed), and that expression patterns correlate with recurrent AML mutations [1].

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