Three-dimensional regulation ofHOXAcluster genes by acis-element in hematopoietic stem cell and leukemia

Abstract

Proper gene regulation is crucial for cellular differentiation, and dysregulation of key genes can lead to diseased states such as cancer. The HOX transcription factors play such a role during hematopoiesis, and aberrant expression of certain HOXA genes is found in certain acute myeloid leukemias (AMLs). While studies have shown that these genes are targeted by a variety of mutant proteins including mutant NPM1, MLL fusions, and NUP98 fusions, little is known about how long-range 3D chromatin interactions regulate the HOXA genes in normal hematopoiesis and leukemia. Here, we report the interaction between the HOXA cluster with a ~1.3 Mb upstream DNA methylation Canyon termed "Geneless Canyon" (GLC) in human CD34+/CD38-hematopoietic stem cells (HSCs) and AML cell lines. We show that CRISPR-Cas9 mediated deletion of the whole GLC region reduces the expression of the distal HOXA genes and compromises HSC and leukemia cells self-renewal. This long-range chromatin interaction brings the HOXA cluster in contact with the nuclear pore complex (NPC) at the nuclear periphery, which promotes HOXA gene expression and maintains HSC and leukemia cell self-renewal. These findings reveal how long-range 3D chromatin organization regulates key transcription factor genes in both normal and diseased hematopoietic cells.

Boundary stacking interactions enable cross-TAD enhancer-promoter communication during limb development

“…Many of these islands, as well as the genes they regulate, are closely linked to CTCF borders 13 . Similarly in human hematopoietic stem cells, enhancers of anterior Hoxa genes, located 1.3 Mb apart from their promoters and separated by TAD borders, are themselves juxtaposed to a strong TAD border 11,63 . In Drosophila, the promoter of the Hox gene Abd-B sits near a boundary and communicates across intervening borders to its distal enhancers iab-7 and iab-5 10 , as does the Hox gene Scr, whose enhancers also bypass the intervening gene ftz 62 .…”

“…Nonetheless, several developmentally important enhancers are separated by TAD borders and CTCF bound insulators from the genes they control. These include genes with key roles in axial patterning 10 , hematopoiesis 11 and limb patterning 12,13 . As candidate enhancer-promoter (E-P) interactions are frequently hypothesized and tested based on linear proximity to a gene, guided by previously mapped TAD boundaries, and studied in cell culture, it is likely that the genomewide frequency of TAD border-bypassing E-P pairs is underestimated.…”

Toward an understanding of the relation between gene regulation and 3D genome organization

“…DNA methylation canyons [49], characterized by low DNA methylation and high H3K27me3 levels, can form cell‐type specific and long‐range chromatin interactions that are independent of CTCF and cohesin, contributing to the formation of sub‐compartments. Similarly, specific spatial interactions between HOXA genes and DNA methylation canyon in acute myeloid leukemia promote HOXA genes expression [50], again emphasizing the vital role of epigenetic information in genome architecture. Cai et al [51] identified H3K27me3‐rich regions, termed as super‐silencers, and found that these regions (similar chromatin state) prefer to spatially interact with each other, in association with gene regulation ( e.g.…”

IKAROS and MENIN coordinate therapeutically actionable leukemogenic gene expression in MLL-r acute myeloid leukemia

“…The cBio Cancer Genomics Portal (cBIOPortal) 34 , 90 was used to examine IKZF1 gene expression across a range cancer subtypes utilizing data from The Cancer Genome Atlas (TCGA) ( https://www.cancer.gov/tcga ). For ABC enhancer predictions, average Hi-C matrix data was utilized, as recommended 45 , and obtained from the Broad Institute of MIT and Harvard ( https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction ) as well as an additional publicly available HiC dataset for MV4;11 91 .…”