CENP-A nucleosomes localize to transcription factor hotspots and subtelomeric sites in human cancer cells

Abstract

BackgroundThe histone H3 variant CENP-A is normally tightly regulated to ensure only one centromere exists per chromosome. Native CENP-A is often found overexpressed in human cancer cells and a range of human tumors. Consequently, CENP-A misregulation is thought to contribute to genome instability in human cancers. However, the consequences of such overexpression have not been directly elucidated in human cancer cells.ResultsTo investigate native CENP-A overexpression, we sought to uncover CENP-A-associated defects in human cells. We confirm that CENP-A is innately overexpressed in several colorectal cancer cell lines. In such cells, we report that a subset of structurally distinct CENP-A-containing nucleosomes associate with canonical histone H3, and with the transcription-coupled chaperones ATRX and DAXX. Furthermore, such hybrid CENP-A nucleosomes localize to DNase I hypersensitive and transcription factor binding sites, including at promoters of genes across the human genome. A distinct class of CENP-A hotspots also accumulates at subtelomeric chromosomal locations, including at the 8q24/Myc region long-associated with genomic instability. We show this 8q24 accumulation of CENP-A can also be seen in early stage primary colorectal tumors.ConclusionsOur data demonstrate that excess CENP-A accumulates at noncentromeric locations in the human cancer genome. These findings suggest that ectopic CENP-A nucleosomes could alter the state of the chromatin fiber, potentially impacting gene regulation and chromosome fragility.Electronic supplementary materialThe online version of this article (doi:10.1186/1756-8935-8-2) contains supplementary material, which is available to authorized users.

Posttranslational mechanisms controlling centromere function and assembly

“…CENP-A overexpression and misincorporation at non-centromeric loci is observed in many cancers, and serves as a potent prognostic marker in conjunction with other centromere genes [75–78]. Inhibition of CENP-A amino terminal methylation and hyperphosphorylation of Ser18 by cyclin E1/CDK2 contributes to chromosome instability [11,12 •• ], suggesting that perturbations in posttranslational modifications of CENP-A may contribute to cancer phenotypes.…”

Essential role for centromeric factors following p53 loss and oncogenic transformation

“…It is equally unknown whether this up-regulation is limited to particular types of cancer or at what point it occurs during tumor evolution. Initial work in human cancer cell lines focusing on exogenously overexpressed CENP-A showed that it can mislocalize outside the centromere in euchromatin, which is equally the case for the endogenously up-regulated protein (Athwal et al 2015). Given how H3.1 and H3.3 oncohistones harboring K-to-M mutations contribute to cell type-specific tumors such as glioblastomas, chondroblastomas, and sarcomas (Schwartzentruber et al 2012;Sturm et al 2012;Fang et al 2016;Lu et al 2016), a tempting hypothesis could be that aberrant CENP-A expression might drive tumorigenesis in a cell type-specific manner.…”

Posttranslational modifications of CENP-A: marks of distinction

“…On the other hand, CENP-A overexpression is associated with its mislocalization outside the centromere to euchromatic regions in tumorigenesis (Allshire and Karpen 2008; Amato et al 2009; Athwal et al 2015; Filipescu et al 2017; Hu et al 2010; Lacoste et al 2014; Li et al 2011; Shrestha et al 2017; Tomonaga et al 2003; Wu et al 2012; Zhang et al 2016). Therefore, in normal conditions, there must exist a mechanism to eliminate CENP-A from non-centromeric loci.…”