QKI-Mediated Alternative Splicing of the Histone Variant MacroH2A1 Regulates Cancer Cell Proliferation

Abstract

The histone variant macroH2A1 contains a carboxyl-terminal ϳ30-kDa domain called a macro domain. MacroH2A1 is produced as one of two alternatively spliced forms, macroH2A1.1 and macroH2A1.2. While the macro domain of macroH2A1.1 can interact with NAD ؉ -derived small molecules, such as poly(ADP-ribose), macroH2A1.2's macro domain cannot. Here, we show that changes in the alternative splicing of macroH2A1 pre-mRNA, which lead to a decrease in macroH2A1.1 expression, occur in a variety of cancers, including testicular, lung, bladder, cervical, breast, colon, ovarian, and endometrial. Furthermore, reintroduction of macroH2A1.1 suppresses the proliferation of lung and cervical cancer cells in a manner that requires the ability of macroH2A1.1 to bind NAD ؉ -derived metabolites. MacroH2A1.1-mediated suppression of proliferation occurs, at least in part, through the reduction of poly(ADP-ribose) polymerase 1 (PARP-1) protein levels. By analyzing publically available expression and splicing microarray data, we identified splicing factors that correlate with alterations in macroH2A1 splicing. Using RNA interference, we demonstrate that one of these factors, QKI, regulates the alternative splicing of macroH2A1 pre-mRNA, resulting in increased levels of macroH2A1.1. Finally, we demonstrate that QKI expression is significantly reduced in many of the same cancer types that demonstrate a reduction in macroH2A1.1 splicing.

Tumor microenvironment–associated modifications of alternative splicing

“…6A; Supplemental Table S4), and suggesting that breast and ovarian cancer use similar mechanisms for modifying the splicing patterns of tumor-associated ASEs. Consistently, an independent study using a large number of breast cancer tissues concluded that QKI expression is reduced in breast tumors (P-value <3.0 × 10 −3 , t-test) (Novikov et al 2011). In our hands, however, the most striking difference between tumor and normal breast tissues was not the change in global expression but rather in the pattern of QKI splicing ( Fig.…”

“…Closer examination of the effects of knocking down cancer-associated splicing factors on CSS ASEs revealed two groups of splicing factors. The first group includes core spliceosomal factors such as SNRPD2 (Schumperli and Pillai 2004) and SNRPG (Ma et al 2005), while the second includes alternative splicing regulators RBFOX2 (Sun et al 2012) and QKI (Novikov et al 2011). Both groups are underexpressed in the tumor microenvironment and modified the splicing of three out of five CSS ASEs in the SKOV3ip1 cell line (Fig.…”

MacroH2A in Stem Cells: A Story Beyond Gene Repression

“…In this context, it is interesting to point out that melanoma cells are dedifferentiated cells that reactivate embryonic signaling pathways [54]. Others could point out functional differences between macroH2A1 splice variants in different types of cancer [55,56]. Ongoing and future studies are likely to reveal the importance, the regulation and the molecular function of macroH2A-containing epigenetic mechanisms in a larger number of physiological and pathological processes.…”

MacroH2A suppresses the proliferation of the B16 melanoma cell line

“…In the present study, the artificial altering of macroH2A expression was performed by the interference and overex- (25)(26)(27)(28)(29)(30). In these cancer types, the expression levels of macroH2A decreased significantly in tumor tissues compared with normal tissues.…”