Exploring a Link between Histone Demethylases and Alternative Polyadenylation
Lauren P. Blair1, Ramon Lorenzo D. Labitigan1, Zongzhi Liu1, Stephanie Byrum2, Alan J. Tackett2 and Qin Yan1
1Department of Pathology, Yale School of Medicine, New Haven, CT and 2Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
ABSTRACT
Many recent reports in both mainstream and scientific media have centered on the concept that “DNA is not destiny.” The key component of this phenomenon is epigenetics. Gene expression is regulated epigenetically on many levels. One key mechanism is the addition and removal of modifications to the N-terminal tails of histones. Jhd2 is a lysine demethylase found in Saccharomyces cerevisiae. It is the only demethylase capable of removing the activating H3K4me3 mark. Many epigenetic regulators have been shown to work as part of one or more complexes. Although Jhd2 and its human homolog, PLU1, are both major players in transcription in yeast and humans, they have not been comprehensively reported as being associated with any established complexes. In an effort to study the involvement of histone demethylases in cellular processes, we have affinity purified a TAP-tagged version of Jhd2. We found that it purifies with multiple components of yeast polyadenylation machinery. Specifically, Jhd2 co-purifies with Cpf11 and Yra1 but not Clp1. Recent reports note that Yra1 competes with Clp1 for binding Cpf11 resulting in alternative polyadenylation over canonical polyadenylation. The link between polyadenylation and demethylases has been recorded in plants but not in yeast or mammals.
PLU1, a human homolog of Jhd2, is upregulated in cancer tissue but not in normal tissue. This makes it an ideal target for cancer therapies. In addition to our yeast polyadenylation studies, we have found that PLU1 expression has an effect on the alternative polyadenylation (APA) of the oncogene CCND1. This alternative polyadenylation results in a loss of miRNA sites and therefore allows CCND1 to escape degradation by the RISC complex. Studies have shown that this form of APA is used commonly in cancer tissues as a mechanism for oncogenes to elude the normal degradation machinery in the cell. This phenomenon results in increased cell proliferation and tumor progression. We have developed a system for identifying transcripts whose APA is directly affected by PLU1 expression. Our system involves a comparison of gene expression and protein expression profiles from normal and PLU1 knockdown cell lines. Thus far, we have identified RAD23B as a potential target.
By elucidating the novel mechanism of histone demethylase involvement in APA in yeast and human cells, we will attain a better understanding of the mechanisms by which cancer progresses. These studies have the potential to lead to development of new drugs to treat cancer or novel uses for existing drugs targeted at the processes outlined here.
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