Abstract
Epigenetic cellular memory mechanisms that involve polycomb and trithorax group of proteins are well conserved across metazoans. The cis-acting elements interacting with these proteins, however, are poorly understood in mammals. In a directed search we identified a potential polycomb responsive element with 25 repeats of YY1 binding motifthatwe designate PRE-PIK3C2B as it occurs in the first intron of human PIK3C2B gene. It down regulates reporter gene expression in HEK cells and the repression is dependent on polycomb group of proteins (PcG). We demonstrate that PRE-PIK3C2B interacts directly with YY1 in vitro and recruits PRC2 complex in vivo. The localization of PcG proteins including YY1 to PRE-PIK3C2B in HEK cells is decreased on knock-down of either YY1 or SUZ12. Endogenous PRE-PIK3C2B shows bivalent marking having H3K27me3 and H3K4me3 for repressed and active state respectively. In transgenic Drosophila, PRE-PIK3C2B down regulates mini-white expression, exhibits variegation and pairing sensitive silencing (PSS), which has not been previously demonstrated for mammalian PRE. Taken together, our results strongly suggest that PRE-PIK3C2B functions as a site of interaction for polycomb proteins.
Highlights
During development, the transcription status of the genes is maintained from embryonic to adult stages through mitotic or cellular memory mechanisms, which leads to the establishment of different cell lineages
We aimed at identifying putative PREs in the human genome based on in silico analysis for the occurrence of common motifs for binding of polycomb complexes
The gene set we selected for analysis shows over or under expression in acute lymphoblastic leukemia (ALL) patients with t(11:4) translocation and detected a high density of YY1 binding motif in the first intron of PIK3C2B
Summary
The transcription status of the genes is maintained from embryonic to adult stages through mitotic or cellular memory mechanisms, which leads to the establishment of different cell lineages. The polycomb (PcG) and trithorax (TrxG) group of proteins, discovered in the context of regulation of homeotic genes in Drosophila, function through their interaction with chromatin as multi-protein complexes [1]. These genes are well conserved in metazoans and their mammalian counterparts are transcription regulators that help in maintaining cell identity through chromatin modification [2,3]. In Drosophila, PcG/TrxG proteins regulate their target genes by binding to specific DNA elements called Polycomb/trithorax response elements (PRE/ TREs) which interact with both activating and repressive complexes and PRE/TREs recruit PcG/TrxG complexes at multiple loci as seen on polytene chromosomes [9,10]. Recent work has suggested the possible additional roles for proteins such as the corepressor CtBP, the DNA binding factor Grainyhead(GRH) and members of the Sp1/KLF family, which are DNA binding factors [14,15,16]
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