Proliferating Cell Nuclear Antigen Associates with Histone Deacetylase Activity, Integrating DNA Replication and Chromatin Modification

Abstract

Faithful inheritance of the chromatin structure is essential for maintaining the gene expression integrity of a cell. Histone modification by acetylation and deacetylation is a critical control of chromatin structure. In this study, we test the hypothesis that histone deacetylase 1 (HDAC1) is physically associated with a basic component of the DNA replication machinery as a mechanism of coordinating histone deacetylation and DNA synthesis. Proliferating cell nuclear antigen (PCNA) is a sliding clamp that serves as a loading platform for many proteins involved in DNA replication and DNA repair. We show that PCNA interacts with HDAC1 in human cells and in vitro and that a considerable fraction of PCNA and HDAC1 colocalize in the cell nucleus. PCNA associates with histone deacetylase activity that is completely abolished in the presence of the HDAC inhibitor trichostatin A. Trichostatin A treatment arrests cells at the G 2 -M phase of the cell cycle, which is consistent with the hypothesis that the proper formation of the chromatin after DNA replication may be important in signaling the progression through the cell cycle. Our results strengthen the role of PCNA as a factor coordinating DNA replication and epigenetic inheritance.Epigenetic markings play an essential role in regulating the gene expression program of vertebrate cells. One of the fundamental challenges of cell division is therefore coordinating the processes of genetic and epigenetic inheritance. The cell must possess multiple mechanisms to coordinate these processes (1). For example, DNA methylation is coordinated with DNA replication (2) by physical association of maintenance DNA methyltransferase 1 with the DNA replication fork protein PCNA 1 (3). Inhibition of DNA methyltransferase 1 leads to inhibition of initiation of DNA replication (4).Similar to DNA methylation, DNA replication-coupled chromatin assembly is essential for the inheritance of the epigenetic code. The specific targeting of nucleosome assembly to the newly synthesized DNA is achieved by direct interaction of histone chaperone CAF-1 with PCNA (5). PCNA is a homotrimeric protein that forms a sliding clamp around DNA and functions as a DNA polymerase processivity factor during replication and nucleotide excision repair. Through its multiple protein-protein interactions, PCNA coordinates events in replication, epigenetic inheritance, repair, and cell cycle control (6). A recent study in Saccharomyces cerevisiae has shown that several mutations in PCNA decrease silencing at telomeres and at the mating-type HMR locus (7). Furthermore, mutations in the Drosophila PCNA gene mus209 suppress repression in the vicinity of heterochromatin (8). The disruption of epigenetic silencing has been attributed to the inability of some of these mutants to associate with CAF-1. However, synergism of several PCNA mutants with CAF-1 mutants suggested that PCNA may participate in silencing through another factor.During nucleosome assembly, histones H3 and H4 undergo transient acetylation before their deposi...

Epigenetic inheritance: Uncontested?

“…Similarly, many histone modifiers have been reported to localize to the replication forks, suggesting potential replication-coupled reestablishment of histone modifications on the nascent chromatin. These include PCNA-mediated replication-coupled recruitment of HDACs [45]; CAF-1-mediated MBD1 and SETDB1 recruitment during heterochromatin DNA replication [46][47][48]; and DNMT1-mediated replicationcoupled recruitment of G9a [49]. Finally, the PRC2 complex has also been reported to localize to the replication foci throughout S phase [50].…”

Nucleosome assembly and epigenetic inheritance

“…PCNA directly interacts with a series of chromatin modifying enzymes, and potentially recruits them to replication foci. These factors include CAF-1 (Shibahara and Stillman 1999;Moggs et al, 2000), HDACs (Milutinovic et al, 2002), ATP dependent chromatin remodeling complex WSTF-SNF2h (Poot et al, 2004), histone lysine methyltransferse PR-SET7 (Jørgensen et al, 2007;Huen et al, 2008) and DNA methyltransferase DNMT1 (Leonhardt et al, 1992;Chuang et al, 1997). CAF-1 is also reported to interact with chromatin factors, including MBD1 (methyl CpG-binding protein 1) and SETDB1 during heterochromatin DNA replication (Reese et al, 2003;Sarraf and Stancheva, 2004).…”

Heterochromatin?many flavours, common themes

“…(81) PCNA recruits the maintenance DNA methyltransferase DNMT1. (83) The origin recognition complex (ORC) and the replication of heterochromatin ORC is a six-subunit, DNA-binding complex necessary for initiation and temporal control of eukaryotic replication. ORC may also recruit proteins involved in the maintenance of heterochromatin.…”