Profiling of the Chromatin-associated Proteome Identifies HP1BP3 as a Novel Regulator of Cell Cycle Progression

Abstract

The chromatin-associated proteome (chromatome) regulates cellular gene expression by restricting access of transcriptional machinery to template DNA, and dynamic re-modeling of chromatin structure is required to regulate critical cell functions including growth and replication, DNA repair and recombination, and oncogenic transformation in progression to cancer. Central to the control of these processes is efficient regulation of the host cell cycle, which is maintained by rapid changes in chromatin conformation during normal cycle progression. A global overview of chromatin protein organization is therefore essential to fully understand cell cycle regulation, but the influence of the chromatome and chromatin binding topology on host cell cycle progression remains poorly defined. Here we used partial MNase digestion together with iTRAQ-based high-throughput quantitative proteomics to quantify chromatin-associated proteins during interphase progression. We identified a total of 481 proteins with high confidence that were involved in chromatin-dependent events including transcriptional regulation, chromatin reorganization, and DNA replication and repair, whereas the quantitative data revealed the temporal interactions of these proteins with chromatin during interphase progression. When combined with biochemical and functional assays, these data revealed a strikingly dynamic association of protein HP1BP3 with the chromatin complex during different stages of interphase, and uncovered a novel regulatory role for this molecule in transcriptional regulation. We report that HP1BP3 protein maintains heterochromatin integrity during G 1-S progression and regulates the duration of G 1 phase to critically influence cell proliferative capacity. Molecular & Cellular

Systems genetics identifies Hp1bp3 as a novel modulator of cognitive aging

“…Functions of Hp1bp3 that have been identified include regulation of chromatin structure (Dutta, et al, 2014), gene expression (Garfinkel, et al, 2015b), cell cycle progression (Dutta, et al, 2014), and insulin signaling (Garfinkel, et al, 2015a), several of which were supported by our analyses. For example, positive correlates of Hp1bp3 were significantly enriched both in nuclear localization (Figure 6a) and insulin signaling (Fig 6b).…”

“…A number of studies suggest this family of proteins play a highly specific role in gene expression, possibly due to their role in chromatin organization (Garfinkel, et al, 2015b). It is thought that Hp1bp3 contributes to the inter-conversion of heterochromatin and euchromatin (Dutta, et al, 2014), thereby activating or silencing specific genes as needed. As long-term memory and cognition depend on de novo gene expression in response to a learning and/or training event (Cavallaro, et al, 2002), it is possible that Hp1bp3 is regulating the transcription of specific genes necessary for successful cognitive function.…”

Quantitative Profiling of Chromatome Dynamics Reveals a Novel Role for HP1BP3 in Hypoxia-induced Oncogenesis

“…S6A and S6B). Indeed, we have previously demonstrated that HP1BP3 plays an important role in the maintenance of heterochromatin integrity, and that depletion of HP1BP3 increases the MNase sensitivity of chromatin samples (38). Accordingly, our MNase digestion experiments confirmed that hypoxia increased chromatin resistance to nuclease activity, suggesting that these samples contained increased proportions of heterochromatin compaction (Fig.…”

“…7A). DSB repair by homologous recombination is restricted to the late S and G 2 phases of the cell cycle, whereas NHEJ repair of DSBs can occur throughout interphase (47,48), and our previous analyses of cellcycle-associated changes in the chromatome suggested that NHEJ repair mechanisms operate throughout interphase but are particularly active during G 1 and G 2 (38). Our findings are therefore consistent with the concept that hypoxia induces G 0 -G 1 cycle arrest to enhance NHEJ-mediated repair of DSBs and increase cancer cell resistance to radio-and chemotherapy.…”

Replication of Epigenetic Postpartum Depression Biomarkers and Variation with Hormone Levels

“…HP1BP3 associates with ERβ in culture (Nassa et al, 2011), binds to chromatin specifically at the repressive histone 3 lysine 9 trimethylation (H3K9me3) mark, and is expressed in most tissues with 10-fold higher levels in the brain (Garfinkel et al, 2015). Knockdown of HP1BP3 by siRNA in culture leads to significant expression changes in hundreds of genes, suggesting it is involved in transcriptional regulation (Dutta et al, 2014;Garfinkel et al, 2015). Interestingly, some genes with the most significantly altered expression in culture experiments are known to mediate progesterone inhibition of estradiol signaling in the uterus, such as MIG-6 (Yoo et al, 2015).…”