Phosphatidylinositol-4-phosphate 5-Kinase 1α Modulates Ribosomal RNA Gene Silencing through Its Interaction with Histone H3 Lysine 9 Trimethylation and Heterochromatin Protein HP1-α

• Published in: The Journal of biological chemistry Vol. 290; no. 34; pp. 20893 - 20903
• Main Authors: Chakrabarti, Rajarshi, Sanyal, Sulagna, Ghosh, Amit, Bhar, Kaushik, Das, Chandrima, Siddhanta, Anirban
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 21.08.2015; American Society for Biochemistry and Molecular Biology
• Subjects: Cell Biology; Cell Cycle; Cell Line, Tumor; Cell Nucleolus - genetics; Cell Nucleolus - metabolism; chromatin immunoprecipitation (ChIP); Chromosomal Proteins, Non-Histone - genetics; Chromosomal Proteins, Non-Histone - metabolism; DNA, Ribosomal - genetics; DNA, Ribosomal - metabolism; Epigenesis, Genetic; Gene Silencing; H3K9me3; HEK293 Cells; Heterochromatin - chemistry; Heterochromatin - metabolism; histone; Histones - genetics; Histones - metabolism; HP1α; Humans; Lysine - metabolism; MCF-7 Cells; Methylation; nucleolus; Phosphatidylinositol 4,5-Diphosphate - biosynthesis; phosphatidylinositol-4-phosphate 5-kinase 1α; Phosphotransferases (Alcohol Group Acceptor) - genetics; Phosphotransferases (Alcohol Group Acceptor) - metabolism; rDNA; Signal Transduction; small ubiquitin-like modifier (SUMO); Sumoylation; rDNA; sumoylation; H3K9me3; nucleolus; HP1α; histone; small ubiquitin-like modifier (SUMO); phosphatidylinositol-4-phosphate 5-kinase 1α; chromatin immunoprecipitation (ChIP)
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M114.633727

Phosphoinositide signaling has been implicated in the regulation of numerous cellular processes including cytoskeletal dynamics, cellular motility, vesicle trafficking, and gene transcription. Studies have also shown that nuclear phosphoinositide(s) regulates processes such as mRNA export, cell cycle progression, gene transcription, and DNA repair. We have shown previously that the nuclear form of phosphatidylinositol-4-phosphate 5-kinase 1α (PIP5K), the enzyme responsible for phosphatidylinositol 4,5-bisphosphate synthesis, is modified by small ubiquitin-like modifier (SUMO)-1. In this study, we have shown that due to the site-specific Lys to Ala mutations of PIP5K at Lys-244 and Lys-490, it is unable to localize in the nucleus and nucleolus, respectively. Furthermore, by using chromatin immunoprecipitation assays, we have observed that PIP5K associates with the chromatin silencing complex constituted of H3K9me3 and heterochromatin protein 1α at multiple ribosomal DNA (rDNA) loci. These interactions followed a definite cyclical pattern of occupancy (mostly G1) and release from the rDNA loci (G1/S) throughout the cell cycle. Moreover, the immunoprecipitation results clearly demonstrate that PIP5K SUMOylated at Lys-490 interacts with components of the chromatin silencing machinery, H3K9me3 and heterochromatin protein 1α. However, PIP5K does not interact with the gene activation signature protein H3K4me3. This study, for the first time, demonstrates that PIP5K, an enzyme actively associated with lipid modification pathway, has additional roles in rDNA silencing. Background: Cell cycle-specific localization and nuclear function of Phosphatidylinositol-4-phosphate 5-kinase1α (PIP5K) is unclear. Results: SUMOylation of PIP5K at Lys-244 and Lys-490 directs its nuclear entry and its interaction with H3K9me3/HP1-α, respectively. Conclusion: PIP5K functions as a member of the rDNA silencing complex. Significance: Our results indicate a possible novel epigenetic role of PIP5K per se in silencing of rDNA.