Lamins, the nuclear intermediate filaments, are important regulators of nuclear structural integrity as well as nuclear functional processes such as DNA transcription, replication and repair, and epigenetic regulations. A portion of phosphorylated lamin A/C localizes to the nuclear interior in interphase, forming a lamin A/C pool with specific properties and distinct functions. Nucleoplasmic lamin A/C molecular functions are mainly dependent on its binding partners; therefore, revealing new interactions could give us new clues on the lamin A/C mechanism of action. In the present study, we show that lamin A/C interacts with nuclear phosphoinositides (PIPs), and with nuclear myosin I (NM1). Both NM1 and nuclear PIPs have been previously reported as important regulators of gene expression and DNA damage/repair. Furthermore, phosphorylated lamin A/C forms a complex with NM1 in a phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2)-dependent manner in the nuclear interior. Taken together, our study reveals a previously unidentified interaction between phosphorylated lamin A/C, NM1, and PI(4,5)P2 and suggests new possible ways of nucleoplasmic lamin A/C regulation, function, and importance for the formation of functional nuclear microdomains.

• Keywords
• NM1, PI(4,5)P2, cell nucleus, lamin A/C, nuclear lamina, nuclear myosin 1, nucleoplasm, phosphoinositides, phosphorylation,
• MeSH
• Cell Nucleus * metabolism   MeSH
• Interphase MeSH
• Intermediate Filaments metabolism   MeSH
• Lamin Type A * metabolism   MeSH
• Humans MeSH
• Cell Line, Tumor MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Lamin Type A * MeSH

Here, we provide evidence for the presence of Myosin phosphatase rho-interacting protein (MPRIP), an F-actin-binding protein, in the cell nucleus. The MPRIP protein binds to Phosphatidylinositol 4,5-bisphosphate (PIP2) and localizes to the nuclear speckles and nuclear lipid islets which are known to be involved in transcription. We identified MPRIP as a component of RNA Polymerase II/Nuclear Myosin 1 complex and showed that MPRIP forms phase-separated condensates which are able to bind nuclear F-actin fibers. Notably, the fibrous MPRIP preserves its liquid-like properties and reforms the spherical shaped condensates when F-actin is disassembled. Moreover, we show that the phase separation of MPRIP is driven by its long intrinsically disordered region at the C-terminus. We propose that the PIP2/MPRIP association might contribute to the regulation of RNAPII transcription via phase separation and nuclear actin polymerization.

• Keywords
• MPRIP, PIP2, actin, nucleus, phase separation,
• MeSH
• Adaptor Proteins, Signal Transducing chemistry   metabolism   MeSH
• Actins metabolism   MeSH
• Cell Nucleus drug effects   metabolism   MeSH
• Phosphatidylinositol 4,5-Diphosphate metabolism   MeSH
• Glycols pharmacology   MeSH
• Humans MeSH
• Myosin Type I metabolism   MeSH
• Cell Line, Tumor MeSH
• Protein Domains MeSH
• RNA Polymerase II metabolism   MeSH
• Subcellular Fractions metabolism   MeSH
• Protein Binding drug effects   MeSH
• Green Fluorescent Proteins metabolism   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Adaptor Proteins, Signal Transducing MeSH
• Actins MeSH
• Phosphatidylinositol 4,5-Diphosphate MeSH
• Glycols MeSH
• hexamethylene glycol MeSH Browser
• MPRIP protein, human MeSH Browser
• MYO1C protein, human MeSH Browser
• Myosin Type I MeSH
• RNA Polymerase II MeSH
• Green Fluorescent Proteins MeSH

Specific nuclear sub-compartments that are regions of fundamental processes such as gene expression or DNA repair, contain phosphoinositides (PIPs). PIPs thus potentially represent signals for the localization of specific proteins into different nuclear functional domains. We performed limited proteolysis followed by label-free quantitative mass spectrometry and identified nuclear protein effectors of the most abundant PIP-phosphatidylinositol 4,5-bisphosphate (PIP2). We identified 515 proteins with PIP2-binding capacity of which 191 'exposed' proteins represent a direct PIP2 interactors and 324 'hidden' proteins, where PIP2 binding was increased upon trypsin treatment. Gene ontology analysis revealed that 'exposed' proteins are involved in the gene expression as regulators of Pol II, mRNA splicing, and cell cycle. They localize mainly to non-membrane bound organelles-nuclear speckles and nucleolus and are connected to the actin nucleoskeleton. 'Hidden' proteins are linked to the gene expression, RNA splicing and transport, cell cycle regulation, and response to heat or viral infection. These proteins localize to the nuclear envelope, nuclear pore complex, or chromatin. Bioinformatic analysis of peptides bound in both groups revealed that PIP2-binding motifs are in general hydrophilic. Our data provide an insight into the molecular mechanism of nuclear PIP2 protein interaction and advance the methodology applicable for further studies of PIPs or other protein ligands.

• Keywords
• limited proteolysis, mass spectrometry, nucleus, phosphatidylinositol 4,5-bisphosphate, phosphoinositides,
• MeSH
• Cell Nucleus metabolism   MeSH
• Phosphatidylinositol 4,5-Diphosphate metabolism   MeSH
• Gene Ontology MeSH
• HeLa Cells MeSH
• Mass Spectrometry * MeSH
• Hydrophobic and Hydrophilic Interactions MeSH
• Humans MeSH
• Peptides metabolism   MeSH
• Proteolysis * MeSH
• Proteome chemistry   metabolism   MeSH
• Gene Expression Regulation MeSH
• Amino Acid Sequence MeSH
• Trypsin metabolism   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Phosphatidylinositol 4,5-Diphosphate MeSH
• Peptides MeSH
• Proteome MeSH
• Trypsin MeSH

Phosphoinositides are glycerol-based phospholipids, and they play essential roles in cellular signalling, membrane and cytoskeletal dynamics, cell movement, and the modulation of ion channels and transporters. Phosphoinositides are also associated with fundamental nuclear processes through their nuclear protein-binding partners, even though membranes do not exist inside of the nucleus. Phosphatidylinositol 4-phosphate (PI(4)P) is one of the most abundant cellular phosphoinositides; however, its functions in the nucleus are still poorly understood. In this study, we describe PI(4)P localisation in the cell nucleus by super-resolution light and electron microscopy, and employ immunoprecipitation with a specific anti-PI(4)P antibody and subsequent mass spectrometry analysis to determine PI(4)P's interaction partners. We show that PI(4)P is present at the nuclear envelope, in nuclear lamina, in nuclear speckles and in nucleoli and also forms multiple small foci in the nucleoplasm. Nuclear PI(4)P undergoes re-localisation to the cytoplasm during cell division; it does not localise to chromosomes, nucleolar organising regions or mitotic interchromatin granules. When PI(4)P and PI(4,5)P2 are compared, they have different nuclear localisations during interphase and mitosis, pointing to their functional differences in the cell nucleus. Mass spectrometry identified hundreds of proteins, including 12 potentially novel PI(4)P interactors, most of them functioning in vital nuclear processes such as pre-mRNA splicing, transcription or nuclear transport, thus extending the current knowledge of PI(4)P's interaction partners. Based on these data, we propose that PI(4)P also plays a role in essential nuclear processes as a part of protein-lipid complexes. Altogether, these observations provide a novel insight into the role of PI(4)P in nuclear functions and provide a direction for further investigation.

• Keywords
• PI(4)P, nucleus, phosphoinositides,
• MeSH
• Cell Nucleolus metabolism   ultrastructure   MeSH
• Cell Nucleus metabolism   ultrastructure   MeSH
• Cell Cycle MeSH
• Phosphatidylinositol Phosphates metabolism   MeSH
• Nuclear Proteins metabolism   MeSH
• Nuclear Envelope metabolism   ultrastructure   MeSH
• Humans MeSH
• Cell Line, Tumor MeSH
• Proteome metabolism   MeSH
• Cluster Analysis MeSH
• Protein Binding MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Phosphatidylinositol Phosphates MeSH
• Nuclear Proteins MeSH
• phosphatidylinositol 4-phosphate MeSH Browser
• Proteome MeSH

The many functions of phosphoinositides in cytosolic signaling were extensively studied; however, their activities in the cell nucleus are much less clear. In this review, we summarize data about their nuclear localization and metabolism, and review the available literature on their involvements in chromatin remodeling, gene transcription, and RNA processing. We discuss the molecular mechanisms via which nuclear phosphoinositides, in particular phosphatidylinositol (4,5)-bisphosphate (PI(4,5)P2), modulate nuclear processes. We focus on PI(4,5)P2's role in the modulation of RNA polymerase I activity, and functions of the nuclear lipid islets-recently described nucleoplasmic PI(4,5)P2-rich compartment involved in RNA polymerase II transcription. In conclusion, the high impact of the phosphoinositide-protein complexes on nuclear organization and genome functions is only now emerging and deserves further thorough studies.

• Keywords
• cell nucleus, gene expression, genome, phosphoinositides,
• MeSH
• Cell Nucleus genetics   metabolism   MeSH
• Eukaryota genetics   metabolism   MeSH
• Phosphatidylinositol 4,5-Diphosphate metabolism   MeSH
• Transcription, Genetic MeSH
• Genome * MeSH
• RNA Processing, Post-Transcriptional MeSH
• Chromatin Assembly and Disassembly MeSH
• RNA Polymerase I metabolism   MeSH
• RNA Polymerase II metabolism   MeSH
• Protein Binding physiology   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH
• Names of Substances
• Phosphatidylinositol 4,5-Diphosphate MeSH
• RNA Polymerase I MeSH
• RNA Polymerase II MeSH

One of the most studied phosphoinositides is phosphatidylinositol 4,5-bisphosphate (PIP2), which localizes to the plasma membrane, nuclear speckles, small foci in the nucleoplasm, and to the nucleolus in mammalian cells. Here, we show that PIP2 also localizes to the nucleus in prophase I, during the gametogenesis of C. elegans hermaphrodite. The depletion of PIP2 by type I PIP kinase (PPK-1) kinase RNA interference results in an altered chromosome structure and leads to various defects during meiotic progression. We observed a decreased brood size and aneuploidy in progeny, defects in synapsis, and crossover formation. The altered chromosome structure is reflected in the increased transcription activity of a tightly regulated process in prophase I. To elucidate the involvement of PIP2 in the processes during the C. elegans development, we identified the PIP2-binding partners, leucine-rich repeat (LRR-1) protein and proteasome subunit beta 4 (PBS-4), pointing to its involvement in the ubiquitin⁻proteasome pathway.

• Keywords
• C. elegans, PPK-1, nucleus, phosphatidylinositol 4,5-bisphosphate,
• MeSH
• Cell Nucleus metabolism   MeSH
• Caenorhabditis elegans genetics   growth & development   metabolism   MeSH
• Chromosomes chemistry   MeSH
• Phosphatidylinositol 4,5-Diphosphate metabolism   MeSH
• Phosphotransferases (Alcohol Group Acceptor) genetics   MeSH
• Gametogenesis * MeSH
• Hermaphroditic Organisms genetics   growth & development   metabolism   MeSH
• Meiotic Prophase I MeSH
• Proteasome Endopeptidase Complex metabolism   MeSH
• Caenorhabditis elegans Proteins genetics   MeSH
• Leucine-Rich Repeat Proteins MeSH
• Proteins metabolism   MeSH
• RNA Interference MeSH
• Gene Expression Regulation, Developmental MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Phosphatidylinositol 4,5-Diphosphate MeSH
• Phosphotransferases (Alcohol Group Acceptor) MeSH
• Ppk-1 protein, C elegans MeSH Browser
• Proteasome Endopeptidase Complex MeSH
• Caenorhabditis elegans Proteins MeSH
• Leucine-Rich Repeat Proteins MeSH
• Proteins MeSH

Even though the majority of knowledge about phospholipids comes from their cytoplasmic functions, in the last decade, it has been shown that nuclear phospholipids and their building blocks, inositol phosphates, have many important roles in the cell nucleus. There are clear connections of phospholipids with the regulation of gene expression and chromatin biology, however, this review focuses on less known functions of nuclear phospholipids in connection with the epigenome regulation. In particular, we highlight the roles of nuclear phospholipids and inositol phosphates that involve histone modifications, such as acetylation or methylation, tightly connected with the cell physiology. This demonstrates the importance of nuclear phospholipids in the regulation of cellular processes, and should encourage further research of nuclear phospholipids and inositol phosphates.

• Keywords
• Acetylation, Inositol phosphate, Methylation, Phosphoinositide, Phospholipids,
• MeSH
• Chromatin chemistry   metabolism   MeSH
• Epigenesis, Genetic * genetics   MeSH
• Phospholipids chemistry   metabolism   MeSH
• Inositol Phosphates chemistry   metabolism   MeSH
• Humans MeSH
• Molecular Structure MeSH
• Gene Expression Regulation MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Review MeSH
• Names of Substances
• Chromatin MeSH
• Phospholipids MeSH
• Inositol Phosphates MeSH