The RNA content is crucial for the formation of nuclear compartments, such as nuclear speckles and nucleoli. Phosphatidylinositol 4,5-bisphosphate (PIP2) is found in nuclear speckles, nucleoli, and nuclear lipid islets and is involved in RNA polymerase I/II transcription. Intriguingly, the nuclear localization of PIP2 was also shown to be RNA-dependent. We therefore investigated whether PIP2 and RNA cooperate in the establishment of nuclear architecture. In this study, we unveiled the RNA-dependent PIP2-associated (RDPA) nuclear proteome in human cells by mass spectrometry. We found that intrinsically disordered regions (IDRs) with polybasic PIP2-binding K/R motifs are prevalent features of RDPA proteins. Moreover, these IDRs of RDPA proteins exhibit enrichment for phosphorylation, acetylation, and ubiquitination sites. Our results show for the first time that the RDPA protein Bromodomain-containing protein 4 (BRD4) associates with PIP2 in the RNA-dependent manner via electrostatic interactions, and that altered PIP2 levels affect the number of nuclear foci of BRD4 protein. Thus, we propose that PIP2 spatiotemporally orchestrates nuclear processes through association with RNA and RDPA proteins and affects their ability to form foci presumably via phase separation. This suggests the pivotal role of PIP2 in the establishment of a functional nuclear architecture competent for gene expression.

• MeSH
• Cell Nucleus * metabolism   genetics   MeSH
• Phosphatidylinositol 4,5-Diphosphate * metabolism   MeSH
• Phosphorylation MeSH
• Nuclear Proteins * metabolism   genetics   MeSH
• Humans MeSH
• Cell Cycle Proteins metabolism   genetics   MeSH
• Bromodomain Containing Proteins MeSH
• RNA metabolism   genetics   MeSH
• Transcription Factors * metabolism   genetics   MeSH
• Protein Binding MeSH
• Intrinsically Disordered Proteins * metabolism   genetics   chemistry   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• BRD4 protein, human MeSH Browser
• Phosphatidylinositol 4,5-Diphosphate * MeSH
• Nuclear Proteins * MeSH
• Cell Cycle Proteins MeSH
• Bromodomain Containing Proteins MeSH
• RNA MeSH
• Transcription Factors * MeSH
• Intrinsically Disordered Proteins * MeSH

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

BACKGROUND: Current biological research extensively describes the interactions of molecules such as RNA with other nucleic acids or proteins. However, the relatively recent discovery of nuclear phospholipids playing biologically relevant processes outside membranes, as well as, RNA-lipid interactions shows the need for new methods to explore the identity of these RNAs. METHODS AND RESULTS: In this study, we describe the method for LIPID-RNA isolation followed by sequencing and analysis of the RNA that has the ability to interact with the selected lipids. Here we utilized specific phospholipid coated beads for selective RNA binding. We tested RNA from organisms belonging to different realms (human, plant, and yeast), and tested their ability to bind a specific lipid. CONCLUSIONS: The results show several RNAs differentially enriched in the pull-down of phosphatidyl Inositol 4,5 bisphosphate coated beads. This method is helpful to screen lipid-binding RNA, which may have relevant biological functions. The method can be used with different lipids and comparison of pull-downs and can narrow the selection of RNAs that interact with a particular lipid for further studies.

• Keywords
• Lipid-RNA, Phase separation, Phosphoinositide, RNA sequence,
• MeSH
• Phospholipids * metabolism   MeSH
• Humans MeSH
• RNA * metabolism   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Phospholipids * MeSH
• RNA * MeSH

Introduction: Imaging of human clinical formalin-fixed paraffin-embedded (FFPE) tissue sections provides insights into healthy and diseased states and therefore represents a valuable resource for basic research, as well as for diagnostic and clinical purposes. However, conventional light microscopy does not allow to observe the molecular details of tissue and cell architecture due to the diffraction limit of light. Super-resolution microscopy overcomes this limitation and provides access to the nanoscale details of tissue and cell organization. Methods: Here, we used quantitative multicolor stimulated emission depletion (STED) nanoscopy to study the nanoscale distribution of the nuclear phosphatidylinositol 4,5-bisphosphate (nPI(4,5)P2) with respect to the nuclear speckles (NS) marker SON. Results: Increased nPI(4,5)P2 signals were previously linked to human papillomavirus (HPV)-mediated carcinogenesis, while NS-associated PI(4,5)P2 represents the largest pool of nPI(4,5)P2 visualized by staining and microscopy. The implementation of multicolor STED nanoscopy in human clinical FFPE skin and wart sections allowed us to provide here the quantitative evidence for higher levels of NS-associated PI(4,5)P2 in HPV-induced warts compared to control skin. Discussion: These data expand the previous reports of HPV-induced increase of nPI(4,5)P2 levels and reveal for the first time the functional, tissue-specific localization of nPI(4,5)P2 within NS in clinically relevant samples. Moreover, our approach is widely applicable to other human clinical FFPE tissues as an informative addition to the classical histochemistry.

• Keywords
• STED nanoscopy, cell nucleus, formalin-fixed paraffin-embedded tissue sections, human papillomavirus (HPV), nuclear architecture, nuclear speckles, phosphatidylinositol 4,5-bisphosphate, quantitative image analysis,
• Publication type
• Journal Article MeSH

The specific post-translational modifications of the C-terminal domain (CTD) of the Rpb1 subunit of RNA polymerase II (RNAPII) correlate with different stages of transcription. The phosphorylation of the Ser5 residues of this domain associates with the initiation condensates, which are formed through liquid-liquid phase separation (LLPS). The subsequent Tyr1 phosphorylation of the CTD peaks at the promoter-proximal region and is involved in the pause-release of RNAPII. By implementing super-resolution microscopy techniques, we previously reported that the nuclear Phosphatidylinositol 4,5-bisphosphate (PIP2) associates with the Ser5-phosphorylated-RNAPII complex and facilitates the RNAPII transcription. In this study, we identified Myosin Phosphatase Rho-Interacting Protein (MPRIP) as a novel regulator of the RNAPII transcription that recruits Tyr1-phosphorylated CTD (Tyr1P-CTD) to nuclear PIP2-containing structures. The depletion of MPRIP increases the number of the initiation condensates, indicating a defect in the transcription. We hypothesize that MPRIP regulates the condensation and transcription through affecting the association of the RNAPII complex with nuclear PIP2-rich structures. The identification of Tyr1P-CTD as an interactor of PIP2 and MPRIP further points to a regulatory role in RNAPII pause-release, where the susceptibility of the transcriptional complex to leave the initiation condensate depends on its association with nuclear PIP2-rich structures. Moreover, the N-terminal domain of MPRIP, which is responsible for the interaction with the Tyr1P-CTD, contains an F-actin binding region that offers an explanation of how nuclear F-actin formations can affect the RNAPII transcription and condensation. Overall, our findings shed light on the role of PIP2 in RNAPII transcription through identifying the F-actin binding protein MPRIP as a transcription regulator and a determinant of the condensation of RNAPII.

• Keywords
• MPRIP, PIP2, RNA polymerase II, phase separation, transcription,
• MeSH
• Actins * metabolism   MeSH
• Myosin-Light-Chain Phosphatase genetics   metabolism   MeSH
• Phosphorylation MeSH
• Transcription, Genetic MeSH
• Humans MeSH
• Phosphoprotein Phosphatases genetics   MeSH
• RNA Polymerase II * chemistry   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Actins * MeSH
• Myosin-Light-Chain Phosphatase MeSH
• MPRIP protein, human MeSH Browser
• Phosphoprotein Phosphatases MeSH
• RNA Polymerase II * 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

Understanding how the packaging of chromatin in the nucleus is regulated and organized to guide complex cellular and developmental programmes, as well as responses to environmental cues is a major question in biology. Technological advances have allowed remarkable progress within this field over the last years. However, we still know very little about how the 3D genome organization within the cell nucleus contributes to the regulation of gene expression. The nuclear space is compartmentalized in several domains such as the nucleolus, chromocentres, telomeres, protein bodies, and the nuclear periphery without the presence of a membrane around these domains. The role of these domains and their possible impact on nuclear activities is currently under intense investigation. In this review, we discuss new data from research in plants that clarify functional links between the organization of different nuclear domains and plant genome function with an emphasis on the potential of this organization for gene regulation.

• Keywords
• 3D Chromatin organization, chromocentres, gene expression, liquid–liquid phase separation (LLPS), nuclear bodies, nuclear domains, nuclear periphery, nucleolus, telomeres, topologically associated domains (TADs),
• MeSH
• Cell Nucleolus MeSH
• Cell Nucleus * MeSH
• Chromatin * MeSH
• Gene Expression Regulation MeSH
• Plants genetics   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH
• Names of Substances
• Chromatin * 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

Fibrillarin is a highly conserved nucleolar methyltransferase responsible for ribosomal RNA methylation across evolution from Archaea to humans. It has been reported that fibrillarin is involved in the methylation of histone H2A in nucleoli and other processes, including viral progression, cellular stress, nuclear shape, and cell cycle progression. We show that fibrillarin has an additional activity as a ribonuclease. The activity is affected by phosphoinositides and phosphatidic acid and insensitive to ribonuclease inhibitors. Furthermore, the presence of phosphatidic acid releases the fibrillarin-U3 snoRNA complex. We show that the ribonuclease activity localizes to the GAR (glycine/arginine-rich) domain conserved in a small group of RNA interacting proteins. The introduction of the GAR domain occurred in evolution in the transition from archaea to eukaryotic cells. The interaction of this domain with phospholipids may allow a phase separation of this protein in nucleoli.

• Keywords
• fibrillarin, nucleolus, phosphoinositides, rRNA, ribonucleolar particle, viral progression,
• MeSH
• Chromosomal Proteins, Non-Histone chemistry   genetics   metabolism   MeSH
• Phospholipids metabolism   MeSH
• HeLa Cells MeSH
• Humans MeSH
• RNA, Small Nucleolar metabolism   MeSH
• Mutation genetics   MeSH
• Protein Domains MeSH
• Recombinant Proteins metabolism   MeSH
• Ribonucleases chemistry   genetics   metabolism   MeSH
• Ribonucleoproteins metabolism   MeSH
• Structure-Activity Relationship MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Chromosomal Proteins, Non-Histone MeSH
• fibrillarin MeSH Browser
• Phospholipids MeSH
• RNA, Small Nucleolar MeSH
• Recombinant Proteins MeSH
• Ribonucleases MeSH
• Ribonucleoproteins MeSH
• RNA, U3 small nucleolar MeSH Browser