Long non-coding RNAs (lncRNAs) interact with a variety of biomolecules, including DNA, mRNAs, microRNA, and proteins, to regulate various cellular processes. Recently, their interactions with lipids have gained increasing attention as an emerging research area. Both lipids and lncRNAs play central roles in cellular regulation, and growing evidence reveals a complex interplay between these molecules. These interactions contribute to key biological functions, such as cancer progression, lipid droplet transport, autophagy, liquid-liquid phase separation, and the formation of organelles without membranes. Understanding the lipid-lncRNA interface opens new avenues for unraveling cellular regulation and disease mechanisms, holding great potential not only for elucidating the fundamental aspects of cellular biology but also for identifying innovative therapeutic targets for metabolic disorders and cancer. This review highlights the biological relevance of lipid-lncRNA interactions by exploring their roles in cellular organization, regulation, and diseases, including metabolic and cancer-related disorders.

• Keywords
• lncRNA, phase separation, phospholipids,
• MeSH
• Humans MeSH
• Lipids * chemistry   MeSH
• Lipid Metabolism * genetics   MeSH
• Neoplasms metabolism   genetics   MeSH
• RNA, Long Noncoding * metabolism   genetics   MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Review MeSH
• Names of Substances
• Lipids * MeSH
• RNA, Long Noncoding * MeSH

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

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

The focal adhesion protein Vinculin (VCL) is ascribed to various cytoplasmic functions; however, its nuclear role has so far been ambiguous. We observed that VCL localizes to the nuclei of mouse primary spermatocytes undergoing first meiotic division. Specifically, VCL localizes along the meiosis-specific structure synaptonemal complex (SC) during prophase I and the centromeric regions, where it remains until metaphase I. To study the role of VCL in meiotic division, we prepared a conditional knock-out mouse (VCLcKO). We found that the VCLcKO male mice were semi-fertile, with a decreased number of offspring compared to wild-type animals. This study of events in late prophase I indicated premature splitting of homologous chromosomes, accompanied by an untimely loss of SCP1. This caused erroneous kinetochore formation, followed by failure of the meiotic spindle assembly and metaphase I arrest. To assess the mechanism of VCL involvement in meiosis, we searched for its possible interacting partners. A mass spectrometry approach identified several putative interactors which belong to the ubiquitin-proteasome pathway (UPS). The depletion of VLC leads to the dysregulation of a key subunit of the proteasome complex in the meiotic nuclei and an altered nuclear SUMOylation level. Taken together, we show for the first time the presence of VCL in the nucleus of spermatocytes and its involvement in proper meiotic progress. It also suggests the direction for future studies regarding the role of VCL in spermatogenesis through regulation of UPS.

• Keywords
• centromere synapsis, fertility, kinetochore, spermatogenesis, ubiquitin–proteasome system, vinculin,
• MeSH
• Centromere MeSH
• Focal Adhesions * MeSH
• Mice MeSH
• Proteasome Endopeptidase Complex * genetics   MeSH
• Spermatogenesis genetics   MeSH
• Vinculin genetics   metabolism   MeSH
• Animals MeSH
• Check Tag
• Male MeSH
• Mice MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Proteasome Endopeptidase Complex * MeSH
• Vcl protein, mouse MeSH Browser
• Vinculin MeSH

Classical models of gene expression were built using genetics and biochemistry. Although these approaches are powerful, they have very limited consideration of the spatial and temporal organization of gene expression. Although the spatial organization and dynamics of RNA polymerase II (RNAPII) transcription machinery have fundamental functional consequences for gene expression, its detailed studies have been abrogated by the limits of classical light microscopy for a long time. The advent of super-resolution microscopy (SRM) techniques allowed for the visualization of the RNAPII transcription machinery with nanometer resolution and millisecond precision. In this review, we summarize the recent methodological advances in SRM, focus on its application for studies of the nanoscale organization in space and time of RNAPII transcription, and discuss its consequences for the mechanistic understanding of gene expression.

• Keywords
• cell nucleus, gene expression, photoactivation, stimulated emission depletion, stochastic optical reconstruction, structured illumination, super-resolution microscopy, transcription factors, transcription foci,
• MeSH
• Microscopy, Fluorescence * methods   MeSH
• Transcription, Genetic * MeSH
• Humans MeSH
• Gene Expression Regulation * MeSH
• RNA Polymerase II metabolism   MeSH
• Transcription Factors metabolism   MeSH
• Protein Binding MeSH
• Single Molecule Imaging methods   MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Review MeSH
• Names of Substances
• RNA Polymerase II MeSH
• Transcription Factors MeSH

Single molecule localization microscopy (SMLM) provided an unprecedented insight into the sub-nuclear organization of proteins and nucleic acids but apart from the nuclear envelope the role of the nuclear lipids in the functional organization of the cell nucleus was less studied. Nevertheless, nuclear lipids and specifically phosphatidylinositol phosphates (PIPs) play increasingly evident roles in gene expression. Therefore, here we provide the SMLM-based approach for the quantitative evaluation of the nuclear PIPs distribution while preserving the context of nuclear architecture. Specifically, on the example of phosphatidylinositol 4,5-bisphosphate (PIP2) we have:•Implemented and optimized the dual-color dSTORM imaging of nuclear PIP2.•Customized the Nearest Neighbor Distance analysis using ImageJ2 plug-in ThunderSTORM to quantitatively evaluate the spatial distribution of nuclear PIP2.•Developed an ImageJ2 tool for the visualization of the Nearest Neighbor Distance analysis results in cellulo.Our customization of the dual-color dSTORM imaging and quantitative analysis provide a tool that is independent of but complementary to the biochemical and lipidomic analyses of the nuclear PIPs. Contrary to the biochemical and lipidomic analyses, the advantage of our analysis is that it preserves the spatial context of the nuclear PIP distribution.

• Keywords
• Cell nucleus, Fibrillarin, ImageJ, Immunofluorescence, Nearest neighbor distance, Nuclear architecture, Nuclear speckles, RNA polymerase II, SON, Super-resolution microscopy, Wide-field microscopy,
• Publication type
• Journal Article 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