Nuclear phosphoinositides and phase separation: Important players in nuclear compartmentalization

Abstract

Nuclear phosphoinositides are recognized as regulators of many nuclear processes including chromatin remodeling, splicing, transcription, DNA repair and epigenetics. These processes are spatially organized in different nuclear compartments. Phase separation is involved in the formation of various nuclear compartments and molecular condensates separated from surrounding environment. The surface of such structures spatiotemporally coordinates formation of protein complexes. PI(4,5)P2 (PIP2) integration into phase-separated structures might provide an additional step in their spatial diversification by attracting certain proteins with affinity to PIP2. Our laboratory has recently identified novel membrane-free PIP2-containing structures, so called Nuclear Lipid Islets (NLIs). We provide an evidence that these structures are evolutionary conserved in different organisms. We hypothesize that NLIs serve as a scaffolding platform which facilitates the formation of transcription factories, thus participating in the formation of nuclear architecture competent for transcription. In this review we speculate on a possible role of NLIs in the integration of various processes linked to RNAPII transcription, chromatin remodeling, actin-myosin interaction, alternative splicing and lamin structures.

Introduction

Phosphatidylinositol phosphates (PIPs) are phospholipids which act as precursors for second messengers or participate in the formation of diverse protein complexes on the surface of various membranous organelles and vesicles (Berridge and Irvine, 1984; Shewan et al., 2011). PIPs play important roles in membrane architecture and cytoskeletal dynamics, vesicular trafficking, signal transduction and neurotransmission (Di Paolo and De Camilli, 2006; Raben and Barber, 2017). Their exact functions depend on their localization and phosphorylation state. PIPs can be phosphorylated by a number of phosphoinositide kinases and dephosphorylated by phosphatases at positions 3, 4, or 5 of the inositol ring giving rise to seven different phosphorylated forms (Shewan et al., 2011). Many enzymes of PIPs metabolism were detected in the nucleus (Barlow et al., 2010). Even though PIPs were identified among the first phospholipids in the nucleus, their nuclear functions have not been described in such details as their cytoplasmic counterparts (Osborne et al., 2001; Shah et al., 2013). Due to the lack of membranous organelles within the nucleus, data describing the presence of nuclear phosphoinositides were considered as controversial. However, an increasing amount of evidences opened a new field in the study of the crucial nuclear processes such as cell cycle progression, cell differentiation and proliferation (Ratti et al., 2018). PIP2 is one of the most abundant phosphoinositides in the nucleus and therefore its possible functions have been extensively studied during the last two decades (Jungmichel et al., 2014). In this review we will focus on the possible role of PIP2 as a determinant of spatial and functional diversification of the nuclear architecture. Several localization studies using different specific tools and imaging approaches showed that PIP2 is enriched in various nuclear compartments: at nuclear speckles, nucleoli, and in the nucleoplasm (Boronenkov et al., 1998; Kalasova et al., 2016; Mazzotti et al., 1995; Mortier et al., 2005; Osborne et al., 2001; Sobol et al., 2013; Ulicna et al., 2018a; Vann et al., 1997; Watt et al., 2002; Yildirim et al., 2013). The first detailed description of the nucleoplasmic PIP2 revealed that it is the major component of the newly discovered NLIs (Sobol et al., 2018). The question, how these aliphatic molecules can be distributed in the membrane-free nuclear environment, remains elusive. One possibility is that lipid acyl groups are bound into the protein hydrophobic cavities as documented by example of SF1 protein. SF1 uses its hydrophobic binding pocket to hide acyl chains of PIP2 and PI(3,4,5)P3 (Blind et al., 2012; Blind et al., 2014). Second possibility is that lipids aggregate and reorient their hydrophobic moieties inward the micellar structures, where they are not in contact with aqueous environment. Third, yet not well described complex RNA folds which might hypothetically participate in lipid aggregation (discussed below). In all these scenarios, the hydrophilic inositol head with the phosphate group(s) remains exposed and accessible for proteins recognizing the negative charge(s). The strong indication that PIP2 may have a role in nuclear processes comes from the work of Lewis et al. (2011), where the authors have identified more than 300 regulatory nuclear proteins which interact with PIP2. In accordance with these important findings, there is a growing number of studies showing that PIP2 is involved in regulation of nuclear pathways. PIP2 has both inducible and repressive functions in processes like pre-mRNA splicing and polyadenylation, rRNA processing, chromatin remodeling, histone acetylation/deacetylation, regulation of RNAPs transcriptional activity (Shah et al., 2013; Ulicna et al., 2018b). These PIP2 functions are realized through the alterations of protein conformation and/or protein localization (Rando et al., 2002; Ulicna et al., 2018a; Yildirim et al., 2013). Hence, the spatial distribution of PIP2 in different parts of the nucleus may result from its binding to various nuclear proteins thus determining the function of PIP2 in the nuclear structures. These nuclear structures are membrane-less so might be formed by the phase separation (Mitrea and Kriwacki, 2016).