Richard Anderson Lab

Research: Phosphoinositide Signaling in the Nucleus

Nuclear Phosphoinositide Signaling Controls Gene Expression

Almost 30 years ago Irvine and Cocco discovered that phosphoinositides could be generated in purified nuclei (see Trends Cell Biol., 20, 25-35). Recently, we have discovered nuclear phosphoinositide signaling pathways that control mRNA processing and ultimately gene expression(Nature, 451:1013-7). Within the nucleus there are phosphoinositide pathways on the inner nuclear envelope. In addition, we discovered a novel phosphoinisitide compartment(s) associated with interchromatin granule clusters or nuclear speckles, which are compartments separate from known membrane structures(Mol Biol Cell, 12:3547-60). We have pioneered the investigation of the role of the nuclear phosphoinositide pathways and have shown that nuclear phosphoinositide pathways control 3’-end processing and polyadenylation of oxidative stress response, DNA damage and apopotosis mRNAs(Nature, 451:1013-7, Mol. Cell, 45, 25–37). These pathways are dependent on a novel non-canonical poly(A) polymerase that we named Star-PAP (for nuclear Speckle Targeted PIPKIa Regulated-Poly(A) Polymerase)(Nature, 451:1013-7). Star-PAP is a nuclear PAP that is a PI4,5P2 effector and requires PI4,5P2 for it’s poly(A) polymerase activity both in vitro and in vivo. In vivo Star-PAP controls the expression of key master genes that regulate cell stress pathways. Recently we have shown that Star-PAP controls expression genome wide.

PIP2 is localized to multiple intranuclear compartments and is positioned to regulate intranuclear organization. Generation of PIP2 is required for Star-PAP control of gene expression through 3’ APA(Trends Cell Biology, 20, 25-35). Disruption of spatial PIP2 synthesis may alter nuclear organization and may block Star-PAP dependent 3’-end processing of genes.

Star-PAP controls genome wide alternative polyadenylation (APA)

Most genes in higher eukaryotes (~70% in humans) have multiple alternative 3’UTRs that are generated by APA. APA is significant as changes in the 3’-UTR control the stability and translation of mRNAs and thus protein expression. Changes in APA are implicated in cancer progression, stem cell differentiation, are cell type specific and are emerging as global regulatory mechanisms. Most recently, we have shown that the nuclear PAPs, PAPa/g and Star-PAP control genome wide APA and 3’-end processing of human genes (Fig. 3). Most significant each of the nuclear PAPs have specificity in controlling sets of genes by APA(Cell, in review). Star-PAP is regulated by the lipid messenger PI4,5P2 that is generated by PIP kinases that directly interact with Star-PAP. In addition, specific signaling pathways regulate the composition of Star-PAP complex which contains different phosphoinositide kinases, protein kinases and other signaling molecules that act as signaling transactivators. These signaling transactivators define Star-PAP’s specificity toward genes and APA sites within a single gene. The canonical PAPa/g also show specificity toward specific genes and APA sites but are regulated differently. The emerging data indicate that APA is regulated genome wide downstream of cellular signals and is a key mechanism for control of gene expression. In humans where the majority of genes have APA sites, the regulation of 3’-end processing may be equally important as 5’ regulation of gene expression.


A current focus is to define the role and mechanisms of APA in expression of a key set of genes that control development, proliferation, cancer and cardiovascular disease. These genes include PTEN, NQO1, MDM2, AKT1-3, and RhoA, that contain between three and nine 3’-end APA sites. Star-PAP modulates a subset of APA sites for each of these genes. Star-PAP controls both distal and proximal APA sites. Significantly, Star-PAP regulated changes in APA have a dramatic impact on protein expression. For example, in the case of the PTEN tumor suppressor, Star-PAP controls all of the signal requlated APA sites (the most distal sites) and the expression of >80% of the cellular PTEN protein.


Star-PAP control of APA regulates expression of key regulatory genes and their expression is tightly controlled by signaling. In higher eukaryotes most genes are regulated by APA. Thus, we hypothesize that 3’-end APA is a mechanism utilized in more complex organisms to fine tune gene expression. Our current objective is to define genome wide APA sites and transactivating factors for Star-PAP that are regulated by specific signaling pathways. A key aspect will be to define Star-PAP spatial modulation by lipid messengers within the nucleus.

Intranuclear spatial control of gene expression

The spatial organization of the nucleus and gene expression is dynamic and changes in disease states. The major cellular function of PIPn isomers is to organize and assemble cellular compartments both temporally and spatially(BioEssays, 35, 513–522). Thus, nuclear PIPn isomers are positioned to play key roles in the organization of nuclear events including gene expression (see Figure). Synthesis of the lipid messenger PI4,5P2 is required for Star-PAP control of 3’UTR processing. As PI4,5P2 is found in membranes, this implies that the intranuclear organization of Star-PAP target gene expression and processing could spatially occur at the inner nuclear envelope (see Figure). Potentially, some Star-PAP target genes upon activation may become docked on the inner nuclear envelope (or nuclear pore complex) or the pre-mRNA maybe localized and processed at the envelope. There is evidence for these models and this could enhance gene expression and export of the resulting mRNA. In this paradigm, if spatial organization of a gene during expression is required for Star-PAP processing, the loss of normal intranuclear organization or changes in PI4,5P2 spatial generation could dramatically change expression, consistent with changes in nuclear organization and expression in transformed cells.


Alternatively, or in addition, there may be islands of phosphoinositides generated within the nucleus at non-membrane structures (see Figure). Our data also supports this model. Combined, these data indicate that lipid messengers are positioned to modulate spatial regulation of gene expression within the nucleus. This putative role for phosphoinositide lipid messengers appears to have evolved in higher eukaryotes and may represent an unexpected mechanism for spatial organization of gene expression and control of 3’-end processing is one example. We are determining if Star-PAP regulated genes are clustered when expressing, if Star-PAP regulated genes move to the nuclear envelop upon expression, the nature of the non-membrane PIP2 compartment and if nuclear PIP kinases modulate nuclear organization by regulation of nuclear actin or other nuclear cytoskeletal components.