Characterization of RNP Networks of PUM1 and PUM2 Post-Transcriptional Regulators in TCam-2 Cells, a Human Male Germ Cell Model

Systematic analysis of the target recognition and repression by the Pumilio proteins

RNA binding proteins orchestrate the post-transcriptional fate of RNA molecules, but the principles of their action remain poorly understood. Pumilio (PUM) proteins bind 3' UTRs of mRNAs and lead to mRNA decay. To comprehensively map the determinants of recognition of sequences by PUM proteins in cells and to study the binding outcomes, we developed a massively parallel RNA assay that profiled thousands of PUM-binding sites in cells undergoing various perturbations or RNA immunoprecipitation. By studying fragments from the NORAD long non-coding RNA, we find two features that antagonize repression by PUM proteins - G/C rich sequences, particularly those upstream of the PUM recognition element, and binding of FAM120A, which limits the repression elicited by PUM-binding sites. We also find that arrays of PUM sites separated by 8-12 bases offer particularly strong repression and use them to develop a particularly sensitive reporter for PUM repression. In contrast, PUM sites separated by shorter linkers, such as some of those found in NORAD, exhibit strong activity interdependence, likely mediated by competition between PUM binding and formation of strong secondary structures. Overall, our findings expand our understanding of the determinants of PUM protein activity in human cells.

Pumilio-1 mediated translational control of claudin-5 at the blood-brain barrier

Claudin-5 is one of the most essential tight junction proteins at the blood-brain barrier. A single nucleotide polymorphism rs10314 is located in the 3'-untranslated region of claudin-5 and has been shown to be a risk factor for schizophrenia. Here, we show that the pumilio RNA-binding protein, pumilio-1, is responsible for rs10314-mediated claudin-5 regulation. The RNA sequence surrounding rs10314 is highly homologous to the canonical pumilio-binding sequence and claudin-5 mRNA with rs10314 produces 25% less protein due to its inability to bind to pumilio-1. Pumilio-1 formed cytosolic granules under stress conditions and claudin-5 mRNA appeared to preferentially accumulate in these granules. Added to this, we observed granular pumilio-1 in endothelial cells in human brain tissues from patients with psychiatric disorders or epilepsy with increased/accumulated claudin-5 mRNA levels, suggesting translational claudin-5 suppression may occur in a brain-region specific manner. These findings identify a key regulator of claudin-5 translational processing and how its dysregulation may be associated with neurological and neuropsychiatric disorders.

The Potential of NORAD-PUMILIO-RALGAPB Regulatory Axis as a Biomarker in Breast Cancer

Introduction: Long non-coding RNAs (LncRNA) represent a heterogeneous family of RNAs that have emerged as regulators of various biological processes through their association with proteins in ribonucleoproteins complexes. The dynamic of these interactions can affect cell metabolism, including cancer development. Annually, breast cancer causes thousands of deaths worldwide, and searching for new biomarkers is pivotal for better diagnosis and treatment. Methods: Based on in silico prediction analysis, we focus on LncRNAs that have binding sites for PUMILIO, an RBP family involved in post-transcriptional regulation and associated with cancer progression. We compared the expression levels of these LncRNAs in breast cancer and non-tumor samples from the TCGA database. We analyzed the impact of overall and disease-free survival associated with the expression of the LncRNAs and co-expressed genes and targets of PUMILIO proteins. Results: Our results found NORAD as the most relevant LncRNA with a PUMILIO binding site in breast cancer, differently expressed between Luminal A and Basal subtypes. Additionally, NORAD was co-expressed in a Basal-like subtype (0.55) with the RALGAPB gene, a target gene of PUMILIO related to chromosome stability during cell division. Conclusion: These data suggest that this molecular axis may provide insights for developing novel therapeutic strategies for breast cancer.

Distinct Roles of NANOS1 and NANOS3 in the Cell Cycle and NANOS3-PUM1-FOXM1 Axis to Control G2/M Phase in a Human Primordial Germ Cell Model

Nanos RNA-binding proteins are critical factors of germline development throughout the animal kingdom and their dysfunction causes infertility. During evolution, mammalian Nanos paralogues adopted divergent roles in germ cell biology. However, the molecular basis behind this divergence, such as their target mRNAs, remains poorly understood. Our RNA-sequencing analysis in a human primordial germ cell model-TCam-2 cell line revealed distinct pools of genes involved in the cell cycle process downregulated upon NANOS1 and NANOS3 overexpression. We show that NANOS1 and NANOS3 proteins influence different stages of the cell cycle. Namely, NANOS1 is involved in the G1/S and NANOS3 in the G2/M phase transition. Many of their cell cycle targets are known infertility and cancer-germ cell genes. Moreover, NANOS3 in complex with RNA-binding protein PUM1 causes 3′UTR-mediated repression of FOXM1 mRNA encoding a transcription factor crucial for G2/M phase transition. Interestingly, while NANOS3 and PUM1 act as post-transcriptional repressors of FOXM1, FOXM1 potentially acts as a transcriptional activator of NANOS3, PUM1, and itself. Finally, by utilizing publicly available RNA-sequencing datasets, we show that the balance between FOXM1-NANOS3 and FOXM1-PUM1 expression levels is disrupted in testis cancer, suggesting a potential role in this disease.

Role of PUM RNA-Binding Proteins in Cancer

Simple Summary

PUM1 and PUM2 are RNA-binding Pumilio proteins controlling the accessibility of hundreds of mRNAs for translation in a variety of human tissues. As a result, PUMs exemplify one of the mechanisms safeguarding the cellular proteome. PUM expression is disturbed in cancer, resulting in dysregulation of their target mRNAs. These targets encode factors responsible for processes usually affected in cancer, such as proliferation, apoptosis, and the cell cycle. This review describes PUM1 and PUM2 ribonucleoprotein networks and highlights the mechanisms underlying the regulatory role of PUM proteins and, most importantly, the emerging impact of PUM dysregulation in cancer. It also emphasizes the importance of upcoming studies on PUM proteins in the context of cancer, as they may provide new therapeutic targets in the future.

Abstract

Until recently, post-transcriptional gene regulation (PTGR), in contrast to transcriptional regulation, was not extensively explored in cancer, even though it seems to be highly important. PUM proteins are well described in the PTGR of several organisms and contain the PUF RNA-binding domain that recognizes the UGUANAUA motif, located mostly in the 3′ untranslated region (3′UTR) of target mRNAs. Depending on the protein cofactors recruited by PUM proteins, target mRNAs are directed towards translation, repression, activation, degradation, or specific localization. Abnormal profiles of PUM expression have been shown in several types of cancer, in some of them being different for PUM1 and PUM2. This review summarizes the dysregulation of PUM1 and PUM2 expression in several cancer tissues. It also describes the regulatory mechanisms behind the activity of PUMs, including cooperation with microRNA and non-coding RNA machineries, as well as the alternative polyadenylation pathway. It also emphasizes the importance of future studies to gain a more complete picture of the role of PUM proteins in different types of cancer. Such studies may result in identification of novel targets for future cancer therapies.