mRNA Localization Research Articles

N6-methyladenosine RNA methylation in liver diseases: from mechanism to treatment.

Epigenetic modification occurring in RNA has become the hotspot of the field. N6-methyladenosine (m6A) methylation is the most abundant RNA internal modification mainly occurring at the consensus motif DR (m6A) CH (D = A/G/U, R = A/G, H = A/C/U) in the 3'-UTR particularly the region near stop codons. The life cycle of m6A methylation includes "writers," "erasers," and "readers", which are responsible for the addition, removal, and recognition of m6A, respectively. m6A modification has been reported changing RNA secondary structure or modulating the stability, localization, transport, and translation of mRNAs to play crucial roles in various physiological and pathological conditions. Liver, as the largest metabolic and digestive organ, modulates vital physiological functions, and its dysfunction gives rise to the occurrence of various diseases. Despite the advanced intervening measures, mortality due to liver diseases is continuously high. Recent studies have explored the roles of m6A RNA methylation in the pathogenesis of liver diseases, providing new insights for studying the molecular mechanism of liver diseases. In the review, we extensively summarize the life cycle of m6A methylation, as well as its function and relevant mechanisms in liver fibrosis (LF), nonalcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), hepatitis virus infection, and hepatocellular carcinoma (HCC), and eventually we explore the potential of m6A as a treatment option for these liver diseases.

Steroidogenic potential of the gonad during sex differentiation in the rice field frog Hoplobatrachus rugulosus (Anura: Dicroglossidae).

Prior studies demonstrated that gonadal differentiation in the rice field frog, Hoplobatrachus rugulosus, was of an undifferentiated type since all individuals had ovaries at complete metamorphosis. However, the steroidogenic potential of the gonad is still unknown. In this study, H. rugulosus were obtained by stimulating fertilization in the laboratory under natural light and temperature conditions. The gonads were collected and their steroidogenic potential was evaluated by determining the expression level of messenger RNA (mRNA) encoding for cytochrome P450 17-hydroxylase/C17-20 lyase (CYP17) and cytochrome P450 aromatase (CYP19) using quantitative real-time RT-PCR and the localization of CYP17 mRNA in tissues by in situ hybridization. The CYP17 mRNA levels in males at 4-11 weeks postmetamorphosis were higher than in female and intersex gonads. This corresponded to their localization in the gonadal tissues, where CYP17 signals were specifically detected in the Leydig cells of the testis at 5-16 weeks postmetamorphosis but was undetectable in all ovary samples. The CYP19 mRNA levels in females at 4-11 weeks postmetamorphosis was higher than in male and intersex gonads, which corresponded with gonadal development, indicating the potential steroidogenic function of the ovary. Based on the present results, the role of CYP17 and CYP19 mRNA in sex differentiation in H. rugulosus may occur after gonadal sex differentiation and the steroidogenic potential of the gonads exhibited a sexual dimorphic pattern. These results provide a crucial basis for further research on the developmental biology in anuran species.

Post-transcriptional checkpoints in autoimmunity.

Post-transcriptional regulation is a fundamental process in gene expression that has a role in diverse cellular processes, including immune responses. A core concept underlying post-transcriptional regulation is that protein abundance is not solely determined by transcript abundance. Indeed, transcription and translation are not directly coupled, and intervening steps occur between these processes, including the regulation of mRNA stability, localization and alternative splicing, which can impact protein abundance. These steps are controlled by various post-transcription factors such as RNA-binding proteins and non-coding RNAs, including microRNAs, and aberrant post-transcriptional regulation has been implicated in various pathological conditions. Indeed, studies on the pathogenesis of autoimmune and inflammatory diseases have identified various post-transcription factors as important regulators of immune cell-mediated and target effector cell-mediated pathological conditions. This Review summarizes current knowledge regarding the roles of post-transcriptional checkpoints in autoimmunity, as evidenced by studies in both haematopoietic and non-haematopoietic cells, and discusses the relevance of these findings for developing new anti-inflammatory therapies.

The Rab5 effector FERRY links early endosomes with mRNA localization

Localized translation is vital to polarized cells and requires precise and robust distribution of different mRNAs and ribosomes across the cell. However, the underlying molecular mechanisms are poorly understood and important players are lacking. Here, we discovered a Rab5 effector, the five-subunit endosomal Rab5 and RNA/ribosome intermediary (FERRY) complex, that recruits mRNAs and ribosomes to early endosomes through direct mRNA-interaction. FERRY displays preferential binding to certain groups of transcripts, including mRNAs encoding mitochondrial proteins. Deletion of FERRY subunits reduces the endosomal localization of transcripts in cells and has a significant impact on mRNA levels. Clinical studies show that genetic disruption of FERRY causes severe brain damage. We found that, in neurons, FERRY co-localizes with mRNA on early endosomes, and mRNA loaded FERRY-positive endosomes are in close proximity of mitochondria. FERRY thus transforms endosomes into mRNA carriers and plays a key role in regulating mRNA distribution and transport.

Preprint Highlight: mRNA Location and Translation Rate Determine Protein Targeting to Dual Destinations

NET1 is a guanine nucleotide exchange factor for RhoA GTPase that plays different roles in the nucleus and cytoplasm. While perinuclear and peripheral mRNA translation sites have been identified, the mechanisms of spatial translation regulation and impacts on protein function are not generally understood. Here, the authors use genetic tools to manipulate NET1 mRNA targeting sequences, as well as proximity ligation, mass spectrometry, and imaging. They show that mRNA localization, translation rate, and the order of appearance of targeting domains during translation determine the extent of protein synthesis in each location, promoting site-specific NET1 function. This novel regulation of protein targeting by RNA translation rate and location uncovers the potential to engineer mRNA localization to optimize protein function and will likely impact research on cell biology, immunology, and beyond. This preprint has been assigned the following badges: New Hypothesis, New Methods, Open Software, Cross-Validation. Read the preprint on bioRxiv ( Gasparski et al., 2023 ): https://doi.org/10.1101/2023.04.24.538105 .

Insulin-like growth factor 1 promotes the gonadal development of Pampus argenteus by regulating energy metabolism†.

Insulin-like growth factor 1 (Igf1) is known to promote ovarian maturation by interacting with other hormones. However, the limited research on the role of Igf1 in the energy metabolism supply of gonads has hindered further exploration. To explore the role of Igf1 in gonadal development of silver pomfret, we analyzed the expression levels and the localization of igf1 mRNA and protein during testicular and ovarian development of silver pomfret. The results of the study showed upregulation of Igf1 in the critical period of vitellogenesis and sperm meiosis, which was found to be mainly expressed in the somatic cells of the gonads. Upon adding E2 and Igf1 to cultured gonadal tissues, the expression of energy-related genes was significantly increased, along with the E2-enhanced effect of Igf1 in the testis. Importantly, stimulation of both ovaries and testes with E2 and Igf1 led to a remarkable increase in the expression of vitellogenesis and meiosis-related genes. Therefore, we conclude that Igf1 promotes vitellogenesis and sperm meiosis by regulating gonadal energy production. Moreover, the expression of Igf1 in gonads is significantly regulated by E2. These findings provide new insights for the research of Igf1 in fish breeding, thus allowing the regulation of energy metabolism between growth and reproduction for successful reproductive outcomes.

The single-cell landscape of alternative transcription start sites of diabetic retina

More than half of mammalian protein-coding genes have multiple transcription start sites. Alternative transcription start site (TSS) modulate mRNA stability, localization, and translation efficiency on post-transcription level, and even generate novel protein isoforms. However, differential TSS usage among cell types in healthy and diabetic retina remains poorly characterized. In this study, by using 5′-tag-based single-cell RNA sequencing, we identified cell type-specific alternative TSS events and key transcription factors for each of retinal cell types. We observed that lengthening of 5′- UTRs in retinal cell types are enriched for multiple RNA binding protein binding sites, including splicing regulators Rbfox1/2/3 and Nova1. Furthermore, by comparing TSS expression between healthy and diabetic retina, we identified elevated apoptosis signal in Müller glia and microglia, which can be served as a putative early sign of diabetic retinopathy. By measuring 5′UTR isoforms in retinal single-cell dataset, our work provides a comprehensive panorama of alternative TSS and its potential consequence related to post-transcriptional regulation. We anticipate our assay can not only provide insights into cellular heterogeneity driven by transcriptional initiation, but also open up the perspectives for identification of novel diagnostic indexes for diabetic retinopathy.

The m6A reader MhYTP2 regulates the stability of its target mRNAs contributing to low nitrogen tolerance in apple (Malus domestica).

Studies have shown that the m6A reader primarily affects genes expression by participating in the regulation of mRNA localization, splicing, degradation, translation, and other metabolic processes. Previously, we discovered that the apple (Malus domestica) m6A reader MhYTP2 bound with and destabilized m6A-modified MdMLO19 mRNA. In addition, it enhanced the translation efficiency of m6A-modified mRNA of MdGDH1L, encoding a glutamate dehydrogenase, which confers resistance to powdery mildew. In this study, we report the function of MhYTP2 in the regulation of resistance to low nitrogen (N). The overexpression of MhYTP2 enhances the resistance of apple to low N. We show that MhYTP2 binds with and stabilizes the mRNAs of MdALN, which participates in the allantoin catabolic process and cellular response to N starvation in apple; MdPIDL, which participates in root hair elongation; MdTTG1, which is involved in the differentiation process of trichomes; and MdATG8A, which is a core participant in the regulation of autophagy. In addition, MhYTP2 accelerates the degradation of MdRHD3 mRNA, which regulates root development. RNA immunoprecipitation-seq and electrophoretic mobility shift assays show that the mRNAs of MdALN, MdATG8A, MdPIDL, MdTTG1, and MdRHD3 are the direct targets of MhYTP2. Overexpressing or knocking down the above genes in MhYTP2 overexpressing plants dismisses the function of MhYTP2 under low N, suggesting the role of MhYTP2 is dependent on those genes. Together, these results demonstrate that MhYTP2 enhances the resistance of apple to N deficiency by affecting the stability of the bound mRNAs.

Improved enzymatic labeling of fluorescent in situ hybridization probes applied to the visualization of retained introns in cells.

Fluorescence in situ hybridization (FISH) is a widely used tool for quantifying gene expression and determining the location of RNA molecules in cells. We present an improved method for FISH probe production that yields high-purity probes with a wide range of fluorophores using standard laboratory equipment at low cost. The method modifies an earlier protocol that uses terminal deoxynucleotidyl transferase to add fluorescently labeled nucleotides to synthetic deoxyoligonucleotides. In our protocol, amino-11-ddUTP is joined to an oligonucleotide pool prior to its conjugation to a fluorescent dye, thereby generating pools of probes ready for a variety of modifications. This order of reaction steps allows for high labeling efficiencies regardless of the GC content or terminal base of the oligonucleotides. The degree of labeling (DOL) for spectrally distinct fluorophores (Quasar, ATTO, and Alexa dyes) was mostly >90%, comparable with commercial probes. The ease and low cost of production allowed the generation of probe sets targeting a wide variety of RNA molecules. Using these probes, FISH assays in C2C12 cells showed the expected subcellular localization of mRNAs and pre-mRNAs for Polr2a (RNA polymerase II subunit 2a) and Gapdh, and of the long noncoding RNAs Malat1 and Neat1 Developing FISH probe sets for several transcripts containing retained introns, we found that retained introns in the Gabbr1 and Noc2l transcripts are present in subnuclear foci separate from their sites of synthesis and partially coincident with nuclear speckles. This labeling protocol should have many applications in RNA biology.

A local translation program regulates centriole amplification in the airway epithelium

Biogenesis of organelles requires targeting of a subset of proteins to specific subcellular domains by signal peptides or mechanisms controlling mRNA localization and local translation. How local distribution and translation of specific mRNAs for organelle biogenesis is achieved remains elusive and likely to be dependent on the cellular context. Here we identify Trinucleotide repeat containing-6a (Tnrc6a), a component of the miRNA pathway, distinctively localized to apical granules of differentiating airway multiciliated cells (MCCs) adjacent to centrioles. In spite of being enriched in TNRC6A and the miRNA-binding protein AGO2, they lack enzymes for mRNA degradation. Instead, we found these apical granules enriched in components of the mRNA translation machinery and newly synthesized proteins suggesting that they are specific hubs for target mRNA localization and local translation in MCCs. Consistent with this, Tnrc6a loss of function prevented formation of these granules and led to a broad reduction, rather than stabilization of miRNA targets. These included downregulation of key genes involved in ciliogenesis and was associated with defective multicilia formation both in vivo and in primary airway epithelial cultures. Similar analysis of Tnrc6a disruption in yolk sac showed stabilization of miRNA targets, highlighting the potential diversity of these mechanisms across organs.

Mammalian Oocytes Store mRNAs in a Mitochondria-Associated Membraneless Compartment

ABSTRACT During the final stages of oocyte growth, transcription ceases only to resume following fertilization. During this cessation, the oocyte and the embryo can only use stores mRNAs to synthesize new products, meaning the storage of maternal mRNAs is critical for generating haploid eggs through meiosis and for early embryonic development. Membraneless storage compartments are well characterized in nonmammalian oocytes but are less understood in more relevant models. Studies have established that RNA-binding proteins YBX2 and ZAR1 are required for maternal mRNA storage in full-grown mouse oocytes, and this study aimed to further characterize the localization of maternal mRNAs and the mechanism that stores them. The potential colocalization between highly expressed RNA-binding proteins and different types of membrane-bound organelles in fully grown mouse oocytes was analyzed, finding the proteins ZAR1, YBX2, DDX6, LSM14B, and 4E-T colocalized with mitochondria. Similar results were found in human, porcine, and bovine oocytes. The localization domain of RNA-binding proteins around mitochondria throughout the cytoplasm was named the mitochondria-associated ribonucleoprotein domain (MARDO). Immunostaining for ZAR1 at various growth stages was performed to determine when the MARDO forms, revealing that formation is directed by an increase in mitochondrial membrane potential during oocyte growth. ZAR1 was observed to be the most highly enriched of these proteins on mitochondria and to be the promoter of MARDO coalescence and mitochondrial clustering. Injections of RNase into mouse oocytes revealed MARDO is a phase-separated compartment regulated by RNA levels, and further analysis identified the disordered N-terminal region of ZAR1 drives MARDO coalescence into a hydrogel-like matrix that sequesters mitochondria. Next, the degradation of MARDO at the meiosis stage when oocytes resume maturation was analyzed. ZAR1 was found to be progressively depleted from the mitochondria during oocyte meiotic maturation. Mass spectrometry revealed phosphorylation as a driving mechanism for this disassembly during maturation. MARDO dissolution accompanied a decrease in ZAR1 levels and occurred during the transition from MI to MII. Treating oocytes with a proteasome inhibitor blocked dissolution of MARDO, whereas impairing spindle assembly causing cell-cycle arrest before MI had no effect. This suggested that proteasome-mediated degradation of ZAR1 underlies MARDO dissolution during oocyte meiotic maturation. Knockout studies in mice confirmed that ZAR1 is essential for MARDO assembly, and in these knockouts more than 1000 mRNAs, many of which were enriched in the MARDO, were reduced by at least 50%, suggesting MARDO disruption also causes mRNA reduction. Many RNA-binding proteins in the MARDO are implicated in translational repression, and by labeling translating ribosomes assembled on mRNAs, it was seen that these active ribosomes were mostly excluded from the MARDO. In addition, ZAR1 was seen to substantially reduce the translation of bound mRNA, suggesting that the maternal mRNAs stored in the MARDO are translationally repressed. This study identified and characterized the MARDO, a mitochondria-associated membraneless compartment that stores maternal mRNAs in mouse, bovine, porcine, and human oocytes.

Abstract A18: STC-15, a novel METTL3 inhibitor, and its combination with Venetoclax confer anti-tumour activity in AML models

Abstract N6-methyladenosine (m6A) is one of the most abundant RNA modifications, which influences mRNA and lncRNA localization, half-life, translation, and splicing. The majority of m6A modifications on cellular mRNAs are deposited by the RNA methyltransferase METTL3. To date, METTL3 has been implicated in the initiation and progression of multiple cancer types, with the highest expression of METTL3 mRNA observed in acute myeloid leukemia (AML). Currently, one line of standard of care therapy for AML patients is Venetoclax, which targets the anti-apoptotic protein BCL2. It was shown that m6A, deposited by METTL3 on BCL2 transcript, affects BCL2 mRNA stability and translation. Storm Therapeutics has developed potent and selective METTL3 inhibitors, including the clinical candidate STC-15. Here, we explore pharmacological inhibition of METTL3 as monotherapy or in combination with Venetoclax in AML models in vitro and in vivo. Sulforhodamine B and CellTiterGloTM assays were used to assess the viability of AML cell lines and patient-derived xenografts (PDXs), respectively, following METTL3 inhibition in vitro. BCL2 protein level was evaluated by Western blotting. SynergyFinder software was used to assess the degree of synergy between METTL3 inhibitors and Venetoclax. Intra-tibial implantation of human-derived AML cells (AML-PDXs) in NSG mice was used to determine single agent and combination therapy efficacy. Multiple AML cells lines and AML-PDXs were sensitive to pharmacological inhibition of METTL3 in vitro, as assessed by loss of viability. Treatment with METTL3 inhibitors led to downregulation of BCL2 protein level in several AML cell lines, as previously suggested by literature. Based on these results, the synergy between METTL3 inhibition and Venetoclax was assessed. Matrix-combination experiments have shown a high degree of synergy between the two drugs (defined by a synergy score >10) in THP-1 and MOLM-13 cell lines. To test METTL3 inhibition as a monotherapy and in combination with Venetoclax in vivo, three AML-PDX studies were initiated. Significantly lower spleen weight was observed in all animals treated with STC-15 or STC-15 + Venetoclax, and reduced number of circulating hCD45+ cells was observed in 2 out of the 3 models. In one of the models, STC-15 monotherapy outperformed Venetoclax (median survival 68 days vs 58 days, respectively), while the combination therapy extended median group survival to 85 days in comparison to 51.5 days in the vehicle group. In conclusion, we demonstrated that METTL3 inhibition results in anti-tumour effects across different AML models. Moreover, we demonstrated a synergistic effect between the novel METTL3 inhibitor STC-15 and Venetoclax, both in vitro and in vivo. These studies provide evidence for the utility of METTL3 inhibitor as a new therapeutic agent to treat AML. Currently, STC-15 is under clinical development (NCT05584111). Citation Format: Lina Vasiliauskaite, Yaara Ofir-Rosenfeld, Mark Albertella, Coralie Hoareau-Aveilla, Jerry McMahon, Oliver Rausch. STC-15, a novel METTL3 inhibitor, and its combination with Venetoclax confer anti-tumour activity in AML models [abstract]. In: Proceedings of the AACR Special Conference: Acute Myeloid Leukemia and Myelodysplastic Syndrome; 2023 Jan 23-25; Austin, TX. Philadelphia (PA): AACR; Blood Cancer Discov 2023;4(3_Suppl):Abstract nr A18.

PO-01-145 DYNAMIC UTR COMPOSITION IMPACTS RNA BINDING PROTEIN COMPLEXING TO CONTROL TRANSLATION AND LIMIT CARDIAC GAP JUNCTION FORMATION DURING STRESS

Translational control has emerged as a critical yet dynamic process, representing one of the most rapid means by which the cardiomyocyte can alter its proteome. Several key cardiac mRNAs, including connexin43 (Cx43, gene name GJA1) are understood to undergo alternative translation initiation with resulting products (ie, GJA1-20k) impacting cardiac function. We previously found alterations to GJA1 mRNA untranslated region (UTR) length occur in aged and stressed heart tissue, suppressing internal translation of GJA1-20k, and limiting Cx43 gap junction formation. Having therefore identified dynamic mRNA cis element-based regulation of Cx43/GJA1-20k translation, we next asked what trans-acting factors are at play to alter GJA1 mRNA translation during stress. The IMP family of RNA binding proteins (RBPs) regulate alternative and canonical translation initiation of several genes, which led us to investigate how they may impact GJA1 mRNA. Using GJA1 as a model RNA, we test the hypothesis that alternative transcription start site usage controls inclusion of cis-acting elements in the mRNA 5’UTR affecting RBP binding and regulation of translation. Pathological hypertrophy was induced by isoproterenol deliverey to adult mice via implanted minipumps. Mouse models are complemented with matured human IPSC-derived cardiomyocytes, primary mouse ventricular cardiomyocytes, exposed to chronic hypoxia or TGF-β in vitro. Single molecule fluorescence in situ hybridization (smFISH) coupled with super-resolution microscopy localize GJA1 mRNA and RBPs. Hypertrophic hearts show reduced GJA1-20k and IMP1 expression. Using smFISH to label GJA1 mRNA, we find IMP1 complexes with GJA1 mRNA predominantly in comparison to IMP2 and 3, and that this complexing is reduced during stress, concomitant with loss of GJA1-20k internal translation. Biochemical assays confirm GJA1 mRNA/IMP1 binding by RNA-IP and synthetic reduction of IMP1 expression by RNAi or CRISPR/Cas9 alters GJA1 mRNA localization, reduces internal translation of GJA1-20k, and limits gap junction formation. We find comparable results during hypoxia in primary mouse cardiomyocytes and human induced pluripotent stem cell derived cardiomyocytes. Dynamic GJA1-5’UTR composition therefore represents a powerful mechanism connecting alterations in transcription to gene-specific translational regulation by RBPs such as IMP1, disruption of intercellular communication during stress, and arrhythmogenesis.

Olfactory receptor OR52N2 for PGE2 in mediation of guppy courtship behaviors

Prostaglandins (PGs) are a type of physiologically active unsaturated fatty acids. As an important sex pheromone, PGs play a vital role in regulating the reproductive behaviors of species by mediating nerve and endocrine responses. In this study, guppy (Poecilia reticulate) was used as the model specie to detect the function of PGE2 in inducing the onset of courtship behaviors. Our results showed that adding PGE2 into the water environment could activate the courtship behavior of male guppy, indicating that the peripheral olfactory system mediated the PGE2 function. Thereafter, the open reading frame (ORF) of olfactory receptor or52n2 was cloned, which was 936 bp in length, coding 311 amino acids. As a typical G protein-coupled receptor, OR52N2 had a conservative seven α-helix transmembrane domains. To confirm the regulatory relationship between OR52N2 and PGE2, dual-luciferase reporter assay was employed to verify the activation of downstream CREB signaling pathways. Results showed that PGE2 significantly enhanced CRE promoter activity in or52n2 ORF transient transfected HEK-293 T cells. Finally, localization of or52n2 mRNA were observed in ciliated receptor cells of the olfactory epithelium using in situ hybridization. Our results provide a novel insight into sex pheromone signaling transduction in reproductive behavior.

The EJC disassembly factor PYM is an intrinsically disordered protein and forms a fuzzy complex with RNA.

The discovery of several functional interactions where one or even both partners remain disordered has demonstrated that specific interactions do not necessarily require well-defined intermolecular interfaces. Here we describe a fuzzy protein-RNA complex formed by the intrinsically unfolded protein PYM and RNA. PYM is a cytosolic protein, which has been reported to bind the exon junction complex (EJC). In the process of oskar mRNA localization in Drosophila melanogaster, removal of the first intron and deposition of the EJC are essential, while PYM is required to recycle the EJC components after localization has been accomplished. Here we demonstrate that the first 160 amino acids of PYM (PYM1-160) are intrinsically disordered. PYM1-160 binds RNA independently of its nucleotide sequence, forming a fuzzy protein-RNA complex that is incompatible with PYM's function as an EJC recycling factor. We propose that the role of RNA binding consists in down-regulating PYM activity by blocking the EJC interaction surface of PYM until localization has been accomplished. We suggest that the largely unstructured character of PYM may act to enable binding to a variety of diverse interaction partners, such as multiple RNA sequences and the EJC proteins Y14 and Mago.

MSLP: mRNA subcellular localization predictor based on machine learning techniques

BackgroundSubcellular localization of messenger RNA (mRNAs) plays a pivotal role in the regulation of gene expression, cell migration as well as in cellular adaptation. Experiment techniques for pinpointing the subcellular localization of mRNAs are laborious, time-consuming and expensive. Therefore, in silico approaches for this purpose are attaining great attention in the RNA community.MethodsIn this article, we propose MSLP, a machine learning-based method to predict the subcellular localization of mRNA. We propose a novel combination of four types of features representing k-mer, pseudo k-tuple nucleotide composition (PseKNC), physicochemical properties of nucleotides, and 3D representation of sequences based on Z-curve transformation to feed into machine learning algorithm to predict the subcellular localization of mRNAs.ResultsConsidering the combination of the above-mentioned features, ennsemble-based models achieved state-of-the-art results in mRNA subcellular localization prediction tasks for multiple benchmark datasets. We evaluated the performance of our method in ten subcellular locations, covering cytoplasm, nucleus, endoplasmic reticulum (ER), extracellular region (ExR), mitochondria, cytosol, pseudopodium, posterior, exosome, and the ribosome. Ablation study highlighted k-mer and PseKNC to be more dominant than other features for predicting cytoplasm, nucleus, and ER localizations. On the other hand, physicochemical properties and Z-curve based features contributed the most to ExR and mitochondria detection. SHAP-based analysis revealed the relative importance of features to provide better insights into the proposed approach.AvailabilityWe have implemented a Docker container and API for end users to run their sequences on our model. Datasets, the code of API and the Docker are shared for the community in GitHub at: https://github.com/smusleh/MSLP.

Phosphorylation controls the oligomeric state of She2 and mRNA localization in yeast.

Messenger RNA (mRNA) localization is an important mechanism controlling local protein synthesis. In budding yeast, asymmetric localization of transcripts such as ASH1 mRNA to the bud tip depends on the She2 RNA-binding protein. She2 assembles as a tetramer to bind RNA, but the regulation of this process as part of the mRNA locasome is still unclear. Here, we performed a phosphoproteomic analysis of She2 in vivo and identified new phosphosites, several of which are located at the dimerization or tetramerization interfaces of She2. Remarkably, phosphomimetic mutations at these residues disrupt the capacity of She2 to promote Ash1 asymmetric accumulation. A detailed analysis of one of these residues, T109, shows that a T109D mutation inhibits She2 oligomerization and its interaction with She3 and the importin-α Srp1. She2 proteins harboring the T109D mutation also display reduced expression. More importantly, this phosphomimetic mutation strongly impairs the capacity of She2 to bind RNA and disrupts ASH1 mRNA localization. These results demonstrate that the control of She2 oligomerization by phosphorylation constitutes an important regulatory step in the mRNA localization pathway.

COL28 promotes proliferation, migration, and EMT of renal tubular epithelial cells

Type XXVIII collagen (COL28) is involved in cancer and lung fibrosis. COL28 polymorphisms and mutations might be involved in kidney fibrosis, but the exact role of COL28 in renal fibrosis is unknown. This study explored the function of COL28 in renal tubular cells by examining the expression of COL28 mRNA and the effects of COL28 overexpression in human tubular cells. COL28 mRNA expression and localization were observed in normal and fibrotic kidney tissues from humans and mice using real-time PCR, western blot, immunofluorescence, and immunohistochemistry. The consequences of COL28 overexpression on cell proliferation, migration, cell polarity, and epithelial-to-mesenchymal transition (EMT) induced by TGF-β1 were examined in human tubular HK-2 cells. COL28 expression was low in human normal renal tissues, mainly observed in the renal tubular epithelial cells and especially in proximal renal tubules. COL28 protein expression in human and mouse obstructive kidney disease was higher than in normal tissues (p < 0.05) and more significant in the UUO2-Week than the UUO1-Week group. The overexpression of COL28 promoted HK-2 cell proliferation and enhanced their migration ability (all p < 0.05). TGF-β1 (10 ng/ml) induced COL28 mRNA expression in HK-2 cells, decreased E-cadherin and increased α-SMA in the COL28-overexpression group compared with controls (p < 0.05). ZO-1 expression decreased while COL6 increased in the COL28-overexpression group compared with controls (p < 0.05). In conclusion, COL28 overexpression promotes the migration and proliferation of renal tubular epithelial cells. The EMT could also be involved. COL28 could be a therapeutic target against renal- fibrotic diseases.

Subcellular mRNA localization and local translation of Arhgap11a in radial glial progenitors regulates cortical development

mRNA localization and local translation enable exquisite spatial and temporal control of gene expression, particularly in polarized, elongated cells. These features are especially prominent in radial glial cells (RGCs), which are neural and glial precursors of the developing cerebral cortex and scaffolds for migrating neurons. Yet the mechanisms by which subcellular RGC compartments accomplish their diverse functions are poorly understood. Here, we demonstrate that mRNA localization and local translation of the RhoGAP ARHGAP11A in the basal endfeet of RGCs control their morphology and mediate neuronal positioning. Arhgap11a transcript and protein exhibit conserved localization to RGC basal structures in mice and humans, conferred by the 5' UTR. Proper RGC morphology relies upon active Arhgap11a mRNA transport and localization to the basal endfeet, where ARHGAP11A is locally synthesized. This translation is essential for positioning interneurons at the basement membrane. Thus, local translation spatially and acutely activates Rho signaling in RGCs to compartmentalize neural progenitor functions.

Localization of Kif1c mRNA to cell protrusions dictates binding partner specificity of the encoded protein.

Subcellular localization of messenger RNA (mRNA) is a widespread phenomenon that can impact the regulation and function of the encoded protein. In nonneuronal cells, specific mRNAs localize to cell protrusions, and proper mRNA localization is required for cell migration. However, the mechanisms by which mRNA localization regulates protein function in this setting remain unclear. Here, we examined the functional consequences of localization of the mRNA encoding KIF1C. KIF1C is a kinesin motor protein required for cell migration and mRNA trafficking, including trafficking of its own mRNA. We show that Kif1c mRNA localization does not regulate KIF1C's protein abundance, distribution, or ability to traffic other mRNAs. Conversely, Kif1c mRNA localization to protrusions is required for directed cell migration. We used mass spectrometry to identify binding partners of endogenous KIF1C, which revealed dramatic dysregulation of the number and identity of KIF1C interactors in response to Kif1c mRNA mislocalization. These results therefore uncovered a mechanistic connection between mRNA localization to cell protrusions and the specificity of protein-protein interactions. We anticipate that this mechanism is not limited to Kif1c and is likely to be a general principle that impacts the functions of proteins encoded by protrusion-enriched mRNAs in nonneuronal cells.