Arginine methylation of RNA-binding proteins regulates cell function and differentiation

ABSTRACT Posttranscriptional controls in higher eukaryotes are central to cell differentiation and developmental programs. These controls reflect sequence-specific interactions of mRNAs with one or more RNA binding proteins. The α-globin poly(C) binding proteins (αCPs) comprise a highly abundant subset of K homology (KH) domain RNA binding proteins and have a characteristic preference for binding single-stranded C-rich motifs. αCPs have been implicated in translation control and stabilization of multiple cellular and viral mRNAs. To explore the full contribution of αCPs to cell function, we have identified a set of mRNAs that associate in vivo with the major αCP2 isoforms. One hundred sixty mRNA species were consistently identified in three independent analyses of αCP2-RNP complexes immunopurified from a human hematopoietic cell line (K562). These mRNAs could be grouped into subsets encoding cytoskeletal components, transcription factors, proto-oncogenes, and cell signaling factors. Two mRNAs were linked to ceroid lipofuscinosis, indicating a potential role for αCP2 in this infantile neurodegenerative disease. Surprisingly, αCP2 mRNA itself was represented in αCP2-RNP complexes, suggesting autoregulatory control of αCP2 expression. In vitro analyses of representative target mRNAs confirmed direct binding of αCP2 within their 3′ untranslated regions. These data expand the list of mRNAs that associate with αCP2 in vivo and establish a foundation for modeling its role in coordinating pathways of posttranscriptional gene regulation.

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The QKI-5 and QKI-6 RNA Binding Proteins Regulate the Expression of MicroRNA 7 in Glial Cells

Molecular and Cellular Biology ◽

10.1128/mcb.01604-12 ◽

2013 ◽

Vol 33 (6) ◽

pp. 1233-1243 ◽

Cited By ~ 47

Author(s):

Yunling Wang ◽

Gillian Vogel ◽

Zhenbao Yu ◽

Stéphane Richard

Keyword(s):

Glial Cells ◽

Rna Splicing ◽

Cellular Localization ◽

Binding Proteins ◽

Rna Binding ◽

Egf Receptor ◽

Cell Function ◽

Rna Binding Proteins ◽

Glioblastoma Cells ◽

Egfr Expression

Thequaking(qkI) gene encodes 3 major alternatively spliced isoforms that contain unique sequences at their C termini dictating their cellular localization. QKI-5 is predominantly nuclear, whereas QKI-6 is distributed throughout the cell and QKI-7 is cytoplasmic. The QKI isoforms are sequence-specific RNA binding proteins expressed mainly in glial cells modulating RNA splicing, export, and stability. Herein, we identify a new role for the QKI proteins in the regulation of microRNA (miRNA) processing. We observed that small interfering RNA (siRNA)-mediated QKI depletion of U343 glioblastoma cells leads to a robust increase in miR-7 expression. The processing from primary to mature miR-7 was inhibited in the presence QKI-5 and QKI-6 but not QKI-7, suggesting that the nuclear localization plays an important role in the regulation of miR-7 expression. The primary miR-7-1 was bound by the QKI isoforms in a QKI response element (QRE)-specific manner. We observed that the pri-miR-7-1 RNA was tightly bound to Drosha in the presence of the QKI isoforms, and this association was not observed in siRNA-mediated QKI or Drosha-depleted U343 glioblastoma cells. Moreover, the presence of the QKI isoforms led to an increase presence of pri-miR-7 in nuclear foci, suggesting that pri-miR-7-1 is retained in the nucleus by the QKI isoforms. miR-7 is known to target the epidermal growth factor (EGF) receptor (EGFR) 3′ untranslated region (3′-UTR), and indeed, QKI-deficient U343 cells had reduced EGFR expression and decreased ERK activation in response to EGF. Elevated levels of miR-7 are associated with cell cycle arrest, and it was observed that QKI-deficient U343 that harbor elevated levels of miR-7 exhibited defects in cell proliferation that were partially rescued by the addition of a miR-7 inhibitor. These findings suggest that the QKI isoforms regulate glial cell function and proliferation by regulating the processing of certain miRNAs.

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In vivo and in vitro arginine methylation of RNA-binding proteins.

Molecular and Cellular Biology ◽

10.1128/mcb.15.5.2800 ◽

1995 ◽

Vol 15 (5) ◽

pp. 2800-2808 ◽

Cited By ~ 214

Author(s):

Q Liu ◽

G Dreyfuss

Keyword(s):

Hela Cells ◽

Posttranslational Modifications ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Arginine Methylation ◽

Hnrnp A1 ◽

Arginine Residues

Heterogenous nuclear ribonucleoproteins (hnRNPs) bind pre-mRNAs and facilitate their processing into mRNAs. Many of the hnRNPs undergo extensive posttranslational modifications including methylation on arginine residues. hnRNPs contain about 65% of the total NG,NG-dimethylarginine found in the cell nucleus. The role of this modification is not known. Here we identify the hnRNPs that are methylated in HeLa cells and demonstrate that most of the pre-mRNA-binding proteins receive this modification. Using recombinant human hnRNP A1 as a substrate, we have partially purified and characterized a protein-arginine N-methyltransferase specific for hnRNPs from HeLa cells. This methyltransferase can methylate the same subset of hnRNPs in vitro as are methylated in vivo. Furthermore, it can also methylate other RNA-binding proteins that contain the RGG motif RNA-binding domain. This activity is evolutionarily conserved from lower eukaryotes to mammals, suggesting that methylation has a significant role in the function of RNA-binding proteins.

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The interactome of Cryptococcus neoformans Rmt5 reveals multiple regulatory points in fungal cell biology and pathogenesis

10.1101/2022.01.13.475903 ◽

2022 ◽

Author(s):

Murat C Kalem ◽

Harini Subbiah ◽

Shichen Shen ◽

Runpu Chen ◽

Luke Terry ◽

...

Keyword(s):

Cryptococcus Neoformans ◽

Cell Biology ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Arginine Methylation ◽

Chromosome 9 ◽

Post Translational Modification ◽

Cellular Processes ◽

Carbon Dioxide Atmosphere

Protein arginine methylation is a key post-translational modification in eukaryotes that modulates core cellular processes, including translation, morphology, transcription, and RNA fate. However, this has not been explored in Cryptococcus neoformans, a human-pathogenic basidiomycetous encapsulated fungus. We characterized the five protein arginine methyltransferases in C. neoformans and highlight Rmt5 as critical regulator of cryptococcal morphology and virulence. An rmt5∆ mutant was defective in thermotolerance, had a remodeled cell wall, and exhibited enhanced growth in an elevated carbon dioxide atmosphere and in chemically induced hypoxia. We revealed that Rmt5 interacts with post-transcriptional gene regulators, such as RNA-binding proteins and translation factors. Further investigation of the rmt5∆ mutant showed that Rmt5 is critical for the homeostasis of eIF2α and its phosphorylation state following 3-amino-1,2,4-triazole-induced ribosome stalling. RNA sequencing of one rmt5∆ clone revealed stable chromosome 9 aneuploidy that was ameliorated by complementation but did not impact the rmt5∆ phenotype. As a result of these diverse interactions and functions, loss of RMT5 enhanced phagocytosis by murine macrophages and attenuated disease progression in mice. Taken together, our findings link arginine methylation to critical cryptococcal cellular processes that impact pathogenesis, including post-transcriptional gene regulation by RNA- binding proteins.

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The Role of Protein Arginine Methylation in mRNP Dynamics

Molecular Biology International ◽

10.4061/2011/163827 ◽

2011 ◽

Vol 2011 ◽

pp. 1-10 ◽

Cited By ~ 28

Author(s):

Michael C. Yu

Keyword(s):

Messenger Rna ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Arginine Methylation ◽

Messenger Ribonucleoprotein ◽

Heterogeneous Nuclear Ribonucleoproteins ◽

Rna Biogenesis ◽

Mrnp Biogenesis

In eukaryotes, messenger RNA biogenesis depends on the ordered and precise assembly of a nuclear messenger ribonucleoprotein particle (mRNP) during transcription. This process requires a well-orchestrated and dynamic sequence of molecular recognition events by specific RNA-binding proteins. Arginine methylation is a posttranslational modification found in a plethora of RNA-binding proteins responsible for mRNP biogenesis. These RNA-binding proteins include both heterogeneous nuclear ribonucleoproteins (hnRNPs) and serine/arginine-rich (SR) proteins. In this paper, I discuss the mechanisms of action by which arginine methylation modulates various facets of mRNP biogenesis, and how the collective consequences of this modification impart the specificity required to generate a mature, translational- and export-competent mRNP.

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Regulation of β-cell function by RNA-binding proteins

Molecular Metabolism ◽

10.1016/j.molmet.2013.09.003 ◽

2013 ◽

Vol 2 (4) ◽

pp. 348-355 ◽

Cited By ~ 10

Author(s):

Maria Grazia Magro ◽

Michele Solimena

Keyword(s):

Binding Proteins ◽

Rna Binding ◽

Cell Function ◽

Rna Binding Proteins ◽

Β Cell ◽

Β Cell Function

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Protein l-Arginine Methylation of RNA-Binding Proteins and Their Impact on Human Diseases

L-Arginine in Clinical Nutrition ◽

10.1007/978-3-319-26009-9_15 ◽

2016 ◽

pp. 189-199

Author(s):

Michael C. Yu ◽

Christopher A. Jackson

Keyword(s):

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Arginine Methylation ◽

Human Diseases ◽

Protein L

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Regulation of Paneth Cell Function by RNA-Binding Proteins and Noncoding RNAs

Cells ◽

10.3390/cells10082107 ◽

2021 ◽

Vol 10 (8) ◽

pp. 2107

Author(s):

Hee K. Chung ◽

Lan Xiao ◽

Krishna C. Jaladanki ◽

Jian-Ying Wang

Keyword(s):

Bacterial Infection ◽

Binding Proteins ◽

Rna Binding ◽

Cell Function ◽

Rna Binding Proteins ◽

Focal Point ◽

Paneth Cell ◽

Noncoding Rnas ◽

Paneth Cells ◽

Mucosal Inflammation

Paneth cells are specialized intestinal epithelial cells that are located at the base of small intestinal crypts and play a vital role in preserving the gut epithelium homeostasis. Paneth cells act as a safeguard from bacterial translocation across the epithelium and constitute the niche for intestinal stem cells in the small intestine by providing multiple niche signals. Recently, Paneth cells have become the focal point of investigations defining the mechanisms underlying the epithelium-microbiome interactions and pathogenesis of chronic gut mucosal inflammation and bacterial infection. Function of Paneth cells is tightly regulated by numerous factors at different levels, while Paneth cell defects have been widely documented in various gut mucosal diseases in humans. The post-transcription events, specific change in mRNA stability and translation by RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) are implicated in many aspects of gut mucosal physiology by modulating Paneth cell function. Deregulation of RBPs and ncRNAs and subsequent Paneth cell defects are identified as crucial elements of gut mucosal pathologies. Here, we overview the posttranscriptional regulation of Paneth cells by RBPs and ncRNAs, with a particular focus on the increasing evidence of RBP HuR and long ncRNA H19 in this process. We also discuss the involvement of Paneth cell dysfunction in altered susceptibility of the intestinal epithelium to chronic inflammation and bacterial infection following disrupted expression of HuR and H19.

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