Vimentin protects differentiating stem cells from stress

Abstract Vimentin is one of the first cytoplasmic intermediate filaments to be expressed in mammalian cells during embryogenesis, but its role in cellular fitness has long been a mystery. Vimentin is acknowledged to play a role in cell stiffness, cell motility, and cytoplasmic organization, yet it is widely considered to be dispensable for cellular function and organismal development. Here, we show that Vimentin plays a role in cellular stress response in differentiating cells, by recruiting aggregates, stress granules, and RNA-binding proteins, directing their elimination and asymmetric partitioning. In the absence of Vimentin, pluripotent embryonic stem cells fail to differentiate properly, with a pronounced deficiency in neuronal differentiation. Our results uncover a novel function for Vimentin, with important implications for development, tissue homeostasis, and in particular, stress response.

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Function of Pumilio Genes in Human Embryonic Stem Cells and Their Effect in Stemness and Cardiomyogenesis

10.1101/751537 ◽

2019 ◽

Author(s):

Isabelle Leticia Zaboroski Silva ◽

Anny Waloski Robert ◽

Guillermo Cabrera Cabo ◽

Lucia Spangenberg ◽

Marco Augusto Stimamiglio ◽

...

Keyword(s):

Stem Cells ◽

Embryonic Stem Cells ◽

Rna Binding ◽

Rna Binding Proteins ◽

Embryonic Stem ◽

Mrna Levels ◽

Human Escs ◽

Mrna Targets ◽

Cardiomyogenic Differentiation

AbstractPosttranscriptional regulation plays a fundamental role in the biology of embryonic stem cells (ESCs). Many studies have demonstrated that multiple mRNAs are coregulated by one or more RNA binding proteins (RBPs) that orchestrate the expression of these molecules. A family of RBPs, known as PUF (Pumilio-FBF), is highly conserved among species and has been associated with the undifferentiated and differentiated states of different cell lines. In humans, two homologs of the PUF family have been found: Pumilio 1 (PUM1) and Pumilio 2 (PUM2). To understand the role of these proteins in human ESCs (hESCs), we first demonstrated the influence of the silencing of PUM1 and PUM2 on pluripotency genes. OCT4 and NANOG mRNA levels decreased significantly with the knockdown of Pumilio, suggesting that PUMILIO proteins play a role in the maintenance of pluripotency in hESCs. Furthermore, we observed that the hESCs silenced for PUM1 and 2 exhibited an improvement in efficiency of in vitro cardiomyogenic differentiation. Using in silico analysis, we identified mRNA targets of PUM1 and PUM2 expressed during cardiomyogenesis. With the reduction of PUM1 and 2, these target mRNAs would be active and could be involved in the progression of cardiomyogenesis.

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CLUH interactome reveals an association to SPAG5 and a proximity to the translation of mitochondrial protein

10.1101/2021.07.08.451585 ◽

2021 ◽

Author(s):

Mickaële Hemono ◽

Alexandre Haller ◽

Johana Chicher ◽

Anne-Marie Duchêne ◽

Richard Patryk Ngondo

Keyword(s):

Mammalian Cells ◽

Rna Binding ◽

Rna Binding Proteins ◽

Mitochondrial Protein ◽

Embryonic Stem ◽

Nuclear Genome ◽

Mrna Translation ◽

Mitochondrial Proteins ◽

Molecular Function ◽

First Time

Mitochondria require thousands of proteins to fulfil their essential function in energy production and other fundamental biological processes. These proteins are mostly encoded by the nuclear genome, translated in the cytoplasm before being imported into the organelle. RNA binding proteins (RBPs) are central players in the regulation of this process by affecting mRNA translation, stability or localization. CLUH is an RBP recognizing specifically mRNAs coding for mitochondrial proteins, but its precise molecular function and interacting partners remain undiscovered in mammals. Here we reveal for the first time CLUH interactome in mammalian cells. Using both co-IP and BioID proximity-labeling approaches, we identify novel molecular partners interacting stably or transiently with CLUH in HCT116 cells and mouse embryonic stem cells. We reveal a stable RNA-independent interaction of CLUH with itself and with SPAG5 in cytosolic granular structures. More importantly, we uncover an unexpected proximity of CLUH to mitochondrial proteins and their cognate mRNAs in the cytosol. Additionally, our data highlight the importance of CLUH TPR domain for its interactions with both proteins and mRNAs. Overall, through the analysis of CLUH interactome, our study sheds a new light on CLUH molecular function by highlighting its association to the translation and subcellular localization of some mRNAs coding for mitochondrial proteins.

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The interactome of CLUH reveals its association to SPAG5 and its co-translational proximity to mitochondrial proteins

BMC Biology ◽

10.1186/s12915-021-01213-y ◽

2022 ◽

Vol 20 (1) ◽

Author(s):

Mickaële Hémono ◽

Alexandre Haller ◽

Johana Chicher ◽

Anne-Marie Duchêne ◽

Richard Patryk Ngondo

Keyword(s):

Mammalian Cells ◽

Rna Binding ◽

Rna Binding Proteins ◽

Embryonic Stem ◽

Nuclear Genome ◽

Mrna Translation ◽

Mitochondrial Proteins ◽

Molecular Function ◽

First Time ◽

Tpr Domain

Abstract Background Mitochondria require thousands of proteins to fulfill their essential function in energy production and other fundamental biological processes. These proteins are mostly encoded by the nuclear genome, translated in the cytoplasm before being imported into the organelle. RNA binding proteins (RBPs) are central players in the regulation of this process by affecting mRNA translation, stability, or localization. CLUH is an RBP recognizing specifically mRNAs coding for mitochondrial proteins, but its precise molecular function and interacting partners remain undiscovered in mammals. Results Here we reveal for the first time CLUH interactome in mammalian cells. Using both co-IP and BioID proximity-labeling approaches, we identify novel molecular partners interacting stably or transiently with CLUH in HCT116 cells and mouse embryonic stem cells. We reveal stable RNA-independent interactions of CLUH with itself and with SPAG5 in cytosolic granular structures. More importantly, we uncover an unexpected proximity of CLUH to mitochondrial proteins and their cognate mRNAs in the cytosol. We show that this interaction occurs during the process of active translation and is dependent on CLUH TPR domain. Conclusions Overall, through the analysis of CLUH interactome, our study sheds a new light on CLUH molecular function by revealing new partners and by highlighting its link to the translation and subcellular localization of some mRNAs coding for mitochondrial proteins.

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Interaction of Sox2 with RNA binding proteins in mouse embryonic stem cells

Experimental Cell Research ◽

10.1016/j.yexcr.2019.05.006 ◽

2019 ◽

Vol 381 (1) ◽

pp. 129-138 ◽

Cited By ~ 3

Author(s):

Samudyata ◽

Paulo P. Amaral ◽

Pär G. Engström ◽

Samuel C. Robson ◽

Michael L. Nielsen ◽

...

Keyword(s):

Stem Cells ◽

Embryonic Stem Cells ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Embryonic Stem ◽

Mouse Embryonic Stem Cells

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Nanog RNA-binding proteins YBX1 and ILF3 affect pluripotency of embryonic stem cells

Cell Biology International ◽

10.1002/cbin.10539 ◽

2016 ◽

Vol 40 (8) ◽

pp. 847-860 ◽

Cited By ~ 4

Author(s):

Chuanliang Guo ◽

Yan Xue ◽

Guanheng Yang ◽

Shang Yin ◽

Wansheng Shi ◽

...

Keyword(s):

Stem Cells ◽

Embryonic Stem Cells ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Embryonic Stem

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The ancestral gene repertoire of animal stem cells

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1514789112 ◽

2015 ◽

Vol 112 (51) ◽

pp. E7093-E7100 ◽

Cited By ~ 50

Author(s):

Alexandre Alié ◽

Tetsutaro Hayashi ◽

Itsuro Sugimura ◽

Michaël Manuel ◽

Wakana Sugano ◽

...

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Evolutionary Biology ◽

Rna Binding ◽

Germ Line ◽

Rna Binding Proteins ◽

Embryonic Stem ◽

Animal Origin ◽

Gene Repertoire ◽

Ancestral Gene

Stem cells are pivotal for development and tissue homeostasis of multicellular animals, and the quest for a gene toolkit associated with the emergence of stem cells in a common ancestor of all metazoans remains a major challenge for evolutionary biology. We reconstructed the conserved gene repertoire of animal stem cells by transcriptomic profiling of totipotent archeocytes in the demosponge Ephydatia fluviatilis and by tracing shared molecular signatures with flatworm and Hydra stem cells. Phylostratigraphy analyses indicated that most of these stem-cell genes predate animal origin, with only few metazoan innovations, notably including several partners of the Piwi machinery known to promote genome stability. The ancestral stem-cell transcriptome is strikingly poor in transcription factors. Instead, it is rich in RNA regulatory actors, including components of the “germ-line multipotency program” and many RNA-binding proteins known as critical regulators of mammalian embryonic stem cells.

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m5U54 tRNA Hypomodification by Lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs

International Journal of Molecular Sciences ◽

10.3390/ijms22062941 ◽

2021 ◽

Vol 22 (6) ◽

pp. 2941

Author(s):

Marisa Pereira ◽

Diana R. Ribeiro ◽

Miguel M. Pinheiro ◽

Margarida Ferreira ◽

Stefanie Kellner ◽

...

Keyword(s):

Stress Response ◽

Small Rnas ◽

Mammalian Cells ◽

Cellular Stress ◽

Cellular Stress Response ◽

Translation Regulation ◽

Translation Efficiency ◽

Down Regulation ◽

Gene Expression Control ◽

The Impact

Transfer RNA (tRNA) molecules contain various post-transcriptional modifications that are crucial for tRNA stability, translation efficiency, and fidelity. Besides their canonical roles in translation, tRNAs also originate tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs with regulatory functions ranging from translation regulation to gene expression control and cellular stress response. Recent evidence indicates that tsRNAs are also modified, however, the impact of tRNA epitranscriptome deregulation on tsRNAs generation is only now beginning to be uncovered. The 5-methyluridine (m5U) modification at position 54 of cytosolic tRNAs is one of the most common and conserved tRNA modifications among species. The tRNA methyltransferase TRMT2A catalyzes this modification, but its biological role remains mostly unexplored. Here, we show that TRMT2A knockdown in human cells induces m5U54 tRNA hypomodification and tsRNA formation. More specifically, m5U54 hypomodification is followed by overexpression of the ribonuclease angiogenin (ANG) that cleaves tRNAs near the anticodon, resulting in accumulation of 5′tRNA-derived stress-induced RNAs (5′tiRNAs), namely 5′tiRNA-GlyGCC and 5′tiRNA-GluCTC, among others. Additionally, transcriptomic analysis confirms that down-regulation of TRMT2A and consequently m5U54 hypomodification impacts the cellular stress response and RNA stability, which is often correlated with tiRNA generation. Accordingly, exposure to oxidative stress conditions induces TRMT2A down-regulation and tiRNA formation in mammalian cells. These results establish a link between tRNA hypomethylation and ANG-dependent tsRNAs formation and unravel m5U54 as a tRNA cleavage protective mark.

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RALYL increases hepatocellular carcinoma stemness by sustaining the mRNA stability of TGF-β2

Nature Communications ◽

10.1038/s41467-021-21828-7 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Xia Wang ◽

Jin Wang ◽

Yu-Man Tsui ◽

Chaoran Shi ◽

Ying Wang ◽

...

Keyword(s):

Stem Cells ◽

Mrna Stability ◽

Rna Binding ◽

Embryonic Stem ◽

Molecular Characteristics ◽

Specific Gene ◽

Functional Studies ◽

Poor Differentiation ◽

Development In Vitro

AbstractGrowing evidences suggest that cancer stem cells exhibit many molecular characteristics and phenotypes similar to their ancestral progenitor cells. In the present study, human embryonic stem cells are induced to differentiate into hepatocytes along hepatic lineages to mimic liver development in vitro. A liver progenitor specific gene, RALY RNA binding protein like (RALYL), is identified. RALYL expression is associated with poor prognosis, poor differentiation, and metastasis in clinical HCC patients. Functional studies reveal that RALYL could promote HCC tumorigenicity, self-renewal, chemoresistance, and metastasis. Moreover, molecular mechanism studies show that RALYL could upregulate TGF-β2 mRNA stability by decreasing N6-methyladenosine (m6A) modification. TGF-β signaling and the subsequent PI3K/AKT and STAT3 pathways, upregulated by RALYL, contribute to the enhancement of HCC stemness. Collectively, RALYL is a liver progenitor specific gene and regulates HCC stemness by sustaining TGF-β2 mRNA stability. These findings may inspire precise therapeutic strategies for HCC.

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