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YB-1 is important for an early stage embryonic development - Neural tube formation and cell proliferation
Abstract and Figures
The eukaryotic Y-box-binding protein-1 (YB-1) is involved in the transcriptional and translational control of many biological
processes, including cell proliferation. In clinical studies, the cellular level of YB-1 closely correlates with tumor growth
and prognosis. To understand the role of YB-1 in vivo, especially in the developmental process, we generated YB-1 knock-out mice, which are embryonic lethal and exhibit exencephaly
associated with abnormal patterns of cell proliferation within the neuroepithelium. β-Actin expression and F-actin formation
were reduced in the YB-1 null embryo and YB-1-/- mouse embryonic fibroblasts, suggesting that the neural tube defect is caused by abnormal cell morphology and actin assembly
within the neuroepithelium. Fibroblasts derived from YB-1-/- embryos demonstrated reduced growth and cell density. A colony formation assay showed that YB-1-/- mouse embryonic fibroblasts failed to undergo morphological transformation and remained contact-inhibited in culture. These
results demonstrate that YB-1 is involved in early mouse development, including neural tube closure and cell proliferation.
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... Among the YB proteins, YB-1 seems to be developmentally most important: In comparison to the loss of YB-2 and YB-3, YB-1 is mostly embryonic lethal as demonstrated in YB-1 null mutant (YB1 −/− ) mice (Lu et al., 2005;Uchiumi et al., 2006). However, the serious consequences of YB-1 deficiency become only evident after the first trimester, when a functional placenta is already established (Meyer et al., 2020). ...
... After placentation which finishes around gestation days (GD) 14-15 in mice, null mutation and heterozygous YB-1 knockout mice suffer from IUGR (Lu et al., 2005;Uchiumi et al., 2006;Meyer et al., 2020). Despite a small proportion of YB1 −/− mice is born alive, most of them have severe craniofacial defects, multi-organ hypoplasia and do not survive the first day of life (Lu et al., 2005;Uchiumi et al., 2006). ...
... After placentation which finishes around gestation days (GD) 14-15 in mice, null mutation and heterozygous YB-1 knockout mice suffer from IUGR (Lu et al., 2005;Uchiumi et al., 2006;Meyer et al., 2020). Despite a small proportion of YB1 −/− mice is born alive, most of them have severe craniofacial defects, multi-organ hypoplasia and do not survive the first day of life (Lu et al., 2005;Uchiumi et al., 2006). The multi-organ hypoplasia might be a consequence of reduced cell proliferation (Lu et al., 2005). ...
By promoting tissue invasion, cell growth and angiogenesis, the Y-box binding protein (YB-1) became famous as multifunctional oncoprotein. However, this designation is telling only part of the story. There is one particular time in life when actual tumorigenic-like processes become undoubtedly welcome, namely pregnancy. It seems therefore reasonable that YB-1 plays also a crucial role in reproduction, and yet this biological aspect of the cold-shock protein has been overlooked for many years. To overcome this limitation, we would like to propose a new perspective on YB-1 and emphasize its pivotal functions in healthy pregnancy and pregnancy-related complications. Moreover, we will discuss findings obtained from cancer research in the light of reproductive events to elucidate the importance of YB-1 at the feto-maternal interface.
... To further confirm this, we have initiated an experiment to knock out the ybx1 gene from the zebrafish genome, which promises to provide insights into the functional relationship of Ybx1 with its counterpart YB-1 and germ cell-specific YB-2 in the tetrapods. The knockout of YB-1 in the mouse causes embryonic lethality due to its ubiquitous expression and universal functions in somatic cells [40]. In contrast, the disruption of YB-2 gene in the mouse genome leads to infertility without any effect on vitality [41]. ...
As in mammals, ovarian folliculogenesis in teleosts also consists of two phases: the primary growth (PG) and secondary growth (SG) phases, which are analogous to the preantral and antral phases respectively in mammals. In this study, we performed a proteomic analysis on zebrafish follicles undergoing the PG-SG transition aiming to identify factors involved in the event. Numerous proteins showed significant changes, and the most prominent one was Y-box binding protein 1 (YB-1; Ybx1/ybx1), a transcription factor and mRNA-binding protein. YB-1 belongs to the Y-box binding protein family, which also includes the gonad-specific YB-2. Interestingly, phylogenetic analysis showed no YB-2 homologue in zebrafish. Although ybx1 mRNA was expressed in various tissues, its protein Ybx1 was primarily produced in the gonads, similar to YB-2 in other species. In the ovary, Ybx1 protein started to appear in early follicles newly emerged from the germ cell cysts, reached the highest level in late PG oocytes, but decreased precipitously when the follicles entered the SG phase. In PG follicles, Ybx1 might function as a key component of the messenger ribonucleoprotein particles (mRNP) in association with other RNA-binding proteins. Similar to mammalian YB-1, zebrafish Ybx1 also contains functional signals that determine its intracellular localization. In conclusion, Ybx1 may play dual roles of YB-1 and YB-2 in zebrafish. In the ovary, Ybx1 binds mRNAs to stabilize them while preventing their translation. At PG-SG transition, Ybx1 is removed to release the masked mRNAs for translation into functional proteins, leading to follicle activation.
... Short chain enoyl coenzyme A hydratase 1 (ECHS1) protein is an enzyme that belongs to the fatty acid metabolic pathway [34]. This gene has been shown to be involved in colon and breast cancers [35] [36] [37]. Y-box protein (YBX1) is a transcription factor that binds to specific DNA sequences called Y boxes and regulates gene expression. ...
Triple Negative Breast Cancer (TNBC) is a malignant form of cancer with very high mortality and morbidity. Epithelial to Mesenchymal Transition (EMT) is the most common pathophysiological change observed in cancer cells of epithelial origin that promotes metastasis, drug resistance and cancer stem cell formation. Since the information regarding differential gene expression in TNBC cells and cell signaling events leading to EMT is limited, this investigation was done by comparing transcriptomic data generated by RNA isolation and sequencing of a EMT model TNBC cell line in comparison to regular TNBC cells. RNA sequencing and Ingenuity Pathway Software Analysis (IPA) of the transcriptomic data revealed several upregulated and down-regulated gene expressions along with novel core canonical pathways including Sirtuin signaling, Oxidative Phosphorylation and Mitochondrial dysfunction events involved in EMT changes of the TNBC cells.
... Here, we report disease-specific upregulation of YBX3 transcripts within different compartments of the kidney in patient biopsies, which agrees with our previous immune histochemical findings [7]. Since growth and kidney function do not appear to be influenced by the deletion of Ybx3, we can conclude that DbpA is not as essential for development as Ybx1 has been shown to be [56,57]. Following disease onset, we showed a strong induction of the short (50 kDa) isoform of the Ybx3 protein (DbpA_b) in the kidney interstitium, where the DbpA-positive cells reside. ...
DNA-binding protein A (DbpA) belongs to the Y-box family of cold shock domain proteins that exert transcriptional and translational activities in the cell via their ability to bind and regulate mRNA. To investigate the role of DbpA in kidney disease, we utilized the murine unilateral ureter obstruction (UUO) model, which recapitulates many features of obstructive nephropathy seen in humans. We observed that DbpA protein expression is induced within the renal interstitium following disease induction. Compared with wild-type animals, obstructed kidneys from Ybx3-deficient mice are protected from tissue injury, with a significant reduction in the number of infiltrating immune cells as well as in extracellular matrix deposition. RNAseq data from UUO kidneys show that Ybx3 is expressed by activated fibroblasts, which reside within the renal interstitium. Our data support a role for DbpA in orchestrating renal fibrosis and suggest that strategies targeting DbpA may be a therapeutic option to slow disease progression.
... Aside from tRF-Gly TCC and RUNX2 as PBC components, we identified YBX1 as the master regulator mediating these molecules' effects on PBC progression. YBX1 is one of the most overexpressed oncogenes observed in human cancer and is highly heterogeneous with several variants and post-translational modifications [47,48]. YBX1 was previously identified as a critical regulator of HIF1A expression in sarcoma leading to enhanced metastatic capacity in vivo [49]. ...
Primary bone cancer (PBC) comprises several subtypes each underpinned by distinctive genetic drivers. This
driver diversity produces novel morphological features and clinical behaviour that serendipitously makes PBC an
excellent metastasis model. Here, we report that some transfer RNA-derived small RNAs termed tRNA fragments
(tRFs) perform as a constitutive tumour suppressor mechanism by blunting a potential pro-metastatic protein-
RNA interaction. This mechanism is reduced in PBC progression with a gradual loss of tRNAGlyTCC cleavage into
5′ end tRF-GlyTCC when comparing low-grade, intermediate-grade and high-grade patient tumours. We detected
recurrent activation of miR-140 leading to upregulated RUNX2 expression in high-grade patient tumours. Both
tRF-GlyTCC and RUNX2 share a sequence motif in their 3′ ends that matches the YBX1 recognition site known to
stabilise pro-metastatic mRNAs. Investigating some aspects of this interaction network, gain- and loss-of-function
experiments using small RNA mimics and antisense LNAs, respectively, showed that ectopic tRF-GlyTCC reduced
RUNX2 expression and dispersed 3D micromass architecture in vitro. iCLIP sequencing revealed YBX1 physical
binding to the 3′ UTR of RUNX2. The interaction between YBX1, tRF-GlyTCC and RUNX2 led to the development
of the RUNX2 inhibitor CADD522 as a PBC treatment. CADD522 assessment in vitro revealed significant effects
on PBC cell behaviour. In xenograft mouse models, CADD522 as a single agent without surgery significantly
reduced tumour volume, increased overall and metastasis-free survival and reduced cancer-induced bone disease.
Our results provide insight into PBC molecular abnormalities that have led to the identification of new
targets and a new therapeutic.
A rampant and urgent global health issue of the 21st century is the emergence and progression of fatty liver disease (FLD), including alcoholic fatty liver disease and the more heterogenous metabolism‐associated (or non‐alcoholic) fatty liver disease (MAFLD/NAFLD) phenotypes. These conditions manifest as disease spectra, progressing from benign hepatic steatosis to symptomatic steatohepatitis, cirrhosis, and, ultimately, hepatocellular carcinoma. With numerous intricately regulated molecular pathways implicated in its pathophysiology, recent data have emphasized the critical roles of RNA‐binding proteins (RBPs) in the onset and development of FLD. They regulate gene transcription and post‐transcriptional processes, including pre‐mRNA splicing, capping, and polyadenylation, as well as mature mRNA transport, stability, and translation. RBP dysfunction at every point along the mRNA life cycle has been associated with altered lipid metabolism and cellular stress response, resulting in hepatic inflammation and fibrosis. Here, we discuss the current understanding of the role of RBPs in the post‐transcriptional processes associated with FLD and highlight the possible and emerging therapeutic strategies leveraging RBP function for FLD treatment.
This article is categorized under: RNA in Disease and Development > RNA in Disease
Y-box binding protein 1 (YBX1) plays important roles in RNA stabilization, translation, transcriptional regulation, and mitophagy. However, its effects on porcine preimplantation embryos remain unclear. In this study, we knocked down YBX1 in the one-cell (1C) stage embryo via small interfering RNA microinjection to determine its function in porcine embryo development. The mRNA level of YBX1 was found to be highly expressed at the four-cell (4C) stage in porcine embryos compared with one-cell (1C) and two-cell (2C) stages. The number of blastocysts was reduced following YBX1 knockdown. Notably, YBX1 knockdown decreased the phosphatase and tensin homolog-induced kinase 1 (PINK1) and parkin RBR E3 ubiquitin protein ligase (PRKN) mRNA levels. YBX1 knockdown also decreased PINK1, active mitochondria, and sirtuin 1 levels, indicating reduced mitophagy and mitochondrial biogenesis. Furthermore, YBX1 knockdown increased the levels of glucose-regulated protein 78 (GRP78) and calnexin, leading to endoplasmic reticulum (ER) stress. Additionally, YBX1 knockdown increased autophagy and apoptosis. In conclusion, knockdown of YBX1 decreases mitochondrial function, while increasing ER stress and autophagy during embryonic development.
Y-box binding protein 1 (YBX1) is a member of the family of DNA- and RNA-binding proteins that play crucial roles in multiple aspects, including RNA stabilization, translational repression, and transcriptional regulation; however, its roles in embryo development remain less known. In this study, to investigate the function of YBX1 and its mechanism of action in porcine embryo development, YBX1 was knocked down by microinjecting YBX1 siRNA at the one-cell stage. YBX1 is located in the cytoplasm during embryonic development. The mRNA level of YBX1 was increased from the four-cell stage to the blastocyst stage but was significantly decreased in YBX1 knockdown embryos compared with the control. Moreover, the percentage of blastocysts was decreased following YBX1 knockdown compared with the control. Defecting YBX1 expression increased maternal gene mRNA expression and decreased zygotic genome activation (ZGA) gene mRNA expression and histone modification owing to decreased levels of N6-methyladenosine (m6A) writer N6-adenosine-methyltransferase 70 kDa subunit (METTL3) and reader insulin-like growth factor 2 mRNA-binding protein (IGF2BP1). In addition, IGF2BP1 knockdown showed that YBX1 regulated the ZGA process through m6A modification. In conclusion, YBX1 is essential for early embryo development because it regulates the ZGA process.
With the development of sequencing technology, transfer RNA (tRNA)-derived small RNAs (tsRNAs) have received extensive attention as a new type of small noncoding RNAs. Based on the differences in the cleavage sites of nucleases on tRNAs, tsRNAs can be divided into two categories, tRNA halves (tiRNAs) and tRNA-derived fragments (tRFs), each with specific subcellular localizations. Additionally, the biogenesis of tsRNAs is tissue-specific and can be regulated by tRNA modifications. In this review, we first elaborated on the classification and biogenesis of tsRNAs. After summarizing the latest mechanisms of tsRNAs, including transcriptional gene silencing, post-transcriptional gene silencing, nascent RNA silencing, translation regulation, rRNA regulation, and reverse transcription regulation, we explored the representative biological functions of tsRNAs in tumors. Furthermore, this review summarized the clinical value of tsRNAs in cancers, thus providing theoretical support for their potential as novel biomarkers and therapeutic targets.
Regulated mRNA turnover is a highly important process, but its mechanism is poorly understood. Using interleukin-2 (IL-2) mRNA as a model, we described a role for the JNK-signaling pathway in stabilization of IL-2 mRNA during T-cell activation, acting via a JNK response element (JRE) in the 5′ untranslated region (UTR). We have now identified two major RNA-binding proteins, nucleolin and YB-1, that specifically bind to the JRE. Binding of both proteins is required for IL-2 mRNA stabilization induced by T-cell activation signals and for JNK-induced stabilization in a cell-free system that duplicates essential features of regulated mRNA decay. Nucleolin and YB-1 are required for formation of an IL-2 mRNP complex that responds to specific mRNA stabilizing signals.
We have isolated three overlapping genomic clones containing the 5'portion of the human YB-1 gene. These clones span approximately 25 kb of contiguous DNA containing 10 kb of 5' flanking sequence and 15 kb of the gene. The nucleotide sequence of the first exon and of 2000 upstream base pairs (bp) was determined. The first axon is unusually large and contains a 166 bp coding sequence and a 331 bp untranslated region. CpG sequences cover the 5'-end of the YB-1 gene including its first axon and intron as well as the upstream regions. The GC content around the first exon is approximately 70% and a CpG-free region was located in the untranslated sequence. The segment preceding the major transcription initiation site does not contain a TATA box, CCAAT box and the binding sequence for known transcription factors. A transient expression assay using the chloramphenicol acetyltransferase (CAT) gene showed that the sequence from +24 to +281 was critical for CAT expression. Fluorescence in situ hybridization demonstrated the chromosomal locus of YB-1 gene on chromosome 1p34. Polymerase chain reaction analysis on other genomic phage DNAs showed that several clones were derived from pseudogenes.
Overexpression of elongation factor-1 alpha (EF1 alpha) mRNA has been correlated with increased metastatic potential in mammary adenocarcinoma; however, this relationship was not explored at the level of protein expression. As EF1 alpha has been shown in other cell types to be a component of the actin cytoskeleton, a likely effector in metastasis, the actin binding activity of EF1 alpha from metastatic and nonmetastatic rat breast tumors and cell lines was investigated. We have shown that EF1 alpha protein is overexpressed in metastatic compared to nonmetastatic cells and whole tumors. Similarly to other EF1 alpha s, both types of tumor EF1 alpha bind to F-actin, but EF1 alpha from metastatic cells has a reduced affinity for actin. In addition, there is a high correlation between the intracellular distribution of filamentous actin and EF1 alpha in those cytoskeletal structures thought to be important for supporting the cellular motility required for metastasis. Following stimulation with EGF, there is a parallel increase in the amount of F-actin and EF1 alpha associated with the cytoskeleton. The response to EGF can be blocked with cytochalasin D indicating that the binding of EF1 alpha to the cytoskeleton is mediated by F-actin. We propose that a weakened association of EF1 alpha with actin may be related to the metastatic process via an altered organization of the actin cytoskeleton and the differential translation of mRNAs associated with the cytoskeleton.
Stimulation of protein synthesis in response to insulin is concomitant with increased phosphorylation of initiation factors 4B and 4G and ribosomal protein S6 (Morley, S. J., and Traugh, J. A. (1993) Biochimie 75, 985-989) and is due at least in part to multipotential S6 kinase. When elongation factor 1 (EF-1) from rabbit reticulocytes was examined as substrate for multipotential S6 kinase, up to 1 mol/mol of phosphate was incorporated into the alpha, beta, and delta subunits. Phosphorylation of EF-1 resulted in a 2-2. 6-fold stimulation of EF-1 activity, as measured by poly(U)-directed polyphenylalanine synthesis. The rate of elongation was also stimulated by approximately 2-fold with 80 S ribosomes phosphorylated on S6 by multipotential S6 kinase. When the rates of elongation in extracts from serum-fed 3T3-L1 cells and cells serum-deprived for 1.5 h were compared, a 40% decrease was observed upon serum deprivation. The addition of insulin to serum-deprived cells for 15 min stimulated elongation to a rate equivalent to that of serum-fed cells. Similar results were obtained with partially purified EF-1, with both EF-1 and ribosomes contributing to stimulation of elongation. These data are consistent with a ribosomal transit time of 3.2 min for serum-deprived cells and 1.6 min following the addition of insulin for 15 min. Taken together, the data suggest that insulin stimulation involves coordinate regulation of EF-1 and ribosomes through phosphorylation by multipotential S6 kinase.
We have isolated three overlapping genomic clones containing the 5′ portion of the human YB-1 gene. These clones span ∼25
kb of contiguous DNA containing 10 kb of 5′ flanking sequence and 15 kb of the gene. The nucleotide sequence of the first
exon and of 2000 upstream base pairs (bp) was determined. The first exon is unusually large and contains a 166 bp coding sequence
and a 331 bp untranslated region. CpG sequences cover the 5′-end of the YB-1 gene including its first exon and intron as well
as the upstream regions. The GC content around the first exon is ∼70% and a CpG-free region was located in the untranslated
sequence. The segment preceding the major transcription initiation site does not contain a TATA box, CCAAT box and the binding
sequence for known transcription factors. A transient expression assay using the chloramphenicol acetyltransferase (CAT) gene
showed that the sequence from +24 to +281 was critical for CAT expression. Fluorescence in situ hybridization demonstrated the chromosomal locus of YB-1 gene on chromosome 1p34. Polymerase chain reaction analysis on other
genomic phage DNAs showed that several clones were derived from pseudogenes.
The expression of HLA class II genes is regulated by a series of cis-acting elements and trans-acting factors. Several cis-acting elements have been identified and have been termed the Z box, X box, Y box, octamer, and "TATA" box. The Y box contains an inverted CCAAT box. By probing a phage lambda gt11 library with double-stranded oligonucleotides, we have directly isolated a cDNA encoding a Y box-binding protein designated YB-1. YB-1 binding has an absolute requirement for the CCAAT box and relative specificity for the Y box. It has a Mr of 35,414, contains 18% basic residues, and contains putative nuclear localization signals. An inverse correlation of YB-1 and HLA-DR beta chain mRNA levels suggests that YB-1 is a negative regulatory factor.
Members of the Y-box (YB) family of transcription factors are expressed in a wide range of cell types and are implicated in the regulation of a rapidly increasing number of genes. Although the biological activities of YB proteins appear to be varied, distinct patterns, relating to the timing of their expression and the identity of their target genes, are beginning to emerge. A recent report by Ito et al. focusses attention on cell proliferation and adds support to earlier suggestions that a primary function of YB proteins is to help activate growth-associated genes.
The human multidrug resistance 1 (MDR1) gene is an SOS gene that responds to environmental stress including various anticancer agents. The chloramphenicol acetyltransferase (CAT) gene was linked to various lengths of MDR1 promoter, and these constructs were integrated into the genome of human cancer KB cells. Using these cell lines, we previously demonstrated that various environmental stimuli lead to an increased abundance of both CAT enzymatic activity and CAT mRNA in a sequence dependent manner. We examined the molecular mechanism of this stress response using actinomycin D, a potent RNA synthesis inhibitor. We found that CAT activity was significantly increased more than 10 fold by actinomycin D itself without comparable elevation of CAT mRNA. CAT induction was, however, lost in the presence of a deletion from position -136 to -76. Gel mobility shift assays showed that the specific DNA binding activity of the transacting protein, MDR-NF1/YB-1, which binds to the inverted CCAAT box, was augmented in nuclear extracts from the cells treated with actinomycin D. We also found that actinomycin D increased the steady state levels of MDR-NF1/YB-1 mRNA, which encodes the inverted CCAAT box binding protein. These results indicate that MDR-NF1/YB-1 mediates the response of the MDR1 gene to environmental stress.
The Y box-binding protein (YB-1) binds to DNA sequences, present in the control regions of many genes, that contain an inverted CCAAT box. The binding activity of a nuclear factor, designated MDR-NF1, to an inverted CCAAT box in the promoter of the multidrug resistance 1 (MDR1) gene has previously been shown to be increased in nuclear extracts of cells exposed to UV radiation or various anticancer agents. The MDR-NF1 cDNA has now been cloned by screening a human colon library with an active fragment of the MDR1 promoter. The amino acid sequence encoded by the cloned cDNA was identical to that of YB-1. Northern blot analysis revealed that YB-1 mRNA was present in all human tissues examined. Rabbit antibodies were generated against synthetic peptides corresponding to YB-1, and indirect immunofluorescence microscopy with these antibodies showed that the concentration of YB-1 in all cisplatin-resistant cell lines examined was higher than that in the respective drug-sensitive parental cells. Transfection of human epidermoid cancer KB cells with a YB-1 antisense construct established two cell lines with reduced concentrations of YB-1. These transfectants showed increased sensitivity to cisplatin, mitomycin C, and UV radiation but not to vincristine, doxorubicin, camptothecin, or etoposide. Thus, YB-1 may protect cells from the cytotoxic effects of agents that induce cross-linking of DNA, suggesting a novel function of this ancestor DNA-binding protein.
Many mutations cause neural tube closure defects (NTDs, exencephaly or spina bifida) in mice and the gene loci are widely distributed in the mouse genome. This compilation summarizes the map position of 40 mouse NTD mutations and the corresponding human linkage homology of each. It includes the nature of the gene product where known, and whether the NTD is part of a syndrome involving other developmental systems. Also listed are the several mouse strains known to have genetic susceptibility to exencephaly, with multifactorial genetic cause in at least one case. The purposes of this mouse NTD compilation are to enable recognition of patterns in genetic causes of NTDs, of molecular pathways essential for closure of specific regions of the mammalian neural tube, and of candidate regions for mapping loci contributing to human multifactorial NTDs.