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Journal articles on the topic 'Rbpms2'

Author: Grafiati

Published: 4 June 2021

Last updated: 11 February 2022

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1

Sagnol, Sébastien, Yinshan Yang, Yannick Bessin, et al. "Homodimerization of RBPMS2 through a new RRM-interaction motif is necessary to control smooth muscle plasticity." Nucleic Acids Research 42, no. 15 (2014): 10173–84. http://dx.doi.org/10.1093/nar/gku692.

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Abstract In vertebrates, smooth muscle cells (SMCs) can reversibly switch between contractile and proliferative phenotypes. This involves various molecular mechanisms to reactivate developmental signaling pathways and induce cell dedifferentiation. The protein RBPMS2 regulates early development and plasticity of digestive SMCs by inhibiting the bone morphogenetic protein pathway through its interaction with NOGGIN mRNA. RBPMS2 contains only one RNA recognition motif (RRM) while this motif is often repeated in tandem or associated with other functional domains in RRM-containing proteins. Herein, we show using an extensive combination of structure/function analyses that RBPMS2 homodimerizes through a particular sequence motif (D-x-K-x-R-E-L-Y-L-L-F: residues 39–51) located in its RRM domain. We also show that this specific motif is conserved among its homologs and paralogs in vertebrates and in its insect and worm orthologs (CPO and MEC-8, respectively) suggesting a conserved molecular mechanism of action. Inhibition of the dimerization process through targeting a conserved leucine inside of this motif abolishes the capacity of RBPMS2 to interact with the translational elongation eEF2 protein, to upregulate NOGGIN mRNA in vivo and to drive SMC dedifferentiation. Our study demonstrates that RBPMS2 possesses an RRM domain harboring both RNA-binding and protein-binding properties and that the newly identified RRM-homodimerization motif is crucial for the function of RBPMS2 at the cell and tissue levels.

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2

Romano, Shannon, Odelya H. Kaufman, and Florence L. Marlow. "Loss of dmrt1 restores zebrafish female fates in the absence of cyp19a1a but not rbpms2a/b." Development 147, no. 18 (2020): dev190942. http://dx.doi.org/10.1242/dev.190942.

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ABSTRACTSex determination and differentiation is a complex process regulated by multiple factors, including factors from the germline or surrounding somatic tissue. In zebrafish, sex-determination involves establishment of a bipotential ovary that undergoes sex-specific differentiation and maintenance to form the functional adult gonad. However, the relationships among these factors are not fully understood. Here, we identify potential Rbpms2 targets and apply genetic epistasis experiments to decipher the genetic hierarchy of regulators of sex-specific differentiation. We provide genetic evidence that the crucial female factor rbpms2 is epistatic to the male factor dmrt1 in terms of adult sex. Moreover, the role of Rbpms2 in promoting female fates extends beyond repression of Dmrt1, as Rbpms2 is essential for female differentiation even in the absence of Dmrt1. In contrast, female fates can be restored in mutants lacking both cyp19a1a and dmrt1, and prolonged in bmp15 mutants in the absence of dmrt1. Taken together, this work indicates that cyp19a1a-mediated suppression of dmrt1 establishes a bipotential ovary and initiates female fate acquisition. Then, after female fate specification, Cyp19a1a regulates subsequent oocyte maturation and sustains female fates independently of Dmrt1 repression.

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3

Kaufman, Odelya H., KathyAnn Lee, Manon Martin, Sophie Rothhämel, and Florence L. Marlow. "rbpms2 functions in Balbiani body architecture and ovary fate." PLOS Genetics 14, no. 7 (2018): e1007489. http://dx.doi.org/10.1371/journal.pgen.1007489.

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Kaufman, Odelya H., KathyAnn Lee, Manon Martin, Sophie Rothhämel, and Florence L. Marlow. "Correction: rbpms2 functions in Balbiani body architecture and ovary fate." PLOS Genetics 14, no. 10 (2018): e1007768. http://dx.doi.org/10.1371/journal.pgen.1007768.

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5

Notarnicola, Cécile, Caroline Rouleau, Ludovic Le Guen, et al. "The RNA-Binding Protein RBPMS2 Regulates Development of Gastrointestinal Smooth Muscle." Gastroenterology 143, no. 3 (2012): 687–97. http://dx.doi.org/10.1053/j.gastro.2012.05.047.

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6

Hapkova, Ilona, Josef Skarda, Caroline Rouleau, et al. "High expression of the RNA-binding protein RBPMS2 in gastrointestinal stromal tumors." Experimental and Molecular Pathology 94, no. 2 (2013): 314–21. http://dx.doi.org/10.1016/j.yexmp.2012.12.004.

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7

Eugene, Andy R., Jolanta Masiak, and Beata Eugene. "Predicting lithium treatment response in bipolar patients using gender-specific gene expression biomarkers and machine learning." F1000Research 7 (April 18, 2018): 474. http://dx.doi.org/10.12688/f1000research.14451.1.

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Background: We sought to test the hypothesis that transcriptiome-level genes signatures are differentially expressed between male and female bipolar patients, prior to lithium treatment, in a patient cohort who later were clinically classified as lithium treatment responders. Methods: Gene expression study data was obtained from the Lithium Treatment-Moderate dose Use Study data accessed from the National Center for Biotechnology Information’s Gene Expression Omnibus via accession number GSE4548. Differential gene expression analysis was conducted using the Linear Models for Microarray and RNA-Seq (limma) package and the Random Forests machine learning algorithm in R. Results: In pre-treatment lithium responders, the following genes were found having a greater than 0.5 fold-change, and differentially expressed indicating a male bias: RBPMS2, SIDT2, CDH23, LILRA5, and KIR2DS5; while the female-biased genes were: HLA-H, RPS23, FHL3, RPL10A, NBPF14, PSTPIP2, FAM117B, CHST7, and ABRACL. Conclusions: Using machine learning, we developed a pre-treatment gender- and gene-expression-based predictive model selective for lithium responders with an ROC AUC of 0.92 for men and an ROC AUC of 1 for women.

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Eugene, Andy R., Jolanta Masiak, and Beata Eugene. "Predicting lithium treatment response in bipolar patients using gender-specific gene expression biomarkers and machine learning." F1000Research 7 (May 29, 2018): 474. http://dx.doi.org/10.12688/f1000research.14451.2.

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Background: We sought to test the hypothesis that transcriptiome-level genes signatures are differentially expressed between male and female bipolar patients, prior to lithium treatment, in a patient cohort who later were clinically classified as lithium treatment responders. Methods: Gene expression study data was obtained from the Lithium Treatment-Moderate dose Use Study data accessed from the National Center for Biotechnology Information’s Gene Expression Omnibus via accession number GSE4548. Differential gene expression analysis was conducted using the Linear Models for Microarray and RNA-Seq (limma) package and the Random Forests machine learning algorithm in R. Results: In pre-treatment lithium responders, the following genes were found having a greater than 0.5 fold-change, and differentially expressed indicating a male bias: RBPMS2, SIDT2, CDH23, LILRA5, and KIR2DS5; while the female-biased genes were: HLA-H, RPS23, FHL3, RPL10A, NBPF14, PSTPIP2, FAM117B, CHST7, and ABRACL. Conclusions: Using machine learning, we developed a pre-treatment gender- and gene-expression-based predictive model selective for lithium responders with an ROC AUC of 0.92 for men and an ROC AUC of 1 for women.

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Eugene, Andy R., Jolanta Masiak, and Beata Eugene. "Predicting lithium treatment response in bipolar patients using gender-specific gene expression biomarkers and machine learning." F1000Research 7 (December 7, 2018): 474. http://dx.doi.org/10.12688/f1000research.14451.3.

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Background: We sought to test the hypothesis that transcriptome-level gene signatures are differentially expressed between male and female bipolar patients, prior to lithium treatment, in a patient cohort who later were clinically classified as lithium treatment responders. Methods: Gene expression study data was obtained from the Lithium Treatment-Moderate dose Use Study data accessed from the National Center for Biotechnology Information’s Gene Expression Omnibus via accession number GSE4548. Differential gene expression analysis was conducted using the Linear Models for Microarray and RNA-Seq (limma) package and the Decision Tree and Random Forest machine learning algorithms in R. Results: Using quantitative gene expression values reported from patient blood samples, the RBPMS2 and LILRA5 genes classify male lithium responders with an area under the receiver operator characteristic curve (AUROC) of 0.92 and the ABRACL, FHL3, and NBPF14 genes classify female lithium responders AUROC of 1. A Decision Tree rule for establishing male versus female samples, using gene expression values were found to be: if RPS4Y1 ≥ 9.643, patient is a male and if RPS4Y1 < 9.643, patient is female with a probability=100%. Conclusions: We developed a pre-treatment gender- and gene-expression-based predictive model selective for classifying male lithium responders with a sensitivity of 96% using 2-genes and female lithium responders with sensitivity=92% using 3-genes.

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10

Kałużna, Sandra, Mariusz J. Nawrocki, Karol Jopek, et al. "In search of markers useful for evaluation of graft patency - molecular analysis of ‘muscle system process’ for internal thoracic artery and saphenous vein conduits." Medical Journal of Cell Biology 8, no. 1 (2020): 12–23. http://dx.doi.org/10.2478/acb-2020-0002.

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AbstractCoronary artery bypass graft (CABG) is the surgical method most commonly used to treat coronary artery disease (CAD). The vessels that are used in CABG are usually the internal thoracic artery (ITA) and the saphenous vein (SV). Transplant patency is one of the most important factors affecting transplant success. In this study, we used an expressive microarray method, approved by RT-qPCR, for transcriptome analysis of arterial and venous grafts. In the search for potential molecular factors, we analyzed gene ontologies of different expression based on the muscular system. Among interesting groups, we distinguished muscle cell proliferation, muscle contraction, muscle system process, regulation of smooth muscle cell proliferation and smooth muscle cell proliferation. The highest increase in gene expression was observed in: ACTN2, RBPMS2, NR4A3, KCNA5, while the smallest decrease in expression was shown by the P2RX1, KCNH2, DES and MYOT genes. Particularly noteworthy are the ACTN2 and NR4A3 genes, which can have a significant impact on vascular patency. ACTN2 is a gene that can affect the formation of atherosclerotic plaques, while NR4A3 occurs in 4 of the 5 ontological groups discussed and can affect the inflammatory process in the blood vessel. To summarize, the presented study provided valuable insight into the molecular aspects characterizing the vessels used in CABG, and in particular identified genes that may be the target for further studies on duct patency.Running title: CABG grafts’ molecular analysis of ‘muscle system process’

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11

Abdalla, Emhimad, Bayode Makanjuola, Benjamin Wood, Christine F. Baes, and Ryley J. Vanderhout. "PSIII-16 Genome-wide association mapping and functional analysis of body weight, feed intake and walking ability in turkeys." Journal of Animal Science 98, Supplement_4 (2020): 234–35. http://dx.doi.org/10.1093/jas/skaa278.429.

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Abstract The underlying genetic mechanisms affecting turkey growth traits have not been widely investigated. Over the last few years, genome-wide association studies (GWAS) became the de facto approach to identify candidate regions associated with complex phenotypes and diseases in livestock. In the present study, we performed GWAS to identify regions associated with growth traits, feed intake and walking ability in a breeding turkey line. This was followed by studying the functional evidence that may support the impact of those regions on the economic traits in turkeys. A total of 31,950 phenotypic records for body weight, feed intake and walking ability with genomic (56,393 SNP) data were provided by Hybrid Turkeys, Kitchener, Canada. The analysis was carried out using a mixed linear model with hatch-week-year and sex fitted as fixed effects and the accumulated effect of all markers captured by the genomic relationship matrix fitted as random polygenic effects. Significant markers were observed on several chromosomes across the turkey genome. For example, COL8A1 and RBPMS2 genes were identified on chromosome 1 and 12, respectively, and associated with body weight. Furthermore, a gene-set enrichment analysis was performed for each trait. These functional and positional analyses uncovered a number of gene ontology functional terms, Reactome pathways and Medical Subject Headings that showed significant enrichment of genes associated with the studied traits. Many of the observed gene ontology functional terms (e.g., skeletal muscle tissue growth, regulation of digestive system process, and adult walking behavior) are known to be related to body growth, feed intake and walking ability. The results of this study revealed novel candidate genomic regions and candidate genes that could be managed within a turkey breeding program.

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Patel, Devanshi, Xiaoling Zhang, John J. Farrell, Kathryn L. Lunetta, and Lindsay A. Farrer. "Set-Based Rare Variant Expression Quantitative Trait Loci in Blood and Brain from Alzheimer Disease Study Participants." Genes 12, no. 3 (2021): 419. http://dx.doi.org/10.3390/genes12030419.

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Because studies of rare variant effects on gene expression have limited power, we investigated set-based methods to identify rare expression quantitative trait loci (eQTL) related to Alzheimer disease (AD). Gene-level and pathway-level cis rare-eQTL mapping was performed genome-wide using gene expression data derived from blood donated by 713 Alzheimer’s Disease Neuroimaging Initiative participants and from brain tissues donated by 475 Religious Orders Study/Memory and Aging Project participants. The association of gene or pathway expression with a set of all cis potentially regulatory low-frequency and rare variants within 1 Mb of genes was evaluated using SKAT-O. A total of 65 genes expressed in the brain were significant targets for rare expression single nucleotide polymorphisms (eSNPs) among which 17% (11/65) included established AD genes HLA-DRB1 and HLA-DRB5. In the blood, 307 genes were significant targets for rare eSNPs. In the blood and the brain, GNMT, LDHC, RBPMS2, DUS2, and HP were targets for significant eSNPs. Pathway enrichment analysis revealed significant pathways in the brain (n = 9) and blood (n = 16). Pathways for apoptosis signaling, cholecystokinin receptor (CCKR) signaling, and inflammation mediated by chemokine and cytokine signaling were common to both tissues. Significant rare eQTLs in inflammation pathways included five genes in the blood (ALOX5AP, CXCR2, FPR2, GRB2, IFNAR1) that were previously linked to AD. This study identified several significant gene- and pathway-level rare eQTLs, which further confirmed the importance of the immune system and inflammation in AD and highlighted the advantages of using a set-based eQTL approach for evaluating the effect of low-frequency and rare variants on gene expression.

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13

Pereiro, Xandra, Noelia Ruzafa, J. Haritz Urcola, Sansar C. Sharma, and Elena Vecino. "Differential Distribution of RBPMS in Pig, Rat, and Human Retina after Damage." International Journal of Molecular Sciences 21, no. 23 (2020): 9330. http://dx.doi.org/10.3390/ijms21239330.

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RNA binding protein with multiple splicing (RBPMS) is expressed exclusively in retinal ganglion cells (RGCs) in the retina and can label all RGCs in normal retinas of mice, rats, guinea pigs, rabbits, cats, and monkeys, but its function in these cells is not known. As a result of the limited knowledge regarding RBPMS, we analyzed the expression of RBPMS in the retina of different mammalian species (humans, pigs, and rats), in various stages of development (neonatal and adult) and with different levels of injury (control, hypoxia, and organotypic culture or explants). In control conditions, RBPMS was localized in the RGCs somas in the ganglion cell layer, whereas in hypoxic conditions, it was localized in the RGCs dendrites in the inner plexiform layer. Such differential distributions of RBPMS occurred in all analyzed species, and in adult and neonatal retinas. Furthermore, we demonstrate RBPMS localization in the degenerating RGCs axons in the nerve fiber layer of retinal explants. This is the first evidence regarding the possible transport of RBPMS in response to physiological damage in a mammalian retina. Therefore, RBPMS should be further investigated in relation to its role in axonal and dendritic degeneration.

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14

Akerberg, Alexander A., Caroline E. Burns, and C. Geoffrey Burns. "Exploring the Activities of RBPMS Proteins in Myocardial Biology." Pediatric Cardiology 40, no. 7 (2019): 1410–18. http://dx.doi.org/10.1007/s00246-019-02180-6.

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15

Jaconi, Stefano, Jean-Hilaire Saurat, and Georges Siegenthaler. "Analysis of normal and truncated holo- and apo-retinol-binding protein (RBP) in human serum: altered ratios in chronic renal failure." European Journal of Endocrinology 134, no. 5 (1996): 576–82. http://dx.doi.org/10.1530/eje.0.1340576.

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Jaconi S, Saurat J-H, Siegenthaler G. Analysis of normal and truncated holo- and apo-retinol-binding protein (RBP) in human serum: altered ratios in chronic renal failure. Eur J Endocrinol 1996;134:576–82. ISSN 0804–4643 Retinol, the precursor of the retinoic acid hormone, is transported in the serum by a specific carrier, the retinol-binding protein (RBP). Compared to serum of healthy controls, the serum of patients with chronic renal failure (CRF) contains markedly increased levels of the RBP form truncated at the C-terminal, des(182Leu-183Leu). (RBP2). which suggests that RBP2 is cleared by the kidney in healthy people but accumulates in serum of CRF patients (Jaconi S, et al. J Lipid Res 1995;36:1247–53). To understand better the mechanism of retinol transport, we have developed a new analytical strategy to analyze the various forms of RBP that circulate in the blood: RBP with and without retinol (holo- and apo-RBP, respectively), RBP bound or not to transthyretin (TTR) and to determine in which of these forms RBP2 circulates. We confirm, but now by direct measurement, that holo-RBP and, to a larger extent, apo-RBP are increased in CRF serum compared to normal serum. We also show that almost all apo-RBP and about 50% of total holo-RBP, corresponding to RBP excess in CRF serum, circulate free and are not complexed to TTR, the remaining 50% being complexed to TTR. This observation suggests that the high levels of free holo-RBP, not bound to TTR, which correspond to the increase in total RBPs measured in CRF serum, may alter the tissue uptake of retinol and be responsible for the signs of hypervitaminosis A observed in these patients. Secondly, we found that the truncation resulting in RBP2 does not alter its binding properties for retinol nor those of holo-RBP2 for TTR. We observed that the high amounts of free holo-RBP2 and holo-RBP in sera of CRF patients were low in normal serum, suggesting that these forms are cleared by the kidney in normal conditions. The possible role of free holo-RBPs is discussed in the context of retinol recycling. Georges Siegenthaler, Clinique de Dermatologie, Hôpital Cantonal Universitaire, CH-1211 Geneve 14, Switzerland

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16

Gwangwava, Norman, Khumbulani Mpofu, Nkgatho Tlale, and Yan Yu. "A methodology for design and reconfiguration of reconfigurable bending press machines (RBPMs)." International Journal of Production Research 52, no. 20 (2014): 6019–32. http://dx.doi.org/10.1080/00207543.2014.904969.

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17

Sun, Yan, Lihua Ding, Hao Zhang, et al. "Potentiation of Smad-mediated transcriptional activation by the RNA-binding protein RBPMS." Nucleic Acids Research 34, no. 21 (2006): 6314–26. http://dx.doi.org/10.1093/nar/gkl914.

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18

Luo, Fujun, Xinran Liu, Thomas C. Südhof, and Claudio Acuna. "Efficient stimulus-secretion coupling at ribbon synapses requires RIM-binding protein tethering of L-type Ca2+channels." Proceedings of the National Academy of Sciences 114, no. 38 (2017): E8081—E8090. http://dx.doi.org/10.1073/pnas.1702991114.

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Fast neurotransmitter release from ribbon synapses via Ca2+-triggered exocytosis requires tight coupling of L-type Ca2+channels to release-ready synaptic vesicles at the presynaptic active zone, which is localized at the base of the ribbon. Here, we used genetic, electrophysiological, and ultrastructural analyses to probe the architecture of ribbon synapses by perturbing the function of RIM-binding proteins (RBPs) as central active-zone scaffolding molecules. We found that genetic deletion of RBP1 and RBP2 did not impair synapse ultrastructure of ribbon-type synapses formed between rod bipolar cells (RBCs) and amacrine type-2 (AII) cells in the mouse retina but dramatically reduced the density of presynaptic Ca2+channels, decreased and desynchronized evoked neurotransmitter release, and rendered evoked and spontaneous neurotransmitter release sensitive to the slow Ca2+buffer EGTA. These findings suggest that RBPs tether L-type Ca2+channels to the active zones of ribbon synapses, thereby synchronizing vesicle exocytosis and promoting high-fidelity information transfer in retinal circuits.

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19

Simon, Gregory E. "PBRNs or RBPNs or Both?" Psychiatric Services 66, no. 11 (2015): 1129. http://dx.doi.org/10.1176/appi.ps.661102.

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20

Gupta, Ajay, Jennifer A. Belsky, Kathleen M. Schieffer, et al. "Infantile fibrosarcoma–like tumor driven by novel RBPMS-MET fusion consolidated with cabozantinib." Molecular Case Studies 6, no. 5 (2020): a005645. http://dx.doi.org/10.1101/mcs.a005645.

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21

Yang, Chen, Zezhong Mou, Zheyu Zhang, et al. "Circular RNA RBPMS inhibits bladder cancer progression via miR-330-3p/RAI2 regulation." Molecular Therapy - Nucleic Acids 23 (March 2021): 872–86. http://dx.doi.org/10.1016/j.omtn.2021.01.009.

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22

Aguero, Tristan, Yi Zhou, Malgorzata Kloc, Patrick Chang, Evelyn Houliston, and Mary King. "Hermes (Rbpms) is a Critical Component of RNP Complexes that Sequester Germline RNAs during Oogenesis." Journal of Developmental Biology 4, no. 1 (2016): 2. http://dx.doi.org/10.3390/jdb4010002.

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23

Soufari, Heddy, and Cameron D. Mackereth. "Conserved binding of GCAC motifs by MEC-8, couch potato, and the RBPMS protein family." RNA 23, no. 3 (2016): 308–16. http://dx.doi.org/10.1261/rna.059733.116.

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24

Fu, Jie, Long Cheng, Yu Wang, et al. "The RNA-binding protein RBPMS1 represses AP-1 signaling and regulates breast cancer cell proliferation and migration." Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 1853, no. 1 (2015): 1–13. http://dx.doi.org/10.1016/j.bbamcr.2014.09.022.

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25

Solanki, Ashish K., Altaf A. Kondkar, Joseph Fogerty, et al. "A Functional Binding Domain in the Rbpr2 Receptor Is Required for Vitamin A Transport, Ocular Retinoid Homeostasis, and Photoreceptor Cell Survival in Zebrafish." Cells 9, no. 5 (2020): 1099. http://dx.doi.org/10.3390/cells9051099.

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Dietary vitamin A/all-trans retinol/ROL plays a critical role in human vision. ROL circulates bound to the plasma retinol-binding protein (RBP4) as RBP4-ROL. In the eye, the STRA6 membrane receptor binds to circulatory RBP4 and internalizes ROL. STRA6 is, however, not expressed in systemic tissues, where there is high affinity RBP4 binding and ROL uptake. We tested the hypothesis that the second retinol binding protein 4 receptor 2 (Rbpr2), which is highly expressed in systemic tissues of zebrafish and mouse, contains a functional RBP4 binding domain, critical for ROL transport. As for STRA6, modeling and docking studies confirmed three conserved RBP4 binding residues in zebrafish Rbpr2. In cell culture studies, disruption of the RBP4 binding residues on Rbpr2 almost completely abolished uptake of exogenous vitamin A. CRISPR-generated rbpr2-RBP4 domain zebrafish mutants showed microphthalmia, shorter photoreceptor outer segments, and decreased opsins, which were attributed to impaired ocular retinoid content. Injection of WT-Rbpr2 mRNA into rbpr2 mutant or all-trans retinoic acid treatment rescued the mutant eye phenotypes. In conclusion, zebrafish Rbpr2 contains a putative extracellular RBP4-ROL ligand-binding domain, critical for yolk vitamin A transport to the eye for ocular retinoid production and homeostasis, for photoreceptor cell survival.

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Rastgoo, Nasrin, Maryam Pourabdollah, Jahangir Abdi, Donna Reece, and Hong Chang. "Dysregulation of EZH2/miR-138 axis contributes to drug resistance in multiple myeloma by downregulating RBPMS." Leukemia 32, no. 11 (2018): 2471–82. http://dx.doi.org/10.1038/s41375-018-0140-y.

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27

Rodriguez, Allen R., Luis Pérez de Sevilla Müller, and Nicholas C. Brecha. "The RNA binding protein RBPMS is a selective marker of ganglion cells in the mammalian retina." Journal of Comparative Neurology 522, no. 6 (2014): 1411–43. http://dx.doi.org/10.1002/cne.23521.

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Kwong, Jacky M. K., Ann Quan, Haksu Kyung, Natik Piri, and Joseph Caprioli. "Quantitative Analysis of Retinal Ganglion Cell Survival with Rbpms Immunolabeling in Animal Models of Optic Neuropathies." Investigative Opthalmology & Visual Science 52, no. 13 (2011): 9694. http://dx.doi.org/10.1167/iovs.11-7869.

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29

Sung, Chang-Ky, and Sang Jeong Lee. "Reliable Time Propagation Algorithms for PMF and RBPMF." Sensors 21, no. 1 (2021): 261. http://dx.doi.org/10.3390/s21010261.

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This paper addresses the reliable time propagation algorithms for Point Mass Filter (PMF) and Rao–Blackwellized PMF (RBPMF) for the nonlinear estimaton problem. The conventional PMF and RBPMF process the probability diffusion for the time propagation with the direct sampled-values of the process noise. However, if the grid interval is not dense enough, it fails to represent the statistical characteristics of the noise accurately so the performance might deteriorate. To overcome that problem, we propose time propagation convolution algorithms adopting Moment Matched Gaussian Kernel (MMGK) on regular grids through mass linear interpolation. To extend the dimension of the MMGK that can accurately describe the noise moments up to the kernel length, we propose the extended MMGK based on the outer tensor product. The proposed time propagation algorithms using one common kernel through the mass linear interpolation not only improve the performance of the filter but also significantly reduce the computational load. The performance improvement and the computational load reduction of the proposed algorithms are verified through numerical simulations for various nonlinear models.

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Kim, Jonathan, Yong Zi Tan, Brianna Costabile, Yunting Chen, and Filippo Mancia. "Structural Studies of Retinol-Binding Protein Receptor RBPR2." Biophysical Journal 114, no. 3 (2018): 424a. http://dx.doi.org/10.1016/j.bpj.2017.11.2349.

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Wang, Yanling, Wenyao Wang, Jessica Liu, et al. "Protective Effect of ALA in Crushed Optic Nerve Cat Retinal Ganglion Cells Using a New Marker RBPMS." PLOS ONE 11, no. 8 (2016): e0160309. http://dx.doi.org/10.1371/journal.pone.0160309.

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Paz, Inbal, Idit Kosti, Manuel Ares, Melissa Cline, and Yael Mandel-Gutfreund. "RBPmap: a web server for mapping binding sites of RNA-binding proteins." Nucleic Acids Research 42, W1 (2014): W361—W367. http://dx.doi.org/10.1093/nar/gku406.

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Guymer, Chelsea, Lloyd Damp, Glyn Chidlow, John Wood, Yi Fan Tang, and Robert Casson. "Software for Quantifying and Batch Processing Images of Brn3a and RBPMS Immunolabelled Retinal Ganglion Cells in Retinal Wholemounts." Translational Vision Science & Technology 9, no. 6 (2020): 28. http://dx.doi.org/10.1167/tvst.9.6.28.

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Che, Qi, Miao Liu, Doudou Zhang, et al. "Long Noncoding RNA HUPCOS Promotes Follicular Fluid Androgen Excess in PCOS Patients via Aromatase Inhibition." Journal of Clinical Endocrinology & Metabolism 105, no. 4 (2020): 1086–97. http://dx.doi.org/10.1210/clinem/dgaa060.

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Abstract Context Androgen excess is a key feature of polycystic ovary syndrome (PCOS), but the underlying molecular mechanism remains unclear. Objective To determine the role and mechanism of novel long noncoding RNA (lncRNA) highly up-regulated in PCOS (HUPCOS) in the androgen excess of PCOS patients. Design The lncRNA expression profile in granulosa cells derived from PCOS and non-PCOS women were analyzed by using microarray assay. Human granulosa cell line KGN was used for mechanism investigation. Setting This was a university-based study. Patients Thirty-eight PCOS and 38 control patients were recruited: 8 PCOS and 8 control samples used for microarray discovery, the remaining 30 PCOS cases and 30 controls for quantitative RT-PCR validation. Main Outcome Measures The aberrant expression lncRNA profile of PCOS patients was measured using microarray. The relationship of HUPCOS and follicular fluid testosterone was measured. Aromatase expression were analyzed after HUPCOS downregulation. HUPCOS interaction protein was confirmed by RNA pull-down. Results The significantly elevated lncRNA in PCOS granulosa cells was named HUPCOS, which was positively correlated with follicular fluid testosterone of PCOS patients. HUPCOS downregulation increased aromatase expression and promoted conversion of androgen to estrogen. RNA-binding protein with multiple splicing (RBPMS) was the most likely protein that combined with HUPCOS. Conclusions Our findings suggested that HUPCOS mediated androgen excess in follicular fluid of PCOS patients by suppressing aromatase expression via interaction with RBPMS.

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Hornberg, H., F. Wollerton-van Horck, D. Maurus, et al. "RNA-Binding Protein Hermes/RBPMS Inversely Affects Synapse Density and Axon Arbor Formation in Retinal Ganglion Cells In Vivo." Journal of Neuroscience 33, no. 25 (2013): 10384–95. http://dx.doi.org/10.1523/jneurosci.5858-12.2013.

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Lian, Shuaibin, Liansheng Li, Yongjie Zhou, Zixiao Liu, and Lei Wang. "The co-expression networks of differentially expressed RBPs with TFs and LncRNAs related to clinical TNM stages of cancers." PeerJ 7 (September 17, 2019): e7696. http://dx.doi.org/10.7717/peerj.7696.

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Background RNA-binding proteins (RBPs) play important roles in cellular homeostasis by regulating the expression of thousands of transcripts, which have been reported to be involved in human tumorigenesis. Despite previous reports of the dysregulation of RBPs in cancers, the degree of dysregulation of RBPs in cancers and the intrinsic relevance between dysregulated RBPs and clinical TNM information remains unknown. Furthermore, the co-expressed networks of dysregulated RBPs with transcriptional factors and lncRNAs also require further investigation. Results Here, we firstly analyzed the deviations of expression levels of 1,542 RBPs from 20 cancer types and found that (1) RBPs are dysregulated in almost all 20 cancer types, especially in BLCA, COAD, READ, STAD, LUAD, LUSC and GBM with proportion of deviation larger than 300% compared with non-RBPs in normal tissues. (2) Up- and down-regulated RBPs also show opposed patterns of differential expression in cancers and normal tissues. In addition, down-regulated RBPs show a greater degree of dysregulated expression than up-regulated RBPs do. Secondly, we analyzed the intrinsic relevance between dysregulated RBPs and clinical TNM information and found that (3) Clinical TNM information for two cancer types—CHOL and KICH—is shown to be closely related to patterns of differentially expressed RBPs (DE RBPs) by co-expression cluster analysis. Thirdly, we identified ten key RBPs (seven down-regulated and three up-regulated) in CHOL and seven key RBPs (five down-regulated and two up-regulated) in KICH by analyzing co-expression correlation networks. Fourthly, we constructed the co-expression networks of key RBPs between 1,570 TFs and 4,147 lncRNAs for CHOL and KICH, respectively. Conclusions These results may provide an insight into the understanding of the functions of RBPs in human carcinogenesis. Furthermore, key RBPs and the co-expressed networks offer useful information for potential prognostic biomarkers and therapeutic targets for patients with cancers at the N and M stages in two cancer types CHOL and KICH.

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Li, Bei, Long Fang, Baolong Wang, Zengkun Yang, and Tingbao Zhao. "Identification of Prognostic RBPs in Osteosarcoma." Technology in Cancer Research & Treatment 20 (January 1, 2021): 153303382110049. http://dx.doi.org/10.1177/15330338211004918.

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Osteosarcoma often occurs in children and adolescents and causes poor prognosis. The role of RNA-binding proteins (RBPs) in malignant tumors has been elucidated in recent years. Our study aims to identify key RBPs in osteosarcoma that could be prognostic factors and treatment targets. GSE33382 dataset was downloaded from Gene Expression Omnibus (GEO) database. RBPs extraction and differential expression analysis was performed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed to explore the biological function of differential expression RBPs. Moreover, we constructed Protein-protein interaction (PPI) network and obtained key modules. Key RBPs were identified by univariate Cox regression analysis and multiple stepwise Cox regression analysis combined with the clinical information from Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. Risk score model was generated and validated by GSE16091 dataset. A total of 38 differential expression RBPs was identified. Go and KEGG results indicated these RBPs were significantly involved in ribosome biogenesis and mRNA surveillance pathway. COX regression analysis showed DDX24, DDX21, WARS and IGF2BP2 could be prognostic factors in osteosarcoma. Spearman’s correlation analysis suggested that WARS might be important in osteosarcoma immune infiltration. In conclusion, DDX24, DDX21, WARS and IGF2BP2 might play key role in osteosarcoma, which could be therapuetic targets for osteosarcoma treatment.

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Farazi, T. A., C. S. Leonhardt, N. Mukherjee, et al. "Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets." RNA 20, no. 7 (2014): 1090–102. http://dx.doi.org/10.1261/rna.045005.114.

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van Rooij, Frank J. A., Rehan Qayyum, Albert V. Smith, et al. "Genome-wide Trans-ethnic Meta-analysis Identifies Seven Genetic Loci Influencing Erythrocyte Traits and a Role for RBPMS in Erythropoiesis." American Journal of Human Genetics 100, no. 1 (2017): 51–63. http://dx.doi.org/10.1016/j.ajhg.2016.11.016.

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Konishi, Hiroaki, Shin Kashima, Takuma Goto, et al. "The Identification of RNA-Binding Proteins Functionally Associated with Tumor Progression in Gastrointestinal Cancer." Cancers 13, no. 13 (2021): 3165. http://dx.doi.org/10.3390/cancers13133165.

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Previous investigations have indicated that RNA-binding proteins (RBPs) are key molecules for the development of organs, differentiation, cell growth and apoptosis in cancer cells as well as normal cells. A bioinformatics analysis based on the mRNA expression and a somatic mutational database revealed the association between aberrant expression/mutations of RBPs and cancer progression. However, this method failed to detect functional alterations in RBPs without changes in the expression, thus leading to false negatives. To identify major tumor-associated RBPs, we constructed an siRNA library based on the database of RBPs and assessed the influence on the growth of colorectal, pancreatic and esophageal cancer cells. A comprehensive analysis of siRNA functional screening findings using 1198 siRNAs targeting 416 RBPs identified 41 RBPs in which 50% inhibition of cell growth was observed in cancer cells. Among these RBPs, 12 showed no change in the mRNA expression and no growth suppression in non-cancerous cells when downregulated by specific siRNAs. We herein report for the first time cancer-promotive RBPs identified by a novel functional assessment using an siRNA library of RBPs combined with expressional and mutational analyses.

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Shon, Byung-Sik. "A Study on the Factors Development of Requirement-Based Performance Measurement Elements for Volunteer Institutes." Journal of International Development Cooperation 15, no. 1 (2020): 85–114. http://dx.doi.org/10.34225/jidc.2020.15.1.85.

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Huang, Rongbing, Mengting Han, Liying Meng, and Xing Chen. "Transcriptome-wide discovery of coding and noncoding RNA-binding proteins." Proceedings of the National Academy of Sciences 115, no. 17 (2018): E3879—E3887. http://dx.doi.org/10.1073/pnas.1718406115.

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Transcriptome-wide identification of RNA-binding proteins (RBPs) is a prerequisite for understanding the posttranscriptional gene regulation networks. However, proteomic profiling of RBPs has been mostly limited to polyadenylated mRNA-binding proteins, leaving RBPs on nonpoly(A) RNAs, including most noncoding RNAs (ncRNAs) and pre-mRNAs, largely undiscovered. Here we present a click chemistry-assisted RNA interactome capture (CARIC) strategy, which enables unbiased identification of RBPs, independent of the polyadenylation state of RNAs. CARIC combines metabolic labeling of RNAs with an alkynyl uridine analog and in vivo RNA-protein photocross-linking, followed by click reaction with azide-biotin, affinity enrichment, and proteomic analysis. Applying CARIC, we identified 597 RBPs in HeLa cells, including 130 previously unknown RBPs. These newly discovered RBPs can likely bind ncRNAs, thus uncovering potential involvement of ncRNAs in processes previously unknown to be ncRNA-related, such as proteasome function and intermediary metabolism. The CARIC strategy should be broadly applicable across various organisms to complete the census of RBPs.

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Marondedze, C. "The increasing diversity and complexity of the RNA-binding protein repertoire in plants." Proceedings of the Royal Society B: Biological Sciences 287, no. 1935 (2020): 20201397. http://dx.doi.org/10.1098/rspb.2020.1397.

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Post-transcriptional regulation has far-reaching implications on the fate of RNAs. It is gaining increasing momentum as a critical component in adjusting global cellular transcript levels during development and in response to environmental stresses. In this process, RNA-binding proteins (RBPs) are indispensable chaperones that naturally bind RNA via one or multiple globular RNA-binding domains (RBDs) changing the function or fate of the bound RNAs. Despite the technical challenges faced in plants in large-scale studies, several hundreds of these RBPs have been discovered and elucidated globally over the past few years. Recent discoveries have more than doubled the number of proteins implicated in RNA interaction, including identification of RBPs lacking classical RBDs. This review will discuss these new emerging classes of RBPs, focusing on the current state of the RBP repertoire in Arabidopsis thaliana , including the diverse functional roles derived from quantitative studies implicating RBPs in abiotic stress responses. Notably, this review highlights that 836 RBPs are enriched as Arabidopsis RBPs while 1865 can be classified as candidate RBPs. The review will also outline outstanding areas within this field that require addressing to advance our understanding and potential biotechnological applications of RBPs.

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McBrayer, Samuel K., Benjamin A. Olenchock, Gabriel J. DiNatale, et al. "Autochthonous tumors driven by Rb1 loss have an ongoing requirement for the RBP2 histone demethylase." Proceedings of the National Academy of Sciences 115, no. 16 (2018): E3741—E3748. http://dx.doi.org/10.1073/pnas.1716029115.

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Inactivation of the retinoblastoma gene (RB1) product, pRB, is common in many human cancers. Targeting downstream effectors of pRB that are central to tumorigenesis is a promising strategy to block the growth of tumors harboring loss-of-function RB1 mutations. One such effector is retinoblastoma-binding protein 2 (RBP2, also called JARID1A or KDM5A), which encodes an H3K4 demethylase. Binding of pRB to RBP2 has been linked to the ability of pRB to promote senescence and differentiation. Importantly, genetic ablation of RBP2 is sufficient to phenocopy pRB’s ability to induce these cellular changes in cell culture experiments. Moreover, germline Rbp2 deletion significantly impedes tumorigenesis in Rb1+/− mice. The value of RBP2 as a therapeutic target in cancer, however, hinges on whether loss of RBP2 could block the growth of established tumors as opposed to simply delaying their onset. Here we show that conditional, systemic ablation of RBP2 in tumor-bearing Rb1+/− mice is sufficient to slow tumor growth and significantly extend survival without causing obvious toxicity to the host. These findings show that established Rb1-null tumors require RBP2 for growth and further credential RBP2 as a therapeutic target in human cancers driven by RB1 inactivation.

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Lang, Benjamin, Jae-Seong Yang, Mireia Garriga-Canut, et al. "Matrix-screening reveals a vast potential for direct protein-protein interactions among RNA binding proteins." Nucleic Acids Research 49, no. 12 (2021): 6702–21. http://dx.doi.org/10.1093/nar/gkab490.

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Abstract RNA-binding proteins (RBPs) are crucial factors of post-transcriptional gene regulation and their modes of action are intensely investigated. At the center of attention are RNA motifs that guide where RBPs bind. However, sequence motifs are often poor predictors of RBP-RNA interactions in vivo. It is hence believed that many RBPs recognize RNAs as complexes, to increase specificity and regulatory possibilities. To probe the potential for complex formation among RBPs, we assembled a library of 978 mammalian RBPs and used rec-Y2H matrix screening to detect direct interactions between RBPs, sampling &gt; 600 K interactions. We discovered 1994 new interactions and demonstrate that interacting RBPs bind RNAs adjacently in vivo. We further find that the mRNA binding region and motif preferences of RBPs deviate, depending on their adjacently binding interaction partners. Finally, we reveal novel RBP interaction networks among major RNA processing steps and show that splicing impairing RBP mutations observed in cancer rewire spliceosomal interaction networks. The dataset we provide will be a valuable resource for understanding the combinatorial interactions of RBPs with RNAs and the resulting regulatory outcomes.

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Wurth, Laurence. "Versatility of RNA-Binding Proteins in Cancer." Comparative and Functional Genomics 2012 (2012): 1–11. http://dx.doi.org/10.1155/2012/178525.

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Posttranscriptional gene regulation is a rapid and efficient process to adjust the proteome of a cell to a changing environment. RNA-binding proteins (RBPs) are the master regulators of mRNA processing and translation and are often aberrantly expressed in cancer. In addition to well-studied transcription factors, RBPs are emerging as fundamental players in tumor development. RBPs and their mRNA targets form a complex network that plays a crucial role in tumorigenesis. This paper describes mechanisms by which RBPs influence the expression of well-known oncogenes, focusing on precise examples that illustrate the versatility of RBPs in posttranscriptional control of cancer development. RBPs appeared very early in evolution, and new RNA-binding domains and combinations of them were generated in more complex organisms. The identification of RBPs, their mRNA targets, and their mechanism of action have provided novel potential targets for cancer therapy.

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Akira, Shizuo, and Kazuhiko Maeda. "Control of RNA Stability in Immunity." Annual Review of Immunology 39, no. 1 (2021): 481–509. http://dx.doi.org/10.1146/annurev-immunol-101819-075147.

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Posttranscriptional control of mRNA regulates various biological processes, including inflammatory and immune responses. RNA-binding proteins (RBPs) bind cis-regulatory elements in the 3′ untranslated regions (UTRs) of mRNA and regulate mRNA turnover and translation. In particular, eight RBPs (TTP, AUF1, KSRP, TIA-1/TIAR, Roquin, Regnase, HuR, and Arid5a) have been extensively studied and are key posttranscriptional regulators of inflammation and immune responses. These RBPs sometimes collaboratively or competitively bind the same target mRNA to enhance or dampen regulatory activities. These RBPs can also bind their own 3′ UTRs to negatively or positively regulate their expression. Both upstream signaling pathways and microRNA regulation shape the interactions between RBPs and target RNA. Dysregulation of RBPs results in chronic inflammation and autoimmunity. Here, we summarize the functional roles of these eight RBPs in immunity and their associated diseases.

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Wang, Yanhui, and Yao Chi. "Measuring Spatiotemporal Changes of Rural Basic Public Service in Poverty-stricken Area of China." International Regional Science Review 41, no. 5 (2016): 510–39. http://dx.doi.org/10.1177/0160017616665671.

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To address the development of rural basic public services (RBPS) among contiguous destitute areas of China, we develop a comprehensive RBPS evaluation methodology to examine RBPS development level of 728 poverty-stricken counties, using geographical information system (GIS) to describe their multiscale and multidimensional spatiotemporal change during 2010–2012; besides, we also try to reveal how RBPS interacts with county economy (CE) by integrating Tapio model and weighted Voronoi circle-layer structure. Our results show that (1) at a multiscale of area–province–county, in spite of the overall low level, RBPS is steadily growing during 2010–2012, along with a positive spatial autocorrelation and an obvious nonequilibrium that is high in east China but low in west; however, the RBPS gaps among the whole counties are gradually narrowing, shifting their development grades from a mostly relative shortage or relatively severe shortage in 2010 to a main state of relatively richness or relatively equilibrium in 2012, (2) from a multidimensional view, the RBPS gaps among most dimensions of different areas are gradually narrowing, except for the dimension of social public safety service that shows a significant regional differentiation among different areas. RBPS in Tibetan areas is the most unequalled and falls into the most obvious heterogeneity, and (3) there exist weak correlations between county-level original RBPS and original CE for each year and each circle layer, while significantly positive correlation is found only between mean RBPS and mean CE for four circle-layer subsets of counties, respectively; overall, RBPS development level lags behind that of CE as a main result of the weak decoupling between them. This study may provide a good understanding of the status, regional differences, and evolution of RBPS in poverty-stricken rural China, and serves as a scientific reference regarding decision-making in both promoting intrarural antipoverty harmonious development and constructing the new countryside of China.

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Furukawa, Mari T., Hiroshi Sakamoto, and Kunio Inoue. "Interaction and colocalization of HERMES/RBPMS with NonO, PSF, and G3BP1 in neuronal cytoplasmic RNP granules in mouse retinal line cells." Genes to Cells 20, no. 4 (2015): 257–66. http://dx.doi.org/10.1111/gtc.12224.

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Thomas, Chloe N., Adam M. Thompson, Zubair Ahmed, and Richard J. Blanch. "Retinal Ganglion Cells Die by Necroptotic Mechanisms in a Site-Specific Manner in a Rat Blunt Ocular Injury Model." Cells 8, no. 12 (2019): 1517. http://dx.doi.org/10.3390/cells8121517.

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Closed-globe injury can cause visual loss in military and civilian populations, with retinal cell death, including retinal ganglion cell (RGC) degeneration, leading to irreversible blindness. RGC and optic nerve (ON) degeneration after eye or head injury is termed traumatic optic neuropathy (TON). There are currently no treatments for RGC loss, therefore novel therapeutics to prevent RGC death or promote axonal regeneration are a priority. We investigated necroptotic signaling mechanisms in a rat blunt ocular injury model. After bilateral blunt trauma, protein expression and retinal localization of necroptosis pathway members (receptor interacting protein kinase 1, RIPK1; receptor interacting protein kinase 3, RIPK3; and mixed lineage kinase domain like pseudokinase, MLKL) were assessed by Western blot and immunohistochemistry (IHC), and potent necroptosis inhibitor Necrostatin-1s (Nec-1s) was delivered by intravitreal injection to one eye and vehicle to the contralateral eye. RGC and photoreceptor survival were assessed by cell counting and outer nuclear layer (ONL) thickness measurements on histology. The neuroprotective effects of Nec-1s were assessed in primary retinal culture by βIII-tubulin+ RGC cell counts. MLKL protein expression were upregulated at 48 h after injury and MLKL immunolocalised to retinal binding protein with multiple splice (RBPMS)+ RGC, inner nuclear cells and ONL cells, specifically at the retinal injury site. RIPK3 expression did not increase but RIPK3 co-immunolocalised with RBPMS+ RGC in intact and injured retinae. In vitro, a Nec-1s concentration of 0.01 pg/µL was RGC neuroprotective. In the blunt ocular injury rat model, Nec-1s prevented RGC death at the center of the impact site but did not protect against ONL thinning or provide functional restitution. RGC degeneration in our blunt ocular injury model is site-specific, with necroptosis driving death at the center of the focal impact site.

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