Molecular cloning, characterization, and stress-responsive expression of genes encoding glycine-rich RNA-binding proteins in Camelina sativa L.

We have previously demonstrated that the two paralogous RNA binding protein, PCBP1 and PCBP2, are individually essential for mouse development: Pcbp1 -null embryos are peri-implantation lethal while Pcbp2 -null embryos lose viability at mid-gestation. Mid-gestation Pcbp2 −/− embryos revealed a complex phenotype that included loss of certain hematopoietic determinants. Whether PCBP2 directly contributes to erythropoietic differentiation and whether PCBP1 has a role in this process remained undetermined. Here we selectively inactivate the genes encoding these two RNA-binding proteins during differentiation of the erythroid lineage in the developing mouse embryo. Individual inactivation of either locus fails to impact viability or blood formation. However, combined inactivation of the two loci results in mid-gestational repression of erythroid/hematopoietic gene expression, loss of blood formation, and fetal demise. Orthogonal ex-vivo analyses of primary erythroid progenitors selectively depleted of these two RNA binding proteins revealed that they mediate a combination of overlapping and isoform-specific impacts on hematopoietic lineage transcriptome, impacting both mRNA representation and exon splicing. These data lead us to conclude that PCBP1 and PCBP2 mediate functions critical to differentiation of the erythroid lineage.

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Stress granules as crucibles of ALS pathogenesis

The Journal of Cell Biology ◽

10.1083/jcb.201302044 ◽

2013 ◽

Vol 201 (3) ◽

pp. 361-372 ◽

Cited By ~ 497

Author(s):

Yun R. Li ◽

Oliver D. King ◽

James Shorter ◽

Aaron D. Gitler

Keyword(s):

Motor Neurons ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Stress Granules ◽

Normal Function ◽

Genes Encoding ◽

Als Patients ◽

Lateral Sclerosis ◽

Human Neurodegenerative Disease

Amyotrophic lateral sclerosis (ALS) is a fatal human neurodegenerative disease affecting primarily motor neurons. Two RNA-binding proteins, TDP-43 and FUS, aggregate in the degenerating motor neurons of ALS patients, and mutations in the genes encoding these proteins cause some forms of ALS. TDP-43 and FUS and several related RNA-binding proteins harbor aggregation-promoting prion-like domains that allow them to rapidly self-associate. This property is critical for the formation and dynamics of cellular ribonucleoprotein granules, the crucibles of RNA metabolism and homeostasis. Recent work connecting TDP-43 and FUS to stress granules has suggested how this cellular pathway, which involves protein aggregation as part of its normal function, might be coopted during disease pathogenesis.

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Discovery of novel cold-induced CISP genes encoding small RNA-binding proteins related to cold adaptation in barley

Plant Science ◽

10.1016/j.plantsci.2017.04.011 ◽

2017 ◽

Vol 260 ◽

pp. 129-138 ◽

Cited By ~ 4

Author(s):

Mengchao Ying ◽

Shin-ichiro Kidou

Keyword(s):

Small Rna ◽

Cold Adaptation ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Genes Encoding

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Novel Drosophila melanogaster genes encoding RRM-type RNA-binding proteins identified by a degenerate PCR strategy

Gene ◽

10.1016/0378-1119(94)00840-o ◽

1995 ◽

Vol 154 (2) ◽

pp. 187-192 ◽

Cited By ~ 10

Author(s):

Stéphanie F. Brand ◽

Sébastien Pichoff ◽

Stéphane Noselli ◽

Henri-Marc Bourbon

Keyword(s):

Drosophila Melanogaster ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Degenerate Pcr ◽

Genes Encoding

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Three types of nuclear genes encoding chloroplast RNA-binding proteins (cp29, cp31 and cp33) are present in Arabidopsis thaliana: presence of cp31 in chloroplasts and its homologue in nuclei/cytoplasms

Plant Molecular Biology ◽

10.1007/bf00019319 ◽

1995 ◽

Vol 27 (3) ◽

pp. 529-539 ◽

Cited By ~ 43

Author(s):

Masaru Ohta ◽

Mamoru Sugita ◽

Masahiro Sugiura

Keyword(s):

Arabidopsis Thaliana ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Nuclear Genes ◽

Genes Encoding ◽

Chloroplast Rna

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RBPTD: a database of cancer-related RNA-binding proteins in humans

Database ◽

10.1093/database/baz156 ◽

2020 ◽

Vol 2020 ◽

Cited By ~ 1

Author(s):

Kun Li ◽

Zhi-Wei Guo ◽

Xiang-Ming Zhai ◽

Xue-Xi Yang ◽

Ying-Song Wu ◽

...

Keyword(s):

High Throughput ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Sequencing Data ◽

Dna Copy Number Variation ◽

Expression Of Genes ◽

Number Variation

Abstract RNA-binding proteins (RBPs) play important roles in regulating the expression of genes involved in human physiological and pathological processes, especially in cancers. Many RBPs have been found to be dysregulated in cancers; however, there was no tool to incorporate high-throughput data from different dimensions to systematically identify cancer-related RBPs and to explore their causes of abnormality and their potential functions. Therefore, we developed a database named RBPTD to identify cancer-related RBPs in humans and systematically explore their functions and abnormalities by integrating different types of data, including gene expression profiles, prognosis data and DNA copy number variation (CNV), among 28 cancers. We found a total of 454 significantly differentially expressed RBPs, 1970 RBPs with significant prognostic value, and 53 dysregulated RBPs correlated with CNV abnormality. Functions of 26 cancer-related RBPs were explored by analysing high-throughput RNA sequencing data obtained by crosslinking immunoprecipitation, and the remaining RBP functions were predicted by calculating their correlation coefficient with other genes. Finally, we developed the RBPTD for users to explore functions and abnormalities of cancer-related RBPs to improve our understanding of their roles in tumorigenesis. Database URL: http: //www.rbptd.com

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RNA-Binding Proteins in Pulmonary Hypertension

International Journal of Molecular Sciences ◽

10.3390/ijms21113757 ◽

2020 ◽

Vol 21 (11) ◽

pp. 3757 ◽

Cited By ~ 1

Author(s):

Hui Zhang ◽

R. Dale Brown ◽

Kurt R. Stenmark ◽

Cheng-Jun Hu

Keyword(s):

Gene Expression ◽

Pulmonary Hypertension ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Current Knowledge ◽

Critical Role ◽

Apoptosis Resistance ◽

Aberrant Expression ◽

Expression Of Genes

Pulmonary hypertension (PH) is a life-threatening disease characterized by significant vascular remodeling and aberrant expression of genes involved in inflammation, apoptosis resistance, proliferation, and metabolism. Effective therapeutic strategies are limited, as mechanisms underlying PH pathophysiology, especially abnormal expression of genes, remain unclear. Most PH studies on gene expression have focused on gene transcription. However, post-transcriptional alterations have been shown to play a critical role in inflammation and metabolic changes in diseases such as cancer and systemic cardiovascular diseases. In these diseases, RNA-binding proteins (RBPs) have been recognized as important regulators of aberrant gene expression via post-transcriptional regulation; however, their role in PH is less clear. Identifying RBPs in PH is of great importance to better understand PH pathophysiology and to identify new targets for PH treatment. In this manuscript, we review the current knowledge on the role of dysregulated RBPs in abnormal mRNA gene expression as well as aberrant non-coding RNA processing and expression (e.g., miRNAs) in PH.

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Pathway-guided analysis identifies Myc-dependent alternative pre-mRNA splicing in aggressive prostate cancers

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1915975117 ◽

2020 ◽

Vol 117 (10) ◽

pp. 5269-5279 ◽

Cited By ~ 3

Author(s):

John W. Phillips ◽

Yang Pan ◽

Brandon L. Tsai ◽

Zhijie Xie ◽

Levon Demirdjian ◽

...

Keyword(s):

Alternative Splicing ◽

Rna Splicing ◽

Large Scale ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Mrna Splicing ◽

Cancer Driver ◽

Genes Encoding ◽

Prostate Cancers

We sought to define the landscape of alternative pre-mRNA splicing in prostate cancers and the relationship of exon choice to known cancer driver alterations. To do so, we compiled a metadataset composed of 876 RNA-sequencing (RNA-Seq) samples from five publicly available sources representing a range of prostate phenotypes from normal tissue to drug-resistant metastases. We subjected these samples to exon-level analysis with rMATS-turbo, purpose-built software designed for large-scale analyses of splicing, and identified 13,149 high-confidence cassette exon events with variable incorporation across samples. We then developed a computational framework, pathway enrichment-guided activity study of alternative splicing (PEGASAS), to correlate transcriptional signatures of 50 different cancer driver pathways with these alternative splicing events. We discovered that Myc signaling was correlated with incorporation of a set of 1,039 cassette exons enriched in genes encoding RNA binding proteins. Using a human prostate epithelial transformation assay, we confirmed the Myc regulation of 147 of these exons, many of which introduced frameshifts or encoded premature stop codons. Our results connect changes in alternative pre-mRNA splicing to oncogenic alterations common in prostate and many other cancers. We also establish a role for Myc in regulating RNA splicing by controlling the incorporation of nonsense-mediated decay-determinant exons in genes encoding RNA binding proteins.

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