RNA-binding proteins PCBP1 and PCBP2 are critical determinants of murine erythropoiesis

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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RNA-binding proteins regulate aldosterone homeostasis in human steroidogenic cells

10.1101/2021.02.19.431050 ◽

2021 ◽

Author(s):

Rui Fu ◽

Kimberly Wellman ◽

Amber Baldwin ◽

Juilee Rege ◽

Kathryn Walters ◽

...

Keyword(s):

Gene Expression ◽

Time Course ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Ex Vivo ◽

Human Cell Line ◽

Rna Decay ◽

Type I ◽

Aldosterone Production

ABSTRACTAngiotensin II (AngII) binds to the type I angiotensin receptor in the adrenal cortex to initiate a cascade of events leading to the production of aldosterone, a master regulator of blood pressure. Despite extensive characterization of the transcriptional and enzymatic control of adrenocortical steroidogenesis, there are still major gaps in our knowledge related to precise regulation of AII-induced gene expression kinetics. Specifically, we do not know the regulatory contribution of RNA-binding proteins (RBPs) and RNA decay, which can control the timing of stimulus-induced gene expression. To investigate this question, we performed a high-resolution RNA-seq time course of the AngII stimulation response and 4-thiouridine pulse labeling in a steroidogenic human cell line (H295R). We identified twelve temporally distinct gene expression responses that contained mRNA encoding proteins known to be important for various steps of aldosterone production, such as cAMP signaling components and steroidogenic enzymes. AngII response kinetics for many of these mRNAs revealed a coordinated increase in both synthesis and decay. These findings were validated in primary human adrenocortical cells stimulated ex vivo with AngII. Using a candidate siRNA screen, we identified a subset of RNA-binding protein and RNA decay factors that activate or repress AngII-stimulated aldosterone production. Among the repressors of aldosterone were BTG2, which promotes deadenylation and global RNA decay. BTG2 was induced in response to AngII stimulation and promoted the repression of mRNAs encoding pro-steroidogenic factors indicating the existence of an incoherent feedforward loop controlling aldosterone homeostasis. Together, these data support a model in which coordinated increases in transcription and regulated RNA decay facilitates the major transcriptomic changes required to implement a pro-steroidogenic gene expression program that is temporally restricted to prevent aldosterone overproduction.

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

Plant Physiology and Biochemistry ◽

10.1016/j.plaphy.2013.03.023 ◽

2013 ◽

Vol 68 ◽

pp. 44-51 ◽

Cited By ~ 10

Author(s):

Kyung Jin Kwak ◽

Hunseung Kang ◽

Kyung-Hwan Han ◽

Sung-Ju Ahn

Keyword(s):

Molecular Cloning ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Camelina Sativa ◽

Expression Of Genes ◽

Genes Encoding

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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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RNA-binding proteins in mouse oocytes and embryos: Expression of genes encoding Y box, DEAD box RNA helicase, and polyA binding proteins

Developmental Genetics ◽

10.1002/(sici)1520-6408(1998)23:4<285::aid-dvg4>3.0.co;2-w ◽

1998 ◽

Vol 23 (4) ◽

pp. 285-298 ◽

Cited By ~ 16

Author(s):

Barbara V. Paynton

Keyword(s):

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Rna Helicase ◽

Mouse Oocytes ◽

Dead Box ◽

Expression Of Genes ◽

Genes Encoding

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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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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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The Poly(C) binding protein Pcbp2, and its retrotransposed derivative Pcbp1, are independently essential to mouse development.

Molecular and Cellular Biology ◽

10.1128/mcb.00936-15 ◽

2015 ◽

pp. MCB.00936-15 ◽

Cited By ~ 13

Author(s):

Louis R. Ghanem ◽

Andrew Kromer ◽

Ian M. Silverman ◽

Priya Chatterji ◽

Elizabeth Traxler ◽

...

Keyword(s):

Embryonic Development ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Binding Protein ◽

Post Partum ◽

Null Alleles ◽

Mouse Development ◽

Wide Range

RNA-binding proteins participate in a complex array of post-transcriptional controls essential to cell-type specification and somatic development. Despite their detailed biochemical characterizations, the degree to which each RNA-binding protein impacts on mammalian embryonic development remains incompletely defined and the level of functional redundancy among subsets of these proteins remains open to question. The poly-(C) binding proteins, Pcbp's (αCPs, hnRNPEs), are encoded by a highly conserved and broadly expressed gene family. The two major Pcbp isoforms, Pcbp2 and Pcbp1, are robustly expressed in a wide range of tissues and exert both nuclear and cytoplasmic controls over gene expression. Here we report thatPcbp1-null embryos are rendered nonviable in the peri-implantation stage. In contrast,Pcbp2-null embryos undergo normal development until mid-gestation (12.5-13.5 days post coitum) at which time they undergo a dramatic loss in viability associated with combined cardiovascular and hematopoietic abnormalities. Mice heterozygous for either Pcbp1 or Pcbp2 null alleles display a mild and non-disruptive defect in initial post-partum weight gain. These data reveal thatPcbp1andPcbp2are individually essential for mouse embryonic development, have distinct impacts on embryonic viability, and that Pcpb2 has a nonredundantin vivorole in hematopoiesis. These data further provide direct evidence thatPcbp1, a retrotransposed derivative ofPcpb2, has evolved essential function(s) in the mammalian genome.

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