The RNA-binding protein Secisbp2 differentially modulates UGA codon reassignment and RNA decay

Fradejas‐Villar, Noelia; Seeher, Sandra; Anderson, Christine B.; Doengi, Michael; Carlson, Bradley A.; Hatfield, Dolph L.; Schweizer, Ulrich; Howard, Michael

doi:10.1093/nar/gkw1255

Cited by 45 publications

(52 citation statements)

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“…We examined underlying biological relationships in gene expression profiles among four different cell types using gene hierarchical clustering analyses. RNA-seq-based transcriptomic data of stria melanocytes (our unpublished data), liver cells, and retinal bipolar cells from published studies (Shekhar et al, 2016 ; Fradejas-Villar et al, 2017 ) were also used for comparison. Figure 3A presents the similarity measure of gene expression profiles of the seven cell types using Principal Component Analysis or PCA (Yeung and Ruzzo, 2001 ).…”

Section: Resultsmentioning

confidence: 99%

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Cell-Specific Transcriptome Analysis Shows That Adult Pillar and Deiters' Cells Express Genes Encoding Machinery for Specializations of Cochlear Hair Cells

Liu

Chen

Giffen

et al. 2018

Front. Mol. Neurosci.

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The mammalian auditory sensory epithelium, the organ of Corti, is composed of hair cells and supporting cells. Hair cells contain specializations in the apical, basolateral and synaptic membranes. These specializations mediate mechanotransduction, electrical and mechanical activities and synaptic transmission. Supporting cells maintain homeostasis of the ionic and chemical environment of the cochlea and contribute to the stiffness of the cochlear partition. While spontaneous proliferation and transdifferentiation of supporting cells are the source of the regenerative response to replace lost hair cells in lower vertebrates, supporting cells in adult mammals no longer retain that capability. An important first step to revealing the basic biological properties of supporting cells is to characterize their cell-type specific transcriptomes. Using RNA-seq, we examined the transcriptomes of 1,000 pillar and 1,000 Deiters' cells, as well as the two types of hair cells, individually collected from adult CBA/J mouse cochleae using a suction pipette technique. Our goal was to determine whether pillar and Deiters' cells, the commonly targeted cells for hair cell replacement, express the genes known for encoding machinery for hair cell specializations in the apical, basolateral, and synaptic membranes. We showed that both pillar and Deiters' cells express these genes, with pillar cells being more similar to hair cells than Deiters' cells. The fact that adult pillar and Deiters' cells express the genes cognate to hair cell specializations provides a strong molecular basis for targeting these cells for mammalian hair cell replacement after hair cells are lost due to damage.

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Section: Resultsmentioning

confidence: 99%

“…(A) Principal component analyses of the gene expression profiles of seven different cell types. RNA-seq-based gene expression data of liver cells and retinal bipolar cells were obtained from published work (Shekhar et al, 2016 ; Fradejas-Villar et al, 2017 ). Stria melanocyte dataset was from our own unpublished work.…”

Section: Resultsmentioning

confidence: 99%

Cell-Specific Transcriptome Analysis Shows That Adult Pillar and Deiters' Cells Express Genes Encoding Machinery for Specializations of Cochlear Hair Cells

Liu

Chen

Giffen

et al. 2018

Front. Mol. Neurosci.

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“…3c shows PCA of the gene expression profiles of IHCs and OHCs. Transcriptome data of mouse liver cells from a published study 21 was downloaded and normalized with our data set. As shown, the expression profiles of OHCs are highly reproducible as the data points from three biological and three technical repeats are clustered all together with small variability.…”

Section: Technical Validationmentioning

confidence: 99%

Transcriptomes of cochlear inner and outer hair cells from adult mice

Liu

Giffen

et al. 2018

Sci Data

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Inner hair cells (IHCs) and outer hair cells (OHCs) are the two anatomically and functionally distinct types of mechanosensitive receptor cells in the mammalian cochlea. The molecular mechanisms defining their morphological and functional specializations are largely unclear. As a first step to uncover the underlying mechanisms, we examined the transcriptomes of IHCs and OHCs isolated from adult CBA/J mouse cochleae. One thousand IHCs and OHCs were separately collected using the suction pipette technique. RNA sequencing of IHCs and OHCs was performed and their transcriptomes were analyzed. The results were validated by comparing some IHC and OHC preferentially expressed genes between present study and published microarray-based data as well as by real-time qPCR. Antibody-based immunocytochemistry was used to validate preferential expression of SLC7A14 and DNM3 in IHCs and OHCs. These data are expected to serve as a highly valuable resource for unraveling the molecular mechanisms underlying different biological properties of IHCs and OHCs as well as to provide a road map for future characterization of genes expressed in IHCs and OHCs.

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“…Treatment of the samples was performed as described previously (19) with the exception of the RNase I incubation time, which was reduced to 20 min for the cortex tissue. Raw sequence data and raw counts can be obtained from the NCBI GEO repository entry GSE119681.…”

Section: Ribosome Profiling and Rna-seqmentioning

confidence: 99%

“…Because the R540Q mutation differentially affected selenoprotein expression and SECIS binding in vitro (10), we wanted to more systematically assess how this mutation impinges on the translation of different selenoprotein mRNAs in vivo. Using ribosome profiling (18), we aimed to specifically probe the efficiency of UGA/Sec recoding in mice in the same transcript-specific way as we have assessed it previously in Secisbp2-knockout mice (19).…”

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confidence: 99%

Ribosome profiling of selenoproteins in vivo reveals consequences of pathogenic Secisbp2 missense mutations

Zhao

Bohleber

Seeher

et al. 2019

Journal of Biological Chemistry

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Recoding of UGA codons as selenocysteine (Sec) codons in selenoproteins depends on a selenocysteine insertion sequence (SECIS) in the 3-UTR of mRNAs of eukaryotic selenoproteins. SECIS-binding protein 2 (SECISBP2) increases the efficiency of this process. Pathogenic mutations in SECISBP2 reduce selenoprotein expression and lead to phenotypes associated with the reduction of deiodinase activities and selenoprotein N expression in humans. Two functions have been ascribed to SECISBP2: binding of SECIS elements in selenoprotein mRNAs and facilitation of co-translational Sec insertion. To separately probe both functions, we established here two mouse models carrying two pathogenic missense mutations in Secisbp2 previously identified in patients. We found that the C696R substitution in the RNA-binding domain abrogates SECIS binding and does not support selenoprotein translation above the level of a complete Secisbp2 null mutation. The R543Q missense substitution located in the selenocysteine insertion domain resulted in residual activity and caused reduced selenoprotein translation, as demonstrated by ribosomal profiling to determine the impact on UGA recoding in individual selenoproteins. We found, however, that the R543Q variant is thermally unstable in vitro and completely degraded in the mouse liver in vivo, while being partially functional in the brain. The moderate impairment of selenoprotein expression in neurons led to astrogliosis and transcriptional induction of genes associated with immune responses. We conclude that differential SECISBP2 protein stability in individual cell types may dictate clinical phenotypes to a much greater extent than molecular interactions involving a mutated amino acid in SECISBP2. This work was supported by Deutsche Forschungsgemeinschaft Grants Schw914/2 and Schw914/5 and Universitätsklinikum Bonn. The authors declare that they have no conflicts of interest with the contents of this article. This article was selected as one of our Editors' Picks. This article contains Table S1 and Figs. S1-S3. Raw and processed original data have been deposited in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) under accession number GSE119681. 1 Supported by a BONFOR SciMed scholarship of the medical faculty.

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The RNA-binding protein Secisbp2 differentially modulates UGA codon reassignment and RNA decay

Cited by 45 publications

References 50 publications

Cell-Specific Transcriptome Analysis Shows That Adult Pillar and Deiters' Cells Express Genes Encoding Machinery for Specializations of Cochlear Hair Cells

Cell-Specific Transcriptome Analysis Shows That Adult Pillar and Deiters' Cells Express Genes Encoding Machinery for Specializations of Cochlear Hair Cells

Transcriptomes of cochlear inner and outer hair cells from adult mice

Ribosome profiling of selenoproteins in vivo reveals consequences of pathogenic Secisbp2 missense mutations

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