2016
DOI: 10.1093/nar/gkw1255
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The RNA-binding protein Secisbp2 differentially modulates UGA codon reassignment and RNA decay

Abstract: Dual-assignment of codons as termination and elongation codons is used to expand the genetic code. In mammals, UGA can be reassigned to selenocysteine during translation of selenoproteins by a mechanism involving a 3΄ untranslated region (UTR) selenocysteine insertion sequence (SECIS) and the SECIS-binding protein Secisbp2. Here, we present data from ribosome profiling, RNA-Seq and mRNA half-life measurements that support distinct roles for Secisbp2 in UGA-redefinition and mRNA stability. Conditional deletions… Show more

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Cited by 45 publications
(51 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 RNA-seq-based transcriptomic data of stria melanocytes (our unpublished data), liver cells, and retinal bipolar cells from published studies (Shekhar et al, 2016 ; Fradejas-Villar et al, 2017 ) were also used for comparison.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%
See 1 more Smart Citation
“…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 RNA-seq-based transcriptomic data of stria melanocytes (our unpublished data), liver cells, and retinal bipolar cells from published studies (Shekhar et al, 2016 ; Fradejas-Villar et al, 2017 ) were also used for comparison.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%
“…(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 Stria melanocyte dataset was from our own unpublished work.…”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%
“…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%
“…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).…”
mentioning
confidence: 99%