Howard et al. 2013 (PRJNA197001)

General Details

Title The effects of dietary selenium on selenocysteine incorporation and selenoprotein expression
Organism
Number of Samples 6
Release Date 2013/04/13 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP021058
ENA SRP021058
GEO GSE46038
BioProject PRJNA197001

Publication

Title
Authors Howard MT,Carlson BA,Anderson CB,Hatfield DL
Journal The Journal of biological chemistry
Publication Date 2013 Jul 5
Abstract Incorporation of selenium into ~25 mammalian selenoproteins occurs by translational recoding whereby in-frame UGA codons are redefined to encode the selenium containing amino acid, selenocysteine (Sec). Here we applied ribosome profiling to examine the effect of dietary selenium levels on the translational mechanisms controlling selenoprotein synthesis in mouse liver. Dietary selenium levels were shown to control gene-specific selenoprotein expression primarily at the translation level by differential regulation of UGA redefinition and Sec incorporation efficiency, although effects on translation initiation and mRNA abundance were also observed. Direct evidence is presented that increasing dietary selenium causes a vast increase in ribosome density downstream of UGA-Sec codons for a subset of selenoprotein mRNAs and that the selenium-dependent effects on Sec incorporation efficiency are mediated in part by the degree of Sec-tRNA([Ser]Sec) Um34 methylation. Furthermore, we find evidence for translation in the 5'-UTRs for a subset of selenoproteins and for ribosome pausing near the UGA-Sec codon in those mRNAs encoding the selenoproteins most affected by selenium availability. These data illustrate how dietary levels of the trace element selenium can alter the readout of the genetic code to affect the expression of an entire class of proteins.
PMC PMC3707644
PMID 23696641
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR826795 PRJNA197001 Mus musculus Ribo-Seq
SRR826796 PRJNA197001 Mus musculus Ribo-Seq
SRR826797 PRJNA197001 Mus musculus Ribo-Seq
SRR826798 PRJNA197001 Mus musculus Ribo-Seq
SRR826799 PRJNA197001 Mus musculus Ribo-Seq
SRR826800 PRJNA197001 Mus musculus Ribo-Seq
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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