SPELL - Nematode

Citation	Stadler M, Fire A. Wobble base-pairing slows in vivo translation elongation in metazoans. RNA, 2011.
PubMed ID	22045228
Short Description	Wobble base-pairing slows in vivo translation elongation in metazoans. GEO Record: N.A. Platform: N.A. Download gene-centric, log2 transformed data: WBPaper00040379.ce.rs.csv
# of Conditions	16
Full Description	In the universal genetic code, most amino acids can be encoded by multiple trinucleotide codons, and the choice among available codons can influence position-specific translation elongation rates. By using sequence-based ribosome profiling, we obtained transcriptome-wide profiles of in vivo ribosome occupancy as a function of codon identity in Caenorhabditis elegans and human cells. Particularly striking in these profiles was a universal trend of higher ribosome occupancy for codons translated via G:U wobble base-pairing compared with synonymous codons that pair with the same tRNA family using G:C base-pairing. These data support a model in which ribosomal translocation is slowed at wobble codon positions. Experimental Details: RNASeq.elegans.WBStrain00000001.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP010374.SRX116361 RNASeq.elegans.WBStrain00000001.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP010374.SRX116363 RNASeq.elegans.WBStrain00000001.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP010374.SRX118116 RNASeq.elegans.WBStrain00000001.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP010374.SRX118117 RNASeq.elegans.WBStrain00000001.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP010374.SRX118118 RNASeq.elegans.WBStrain00000001.WBls:0000027.Hermaphrodite.WBbt:0007833.SRP010374.SRX118119 RNASeq.elegans.WBStrain00000001.WBls:0000027.Hermaphrodite.WBbt:0007833.SRP010374.SRX118120 RNASeq.elegans.WBStrain00000001.WBls:0000035.Hermaphrodite.WBbt:0007833.SRP010374.SRX118124 RNASeq.elegans.WBStrain00000001.WBls:0000035.Hermaphrodite.WBbt:0007833.SRP010374.SRX118125 RNASeq.elegans.WBStrain00000001.WBls:0000038.Hermaphrodite.WBbt:0007833.SRP010374.SRX118126 RNASeq.elegans.WBStrain00000001.WBls:0000038.Hermaphrodite.WBbt:0007833.SRP010374.SRX118127 RNASeq.elegans.WBStrain00000001.WBls:0000035.Hermaphrodite.WBbt:0007833.SRP010374.SRX118128 RNASeq.elegans.WBStrain00000001.WBls:0000035.Hermaphrodite.WBbt:0007833.SRP010374.SRX118139 RNASeq.elegans.WBStrain00000001.WBls:0000038.Hermaphrodite.WBbt:0007833.SRP010374.SRX118140 RNASeq.elegans.WBStrain00000001.WBls:0000035.Hermaphrodite.WBbt:0007833.SRP010374.SRX118143 RNASeq.elegans.WBStrain00000001.WBls:0000035.Hermaphrodite.WBbt:0007833.SRP010374.SRX118144.
Tags	Method: RNAseq, Species: Caenorhabditis elegans, Topic: developmental time course