PT  - JOURNAL ARTICLE
AU  - Anneke Brümmer
AU  - Rene Dreos
AU  - Ana Claudia Marques
AU  - Sven Bergmann
TI  - LincRNA sequences are biased to counteract their translation
AID  - 10.1101/737890
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 737890
4099  - http://biorxiv.org/content/early/2019/08/16/737890.short
4100  - http://biorxiv.org/content/early/2019/08/16/737890.full
AB  - Long intergenic non-coding RNAs (lincRNAs) account for a large fraction of transcribed loci in the human genome. While many lincRNAs are retained in the cell nucleus, preventing their association with ribosomes, binding of cytosolic lincRNAs to ribosomes has been observed, but rarely results in translation. This raises the question of how translation of short open reading frames (ORFs) within cytosolic lincRNAs is hindered. Here, we investigate the content of nucleotide triplets in lincRNA putative ORFs (i.e. “codons”) and its potential impact on ribosome binding and translation.We find that lincRNA and mRNA ORFs have distinct codon frequencies, that are well conserved between human and mouse. In lincRNAs, codon frequencies are less correlated with the corresponding tRNA abundance measures than in mRNAs. This correlation is weaker for cytoplasmic lincRNAs and lowest for those without experimental evidence for ribosome binding.Our results suggest that putative lincRNA codons are a substrate of evolutionary forces modulating them to counteract unwanted ribosomal binding and translation. The resulting sequence signatures may help in distinguishing bona-fide lincRNAs with regulatory roles in the cytoplasm from transcripts coding for peptides.