Weak 5′-mRNA secondary structures in short eukaryotic genes

TY - JOUR

T1 - Weak 5′-mRNA secondary structures in short eukaryotic genes

AU - Ding, Yang

AU - Shah, Premal

AU - Plotkin, Joshua B.

PY - 2012/1/1

Y1 - 2012/1/1

N2 - Experimental studies of translation have found that short genes tend to exhibit greater densities of ribosomes than long genes in eukaryotic species. It remains an open question whether the elevated ribosome density on short genes is due to faster initiation or slower elongation dynamics. Here, we address this question computationally using 5′-mRNA folding energy as a proxy for translation initiation rates and codon bias as a proxy for elongation rates. We report a significant trend toward reduced 50-secondary structure in shorter coding sequences, suggesting that short genes initiate faster during translation. We also find a trend toward higher 5′-codon bias in short genes, suggesting that short genes elongate faster than long genes. Both of these trends hold across a diverse set of eukaryotic taxa. Thus, the elevated ribosome density on short eukaryotic genes is likely caused by differential rates of initiation, rather than differential rates of elongation.

AB - Experimental studies of translation have found that short genes tend to exhibit greater densities of ribosomes than long genes in eukaryotic species. It remains an open question whether the elevated ribosome density on short genes is due to faster initiation or slower elongation dynamics. Here, we address this question computationally using 5′-mRNA folding energy as a proxy for translation initiation rates and codon bias as a proxy for elongation rates. We report a significant trend toward reduced 50-secondary structure in shorter coding sequences, suggesting that short genes initiate faster during translation. We also find a trend toward higher 5′-codon bias in short genes, suggesting that short genes elongate faster than long genes. Both of these trends hold across a diverse set of eukaryotic taxa. Thus, the elevated ribosome density on short eukaryotic genes is likely caused by differential rates of initiation, rather than differential rates of elongation.

KW - Codon bias

KW - Gene length

KW - Ribosome density

KW - Translation initiation

UR - http://www.scopus.com/inward/record.url?scp=84875082172&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84875082172&partnerID=8YFLogxK

U2 - https://doi.org/10.1093/gbe/evs082

DO - https://doi.org/10.1093/gbe/evs082

M3 - Article

C2 - 23034215

SN - 1759-6653

VL - 4

SP - 1046

EP - 1053

JO - Genome biology and evolution

JF - Genome biology and evolution

IS - 10

ER -