Reply to Simmonds et al.: Codon pair and dinucleotide bias have not been functionally distinguished

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 28, 2015, Pages E3635-E3636

  Futcher, Bruce ^a   Gorbatsevych, Oleksandr ^a   Shen, Sam H ^a   Stauft, Charles B ^a   Song, Yutong ^a   Wang, Bingyin ^a   Leatherwood, Janet ^a   Gardin, Justin ^a   Yurovsky, Alisa ^a   Mueller, Steffen ^a   Wimmer, Eckard ^a  

^a STONY BROOK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE;

CODON; CODON PAIR; CPG ISLAND; DENGUE VIRUS; GENE FREQUENCY; LETTER; MAMMAL CELL; NONHUMAN; PRIORITY JOURNAL; RNA VIRUS; ANIMAL; ARBOVIRUS; HUMAN; INSECT VECTOR; MAMMAL; PHYSIOLOGY; VIROLOGY; VIRUS GENOME;

ANIMALS; ARBOVIRUSES; GENOME, VIRAL; HUMANS; INSECT VECTORS; MAMMALS;

EID: 84937127379     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1507710112     Document Type: Letter

References (4)

1. Simmonds P, Tulloch F, Evans DJ, Ryan MD (2015) Attenuation of dengue (and other RNA viruses) with codon pair recoding can be explained by increased CpG/UpA dinucleotide frequencies. Proc Natl Acad Sci USA 112:E3633-E3634.
2. Shen SH, et al. (2015) Large-scale recoding of an arbovirus genome to rebalance its insect versus mammalian preference. Proc Natl Acad Sci USA 112(15):4749-4754.
3. Tulloch F, Atkinson NJ, Evans DJ, Ryan MD, Simmonds P (2014) RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies. eLife 3:e04531.
4. Coleman JR, et al. (2008) Virus attenuation by genome-scale changes in codon pair bias. Science 320(5884):1784-1787.