CpG + CpNpG Analysis of Protein-Coding Sequences from Tomato

Asger Hobolth; Rasmus Nielsen; Ying Wang; Feinan Wu; Steven D. Tanksley

doi:10.1093/molbev/msk017

CpG + CpNpG Analysis of Protein-Coding Sequences from Tomato

Asger Hobolth, Rasmus Nielsen, Ying Wang, Feinan Wu, Steven D. Tanksley

15 Citations (Scopus)

Abstract

We develop codon-based models for simultaneously inferring themutational effects of CpG and CpNpG methylation in coding regions.In a data set of 369 tomato genes, we show that there is verylittle effect of CpNpG methylation but a strong effect of CpGmethylation affecting almost all genes. We further show thatthe CpNpG and CpG effects are largely uncorrelated. Our resultssuggest different roles of CpG and CpNpG methylation, with CpNpGmethylation possibly playing a specialized role in defense againsttransposons and RNA viruses.

Original language	English
Journal	Molecular Biology and Evolution
Volume	23
Issue number	6
Pages (from-to)	1318-1323
ISSN	0737-4038
DOIs	https://doi.org/10.1093/molbev/msk017
Publication status	Published - 2006

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title = "CpG + CpNpG Analysis of Protein-Coding Sequences from Tomato",

abstract = "We develop codon-based models for simultaneously inferring the mutational effects of CpG and CpNpG methylation in coding regions. In a data set of 369 tomato genes, we show that there is very little effect of CpNpG methylation but a strong effect of CpG methylation affecting almost all genes. We further show that the CpNpG and CpG effects are largely uncorrelated. Our results suggest different roles of CpG and CpNpG methylation, with CpNpG methylation possibly playing a specialized role in defense against transposons and RNA viruses. ",

author = "Asger Hobolth and Rasmus Nielsen and Ying Wang and Feinan Wu and Tanksley, {Steven D.}",

note = "codon model • context dependency • CpG + CpNpG methylation",

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T1 - CpG + CpNpG Analysis of Protein-Coding Sequences from Tomato

AU - Hobolth, Asger

AU - Nielsen, Rasmus

AU - Wang, Ying

AU - Wu, Feinan

AU - Tanksley, Steven D.

N1 - codon model • context dependency • CpG + CpNpG methylation

PY - 2006

Y1 - 2006

N2 - We develop codon-based models for simultaneously inferring the mutational effects of CpG and CpNpG methylation in coding regions. In a data set of 369 tomato genes, we show that there is very little effect of CpNpG methylation but a strong effect of CpG methylation affecting almost all genes. We further show that the CpNpG and CpG effects are largely uncorrelated. Our results suggest different roles of CpG and CpNpG methylation, with CpNpG methylation possibly playing a specialized role in defense against transposons and RNA viruses.

AB - We develop codon-based models for simultaneously inferring the mutational effects of CpG and CpNpG methylation in coding regions. In a data set of 369 tomato genes, we show that there is very little effect of CpNpG methylation but a strong effect of CpG methylation affecting almost all genes. We further show that the CpNpG and CpG effects are largely uncorrelated. Our results suggest different roles of CpG and CpNpG methylation, with CpNpG methylation possibly playing a specialized role in defense against transposons and RNA viruses.

U2 - 10.1093/molbev/msk017

DO - 10.1093/molbev/msk017

M3 - Journal article

C2 - 16600999

SN - 0737-4038

VL - 23

SP - 1318

EP - 1323

JO - Molecular Biology and Evolution

JF - Molecular Biology and Evolution

IS - 6

ER -

CpG + CpNpG Analysis of Protein-Coding Sequences from Tomato

Abstract

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