Cargando…
GC(3 )biology in corn, rice, sorghum and other grasses
BACKGROUND: The third, or wobble, position in a codon provides a high degree of possible degeneracy and is an elegant fault-tolerance mechanism. Nucleotide biases between organisms at the wobble position have been documented and correlated with the abundances of the complementary tRNAs. We and other...
Autores principales: | , , , |
---|---|
Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2010
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2895627/ https://www.ncbi.nlm.nih.gov/pubmed/20470436 http://dx.doi.org/10.1186/1471-2164-11-308 |
_version_ | 1782183271699841024 |
---|---|
author | Tatarinova, Tatiana V Alexandrov, Nickolai N Bouck, John B Feldmann, Kenneth A |
author_facet | Tatarinova, Tatiana V Alexandrov, Nickolai N Bouck, John B Feldmann, Kenneth A |
author_sort | Tatarinova, Tatiana V |
collection | PubMed |
description | BACKGROUND: The third, or wobble, position in a codon provides a high degree of possible degeneracy and is an elegant fault-tolerance mechanism. Nucleotide biases between organisms at the wobble position have been documented and correlated with the abundances of the complementary tRNAs. We and others have noticed a bias for cytosine and guanine at the third position in a subset of transcripts within a single organism. The bias is present in some plant species and warm-blooded vertebrates but not in all plants, or in invertebrates or cold-blooded vertebrates. RESULTS: Here we demonstrate that in certain organisms the amount of GC at the wobble position (GC(3)) can be used to distinguish two classes of genes. We highlight the following features of genes with high GC(3 )content: they (1) provide more targets for methylation, (2) exhibit more variable expression, (3) more frequently possess upstream TATA boxes, (4) are predominant in certain classes of genes (e.g., stress responsive genes) and (5) have a GC(3 )content that increases from 5'to 3'. These observations led us to formulate a hypothesis to explain GC(3 )bimodality in grasses. CONCLUSIONS: Our findings suggest that high levels of GC(3 )typify a class of genes whose expression is regulated through DNA methylation or are a legacy of accelerated evolution through gene conversion. We discuss the three most probable explanations for GC(3 )bimodality: biased gene conversion, transcriptional and translational advantage and gene methylation. |
format | Text |
id | pubmed-2895627 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-28956272010-07-02 GC(3 )biology in corn, rice, sorghum and other grasses Tatarinova, Tatiana V Alexandrov, Nickolai N Bouck, John B Feldmann, Kenneth A BMC Genomics Research Article BACKGROUND: The third, or wobble, position in a codon provides a high degree of possible degeneracy and is an elegant fault-tolerance mechanism. Nucleotide biases between organisms at the wobble position have been documented and correlated with the abundances of the complementary tRNAs. We and others have noticed a bias for cytosine and guanine at the third position in a subset of transcripts within a single organism. The bias is present in some plant species and warm-blooded vertebrates but not in all plants, or in invertebrates or cold-blooded vertebrates. RESULTS: Here we demonstrate that in certain organisms the amount of GC at the wobble position (GC(3)) can be used to distinguish two classes of genes. We highlight the following features of genes with high GC(3 )content: they (1) provide more targets for methylation, (2) exhibit more variable expression, (3) more frequently possess upstream TATA boxes, (4) are predominant in certain classes of genes (e.g., stress responsive genes) and (5) have a GC(3 )content that increases from 5'to 3'. These observations led us to formulate a hypothesis to explain GC(3 )bimodality in grasses. CONCLUSIONS: Our findings suggest that high levels of GC(3 )typify a class of genes whose expression is regulated through DNA methylation or are a legacy of accelerated evolution through gene conversion. We discuss the three most probable explanations for GC(3 )bimodality: biased gene conversion, transcriptional and translational advantage and gene methylation. BioMed Central 2010-05-16 /pmc/articles/PMC2895627/ /pubmed/20470436 http://dx.doi.org/10.1186/1471-2164-11-308 Text en Copyright ©2010 Tatarinova et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Tatarinova, Tatiana V Alexandrov, Nickolai N Bouck, John B Feldmann, Kenneth A GC(3 )biology in corn, rice, sorghum and other grasses |
title | GC(3 )biology in corn, rice, sorghum and other grasses |
title_full | GC(3 )biology in corn, rice, sorghum and other grasses |
title_fullStr | GC(3 )biology in corn, rice, sorghum and other grasses |
title_full_unstemmed | GC(3 )biology in corn, rice, sorghum and other grasses |
title_short | GC(3 )biology in corn, rice, sorghum and other grasses |
title_sort | gc(3 )biology in corn, rice, sorghum and other grasses |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2895627/ https://www.ncbi.nlm.nih.gov/pubmed/20470436 http://dx.doi.org/10.1186/1471-2164-11-308 |
work_keys_str_mv | AT tatarinovatatianav gc3biologyincornricesorghumandothergrasses AT alexandrovnickolain gc3biologyincornricesorghumandothergrasses AT bouckjohnb gc3biologyincornricesorghumandothergrasses AT feldmannkennetha gc3biologyincornricesorghumandothergrasses |