Analysis of GC-compositional Strand Bias in the Transcription Start Sites of Plant and Fungal Genes
نویسندگان
چکیده
In a recent paper, a GC-compositional strand bias, or GC-skew (=(C-G)/(C+G)) was reported, where C and G denote the numbers of cytosine and guanine residues, respectively, near the transcription start sites (TSS) in Arabidopsis [4]. However, it is unclear whether other eukaryotic species have similar GC-skews, and the biological meaning of that remains unknown. In this study, we conducted comparative analysis using sequences from various eukaryotic genomes animals, fungi, protists, and plants. In addition, we explored the potential of GC-skew as an index for TSS prediction in plants. Finally, we discuss the formation process of GC-skew, based on our results of the analysis.
منابع مشابه
Statistical Characterization of Transcription Start Sites in Plant Genomes
Although large amounts of genomic and full-length cDNA sequence data from plants are now publicly available, knowledge of the promoters and transcription start sites (TSSs) in plants is still limited compared to mammals, such as human and mouse. In a recent paper, a prominent GC-compositional strand bias or GC-skew (=(C-G)/(C+G)), where C and G denote the numbers of cytosine and guanine residue...
متن کاملMeasures of Compositional Strand Bias Related to Replication Machinery and its Applications
The compositional asymmetry of complementary bases in nucleotide sequences implies the existence of a mutational or selectional bias in the two strands of the DNA duplex, which is commonly shaped by strand-specific mechanisms in transcription or replication. Such strand bias in genomes, frequently visualized by GC skew graphs, is used for the computational prediction of transcription start site...
متن کاملThe Inversion of the Control Region in Three Mitogenomes Provides Further Evidence for an Asymmetric Model of Vertebrate mtDNA Replication
Mitochondrial genomes are known to have a strong strand-specific compositional bias that is more pronounced at fourfold redundant sites of mtDNA protein-coding genes. This observation suggests that strand asymmetries, to a large extent, are caused by mutational asymmetric mechanisms. In vertebrate mitogenomes, replication and not transcription seems to play a major role in shaping compositional...
متن کاملCodon bias patterns in photosynthetic genes of halophytic grass Aeluropus littoralis
Codon bias refers to the differences in the frequency of occurrence of synonymous codons in coding DNA. Pattern of codon and optimum codon utilization is significantly different between the lives. This difference is due to the long term function of natural selection and evolution process. Genetics drift, mutation and regulation of gene expression are the main reasons for codon bias. In this stu...
متن کاملExpression pattern analysis of transcription factors from Aeluropus littoralis in response to salt stress and recovery condition.
Salinity is one of the most important abiotic stresses that decrease crop production. Transcription factors (TFs) are prominent regulators in plant responses to abiotic stress. In the present study, the expression pattern of four salt-induced genes encoding transcription factors, namely, MYB, RF2, GTF, and ARID was studied in response to salt stress (sodium chloride) and recovery conditions. Th...
متن کامل