Related Experiment Video
Updated: Dec 16, 2025
14:26
Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
Published on: April 4, 2016
25.7K
The maximality of circular codes in genes statistically verified
1Theoretical Bioinformatics, ICube, CNRS, University of Strasbourg, 300 Boulevard Sébastien Brant, 67400 Illkirch, France.
Bio Systems
|July 6, 2020
Summary
Circular codes in genes exhibit a maximal property with 20 preferred trinucleotides per frame. This finding, statistically verified in bacteria and eukaryotes, offers insights into genetic code evolution.
Area of Science:
- Genetics
- Bioinformatics
- Computational Biology
Background:
- The genetic code's structure and evolution are fundamental to molecular biology.
- Circular codes represent a specific combinatorial property observed in genetic sequences.
- Understanding trinucleotide frequencies is crucial for analyzing gene organization.
Purpose of the Study:
- To investigate the maximality property of circular codes in genes.
- To statistically verify the occurrence of 20 preferential trinucleotides in each reading frame.
- To explore the relationship between circular codes, codon usage, and genetic code evolution.
Main Methods:
- Statistical verification of trinucleotide occurrence frequencies.
- Analysis of gene populations in bacteria and eukaryotes.
- Comparison of classical (population-level) and recent (gene-level) frequency computation methods.
- Examination of historical and theoretical aspects of comma-free and circular codes.
Main Results:
- The maximality of circular codes, characterized by 20 preferential trinucleotides per frame, was statistically confirmed.
- Both classical and recent methods validated this combinatorial property across bacterial and eukaryotic genes.
- The study highlights limitations of the codon usage parameter in identifying circular codes.
Conclusions:
- Circular codes possess a statistically significant maximal property related to trinucleotide frequencies.
- This property is conserved across different domains of life (bacteria and eukaryotes).
- A model of evolutionary trinucleotide permutation is proposed to explain transitions between different circular codes.
Related Concept Videos
02:33Combinatorial Gene Control
9.3K
Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
9.3K
03:06From DNA to Protein
21.5K
The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...
21.5K
02:26Comparing Copy Number Variations and SNPs
18.4K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
18.4K
02:37Gene Duplication and Divergence
7.6K
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
7.6K
01:49Hardy-Weinberg Principle
75.6K
Diploid organisms have two alleles of each gene, one from each parent, in their somatic cells. Therefore, each individual contributes two alleles to the gene pool of the population. The gene pool of a population is the sum of every allele of all genes within that population and has some degree of variation. Genetic variation is typically expressed as a relative frequency, which is the percentage of the total population that has a given allele, genotype or phenotype.
75.6K
03:21Genome Size and the Evolution of New Genes
8.8K
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
8.8K