Related Experiment Video
Updated: Aug 8, 2026
10:50
Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
Published on: September 15, 2010
Predicting regional mutability in antibody V genes based solely on di- and trinucleotide sequence composition
G S Shapiro1, K Aviszus, D Ikle
1Department of Pediatrics, Division of Basic Sciences, National Jewish Medical and Research Center, Denver, CO 80206, USA.
Journal of Immunology (Baltimore, Md. : 1950)
|June 29, 1999
Summary
Somatic mutations in immunoglobulin V genes show a consistent sequence bias across species. This suggests a shared mutation mechanism influences antibody gene evolution in both mice and humans.
Area of Science:
- Immunology
- Genetics
- Molecular Biology
Background:
- Somatic mutations in immunoglobulin V genes are crucial for antibody diversity.
- The distribution of these mutations is not random and suggests sequence-specific targeting.
Purpose of the Study:
- To investigate the sequence-specific mutational bias in immunoglobulin V genes across species.
- To determine if a common mutation mechanism underlies regional mutability patterns in human and mouse Ig V genes.
Main Methods:
- Analysis of di- and trinucleotide mutability patterns in intronic DNA of mouse JH and Jkappa clusters and human VH genes.
- Prediction of regional mutabilities in human and murine germline V genes using identified target preferences.
- Comparison of predicted mutabilities with empirical mutation data from nonproductively rearranged human VH genes.
Main Results:
- A shared di- and trinucleotide mutability preference pattern was identified in mouse and human Ig V genes, indicating a common mutation mechanism.
- Heavy chain genes in both species show higher predicted mutability in CDR1, CDR2, and FR3 compared to FR1 and FR2.
- Light chain genes exhibit an unexpected high mutability prediction for FR2.
Conclusions:
- A common mutation mechanism with regional bias exists for both heavy and light chain immunoglobulin V genes in mice and humans.
- Short nucleotide sequence composition qualitatively, but not quantitatively, explains the observed regional mutational preferences.
More Related Videos
Related Concept Videos
00:36Viral Mutations
A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material for adaptive...
02:05Gene Evolution - Fast or Slow?
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
02:13Overview of Transposition and Recombination
Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
02:53Conservative Site-specific Recombination and Phase Variation
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
The recognition sites for Cre recombinase called LoxP...
02:51Multi-species Conserved Sequences
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...