Hypervariable region

Examples of Hypervariable region in the following topics:

• Nucleic Acid Sequencing and rRNA Analysis

  • In these articles, one pair of primers (although many of them are designed, and provide different results) is used to amplify a region of the 16S rRNA gene.
  • In addition to highly conserved primer binding sites, 16S rRNA gene sequences contain hypervariable regions that can provide species-specific signature sequences useful for bacterial identification.

• Antibody Proteins and Antigen Binding

  • Heavy and light chains, variable and constant regions of an antibody
  • The constant region determines the class of an immunoglobulin.
  • This region is known as the hypervariable region.
  • The variable domain is also referred to as the FV region, and is the most important region for binding to antigens.
  • Scheme of an IgM/IgE with its costant (C) and variable (V) regions: 1) antigen binding fragment 2) Fab region 3) Fc regionblue: heavy chainsyellow: light chains

• Antibody Genes and Diversity

  • This region is known as the hypervariable region.
  • The first stage is called somatic, or V(D)J, which stands for variable, diverse, and joining regions recombination.
  • Several sets of genes are located within each of the three regions.
  • This segment, along with a constant region gene, forms the basis for subsequent antibody production.
  • Somatic hypermutation involves a programmed process of mutation affecting the variable regions of immunoglobulin genes.

• T Cell Receptors

  • Each alpha and beta chain consists of one variable domain (V), one constant domain (C), a hydrophobic transmembrane region, and a short cytoplasmic region .
  • The V regions of the TCR contain short stretches of amino acids where the variability between different TCRs is concentrated, and these form the hypervariable or complementarity-determining regions (CDRs).
  • T cell receptor consists of alpha and beta chains, a transmembrane domain, and a cytoplasmic region.

• Retroviral RNA Genome

  • The RNA genome also has terminal noncoding regions, which are important in replication, and internal regions that encode virion proteins for gene expression.
  • The 5' end includes four regions, which are R, U5, PBS, and L.
  • The L region is an untranslated leader region that give the signal for packaging of genome RNA.
  • The 3' end includes 3 regions, which are PPT (polypurine tract), U3, and R.
  • Inbetween the 5' and 3' region is the protein encoding region of the retrovirus, consisting of gag proteins, protease (PR), pol proteins and env proteins.

• Isotype Class Switching

  • During this process, the constant region portion of the antibody-heavy chain is changed, but the variable region of the heavy chain stays the same (the terms "constant" and "variable" refer to changes or lack thereof between antibodies that target different epitopes).
  • Since the variable region does not change, class switching does not affect antigen specificity.
  • Double-stranded breaks are generated in DNA at conserved nucleotide motifs, called switch (S) regions, which are upstream from gene segments that encode the constant regions of antibody-heavy chains; these occur adjacent to all heavy chain constant region genes with the exception of the δ-chain.
  • DNA is nicked and broken at two selected S-regions by the activity of a series of enzymes, including Activation-Induced (Cytidine) Deaminase (AID), uracil DNA glycosylase and apyrimidic/apurinic (AP)-endonucleases.
  • The intervening DNA between the S-regions is subsequently deleted from the chromosome, removing unwanted μ or δ heavy chain constant region exons and allowing substitution of a γ, α or ε constant region gene segment.

• MHC Polymorphism and Antigen Binding

  • Chickens have among the smallest known MHC regions (19 genes).
  • In humans, the MHC region occurs on chromosome 6 .
  • In humans, the MHC is divided into three regions: classes I, II, and III.
  • The polymorphic regions in each allele are located in the region for peptide contact, which is going to be displayed to the lymphocyte.
  • For this reason, the contact region for each allele of MHC molecule is highly variable, as the polymorphic residues of the MHC will create specific clefts in which only certain types of residues of the peptide can enter.

• Size Variation and ORF Contents in Genomes

  • Normally, inserts which interrupt the reading frame of a subsequent region after the start codon cause frameshift mutation of the sequence and dislocate the sequences for stop codons.
  • Long ORFs are often used, along with other evidence, to initially identify candidate protein coding regions in a DNA sequence .
  • The presence of an ORF does not necessarily mean that the region is ever translated.
  • A simple gene prediction algorithm for prokaryotes might look for a start codon followed by an open reading frame that is long enough to encode a typical protein, where the codon usage of that region matches the frequency characteristic for the given organism's coding regions.

• Edible Algae

  • Edible algae have been used as food for centuries in many coastal regions all over the world.
  • Seaweeds are edible algae that have been used for centuries as food in many coastal regions all over the world.

• Slipped-Strand Mispairing

  • One possibility is if the repeats are located in the promoter region at the RNA polymerase binding site, -10 and -35, upstream of the gene(s).
  • The overlapping promoter regions have repeats of the dinucleotide TA in the -10 and -35 sequences.
  • Through SSM the TA repeat region can undergo addition or subtraction of TA dinucleotides which results in the reversible ON phase or OFF phase of transcription of the hifA and hifB.