Glossary

C

• Class I Elements: (see also)
• Class II Elements: (see also)
• Cre Recombinase: The Cre Recombinase is a DNA breaking and rejoining enzyme (from tyrosine recombinase family) derived from the P1 bacteriophage. It is widely used for conditional mutagenesis of transgenes and insert DNA cassettes into eukaryotic chromosomes. (see also).
• Co-integrate:
• Copy-and-paste transposition model:
• Copy-out–Paste-in transposition model:
• Cut-and-paste transposition model:

D

• Direct Repeats (DRs):
• DDE Domain:
• Donor Primed Replicative Transposition (DPRT):

G

• Group II introns: The group II introns are mobile retroelements that use the combined activities of an autocatalytic RNA and an intron-encoded reverse transcriptase (RT) to propagate efficiently within genomes. They are intimately related with the evolution of eukaryotes, being ancestrally related to nuclear spliceosomal introns, retrotransposons and telomerase (see also).
• Genome decay:
• Genome Rearrangements:

H

• Horizontal gene transfer (or Lateral gene transfer):
• Homologous recombination:

I

• Inverted Repeats (IR):
• Integron: Integrons one class of Mobile Genetic Elements (MGEs) are specific genetic structure composed by genes (named as integron cassettes) that generally allow bacteria to adapt and rapidly evolve through the acquisition, stockpiling, excision, and reordering of open reading frames found the integron cassettes. The integron mobilization is mediated by site-specific recombination reactions by the integrase (see also).
• Invertases:

M

• Mobilome:
• Methylase (Methylation):

P

• Plasmidome:
• plasmid F:
• Pseudogenisation:
• Peel-and-paste (Single-strand) transposition model:
• Phage tyrosine integrase:
• Phage serine integrase:

R

• Resolution site:
• Resolvase:
• Rolling-circle transposition model:

S

• Synaptic complex:
• Serine recombinase: The serine recombinases are a family of DNA breaking and rejoining enzymes. Unlike homologous recombination, the serine recombinases promote rearrangements of DNA by breaking and rejoining strands at precisely defined sequence positions (see also).
• Serine Resolvases: The serine resolvases and the closely related invertases, are a group of site-specific recombinases that, in their native contexts, resolve large fused replicons into smaller separated ones
• Single-strand transposition:
• Site-specific recombination:

T

• Target specificity:
• Transposase:
• Transposome:
• Target Primed Replicative Transposition (TPRT):
• Tyrosine recombinase: Tyrosine site-specific recombinases (YRs) are a family of DNA breaking and rejoining enzymes which use the active site tyrosine nucleophile for DNA strand breakage (see also).

V

• V(D)J Recombination:

X

• Xer Site-Specific Recombination:

See also

The logic behind the TEs nomenclature and naming attribution

The first attempt to create an concise nomenclature system for Transposable Elements started at Stanford University by Campbell and colleagues in 1979 . They classified the prokaryotes elements as simple IS elements to more complex Tn transposons, and self-replicating episomes. In addition, definitions and nomenclature rules for these three classes of prokaryotic TEs were specified (see bellow).

TE nomenclature rules defined by Campbell (1979 and colleagues)

Classes	Definition	Naming rule
IS elements	IS elements contain no known genes unrelated to insertion functions, and are shorter than 2kb.	IS1, IS2, IS3, IS4, IS5, etc, with the numbers italicized
Tn elements	Tn are more complex, often containing two copies of an IS element. They are generally larger than 2kb, and contain additional genes unrelated to insertion functions.	Tn1, Tn2, Tn3, etc, with the numbers italicized
Episomes	Episomes are complex, self-replicating elements, often containing IS and Tn elements. Examples include the phage λ and plasmid F of E. coli.	-

Proposed classification system for eukaryotic Transposable Elements (TEs) (extracted from Wicker et al., 2007).