DNA Repair Mechanisms and Transposon Dynamics

Mismatch Repair (MMR)

Corrects mispaired bases after DNA replication.

Photoreactivation

Uses light to repair UV-induced DNA damage.

Excision Repair

Removes damaged DNA strand, replaces with new.

Base Excision Repair (BER)

Repairs single base damage, replaces 2-10 nucleotides.

Nucleotide Excision Repair (NER)

Repairs bulky DNA lesions like UV-induced dimers.

Transcription-Coupled Repair (TC-NER)

Repairs damage in active gene transcribed strands.

Global Genome Repair (GG-NER)

Repairs damage anywhere in the genome.

Recombination-Repair Systems

Uses recombination to replace damaged double-stranded DNA.

Error-Prone Repair

Repair polymerases synthesize DNA with potential errors.

Mutator

Gene increasing mutation rates, often DNA repair-related.

GATC Methylation

Distinguishes parental from daughter DNA strands.

E. coli Uvr System

Incises damaged DNA, excises, and resynthesizes it.

Xeroderma Pigmentosum (XP)

Disease from mutations in nucleotide excision repair genes.

Glycosylases

Enzymes that remove damaged bases from DNA.

Uracil DNA Glycosylase

Removes uracil from DNA, preventing mutations.

RecA Protein

Triggers SOS response for DNA repair mechanisms.

Nonhomologous End-Joining (NHEJ)

Repairs double-strand breaks by ligating blunt ends.

Chromatin Remodeling

Essential for DNA damage repair in chromatin context.

Histone Modification

Changes in histones that regulate DNA repair processes.

Rad51 Protein

Forms nucleoprotein filament for homologous recombination.

LexA Protein

Represses SOS response, activated by RecA autocleavage.

Polδ/ε Pathway

Replaces long stretches of polynucleotides in repair.

Polβ Pathway

Replaces short stretches of polynucleotides in repair.

Deamination

Conversion of cytosine to uracil or thymine.

Single-Strand Exchange

Uses another duplex to replace gaps in DNA.

MRN Complex

Required for forming single-stranded regions in repair.

TFIIH

Transcription factor involved in nucleotide excision repair.

Repair Genes

Genes responsible for various DNA repair mechanisms.

Replication Errors

Mismatched base pairs introduced during DNA replication.

transposon

A DNA sequence able to insert itself (or a copy of itself) at a new location in the genome without having any sequence relationship with the target locus.

retrovirus

An RNA virus with the ability to convert its sequence into DNA by reverse transcription.

retrotransposon

A transposon that mobilizes via an RNA form; the DNA element is transcribed into RNA, and then reverse-transcribed into DNA, which is inserted at a new site in the genome. It does not have an infective (viral) form.

insertion sequence

A transposon that codes for the enzyme(s) needed for transposition flanked by short inverted terminal repeats.

direct repeat

The target site at which a transposon is inserted is duplicated during the insertion process, characterized by two repeats in direct orientation at the ends of the transposon.

length of direct repeat

5 to 9 bp, characteristic for any particular transposon.

transposase

The enzyme which recognizes the inverted repeats and is responsible for transposition.

composite transposon

Transposons that have a central region flanked by an IS element at each end and can carry other genes in addition to those coding for transposition.

replicative transposition

A mechanism of transposition where the transposon is copied and inserted into a new location.

non-replicative transposition

A mechanism of transposition where the transposon is cut from one location and pasted into another.

conservative transposition

A type of non-replicative transposition where every bond is preserved.

homologous recombination

A process that can cause rearrangement of host DNA through multiple copies of a transposon.

strand transfer complex

A structure formed during transposition where the transposon is connected to the target site through one strand at each end.

Tn10

A transposon that does not transpose when there are multiple copies in the same cell and preferentially jumps in actively dividing cells.

anti-sense RNA

RNA that is complementary to a sense strand of RNA and can regulate gene expression.

Mu (mutator)

A lysogenic bacteriophage and a large DNA transposon that is immune to insertion within and proximal to its insertion site.

autonomous transposons

Transposons that can catalyze their own transposition.

nonautonomous transposons

Transposons that cannot catalyze transposition but can transpose when an autonomous element provides the necessary proteins.

Ac (activator) element

An autonomous transposable element in maize.

Ds element

A nonautonomous transposable element in maize, related to the autonomous activator (Ac) element.

reverse transcriptase

An enzyme that uses single-stranded RNA as a template to synthesize a complementary DNA strand.

integrase

An enzyme responsible for site-specific recombination that inserts one molecule of DNA into another.

gag, pol, and env

The three genes of a typical retrovirus, with Gag and Pol proteins translated from a full-length transcript of the genome.

frameshift

A process required for the translation of Pol, caused by the ribosome.

replication-defective virus

A virus that cannot perpetuate an infective cycle because some of the necessary genes are absent or mutated.

LTR retrotransposons

Retrotransposons that mobilize via an RNA that is similar to retroviral RNA but does not form an infectious particle.

LINEs

A major class of retrotransposons that occupy about 21% of the human genome.

SINEs

A major class of short (less than 500 bp) nonautonomous retrotransposons that occupy about 13% of the human genome.

Alu element

One of a set of dispersed, related sequences, each about 300 bp long, in the human genome (members of the SINE family).