SSR and transposition

What is site-specific recombination (SSR)?

A type of non-homologous recombination where DNA is rearranged at specific defined sequence elements called recombination or att sites.

How does SSR differ from homologous recombination?

SSR changes gene order and structure using defined recombination sites, while homologous recombination exchanges similar DNA sequences.

What are recombination/att sites?

Specific DNA sequences recognized by recombinases; consist of recombinase signal sequences (RSS) and a central crossover region.

What are the two components of a recombination site?

Recombinase Signal Sequences (RSS) and the crossover region.

What are the three DNA rearrangements that SSR can generate?

Insertions, deletions, and inversions.

What happens when recombination occurs at direct repeats?

The DNA segment between repeats is deleted and appears as a circular molecule.

What is insertion in SSR?

The reverse of deletion—circular DNA reinserts into a recombination site.

What happens when recombination occurs at inverted repeats?

The DNA segment between repeats is inverted.

What are the two major families of site-specific recombinases?

Serine recombinases and tyrosine recombinases.

How do serine recombinases work?

They create simultaneous double-stranded breaks in all four strands, swap DNA segments, then rejoin the DNA.

How do tyrosine recombinases work?

They cleave and rejoin one pair of DNA strands at a time, forming a Holliday junction intermediate.

Give an example of SSR in prokaryotes.

Lambda (λ) phage integration and excision from the bacterial genome.

Give an example of SSR in eukaryotes.

Immunoglobulin (Ig) and T-cell receptor (TCR) gene rearrangements.

Why is SSR important in the immune system?

It generates the enormous diversity of antibodies and TCRs by recombining V, D, and J gene segments.

What proteins initiate V(D)J recombination?

RAG1 and RAG2.

What do RAG1/2 proteins recognize?

Recombination Signal Sequences (RSS) flanking V, D, and J segments.

Where does immunoglobulin light chain rearrangement occur?

In developing B cells in the bone marrow.

Where does T-cell receptor gene rearrangement occur?

In the thymus.

What is transposition?

The movement of mobile DNA elements (transposons) from one DNA site to another without needing homologous sequences.

What are transposable elements?

Mobile sequences of DNA that can move within or between chromosomes.

Who discovered transposons?

Barbara McClintock in maize.

How much of the human genome is derived from transposons?

Approximately 50%.

What general effects can transposons have on gene expression?

They can disrupt genes, alter gene expression, or cause chromosomal mutations.

What are insertion sequences (IS elements)?

Simple prokaryotic transposons carrying only a transposase gene flanked by terminal inverted repeats (IRs).

What are terminal inverted repeats (IRs)?

Short DNA sequences at the ends of transposons that are inverted complements of each other.

What are direct repeats flanking transposons?

Short identical sequences created during insertion of a transposon into the target DNA.

How are direct repeats generated during transposition?

Target site duplication occurs when staggered cuts are made in the target DNA before transposon insertion.

What enzyme mediates DNA excision and insertion during transposition?

Transposase (or integrase for some retrotransposons).

What is a composite transposon?

A transposon containing additional genes such as antibiotic resistance flanked by two IS elements.

What is conservative (cut-and-paste) transposition?

The transposon is excised from the donor site and inserted into a new site without leaving a copy behind.

What is replicative transposition?

The transposon is copied; one copy remains at the donor site and one inserts at a new site.

What is retrotransposition?

Transposition via an RNA intermediate that is reverse-transcribed into cDNA and inserted into DNA.

What genes do retrotransposons typically encode?

Reverse transcriptase and integrase.

What are LTR retrotransposons?

Retrotransposons with long terminal repeats flanking their coding sequences.

What are poly-A retrotransposons?

Non-LTR elements with 5’ and 3’ UTRs and a poly-A tail; includes LINEs and SINEs such as Alu elements.

Are most human transposons active or inactive?

Most are inactive “fossils,” but some LINEs and SINEs still transpose.

How can organisms regulate transposons?

By promoter methylation, protein autoregulation, and other silencing mechanisms.

How can transposons contribute to human disease?

By disrupting genes or regulatory regions, causing insertions, deletions, or chromosomal rearrangements.