Transposons Mol Gen

Transposable Elements

Lecture Objectives

• Types of Transposons: Distinguish among various transposons and retroviruses.

• Mechanisms of Transposition: Describe how transposition occurs and its consequences.

• DNA Rearrangements: Explain how transposons induce DNA rearrangements.

• Transposition Mechanisms: Outline both replicative and nonreplicative transposition processes.

• Transposon Families: Describe different transposition families and superfamilies.

• Hybrid Dysgenesis: Explain the role of transposable elements in hybrid dysgenesis.

• P Elements Activation: Describe activation of P elements in the germline.

• Comparison: Compare and contrast retroviruses with transposons.

• Retroelements: Define and describe classes of retroelements including yeast Ty elements, the Alu family, LINEs, and SINEs.

Introduction

• Transposon Definition:

  • A sequence of DNA that can insert itself at new genome locations without sequence similarity to the target locus.

• Retrovirus Definition:

  • An RNA virus that converts its RNA sequence into DNA via reverse transcription.

  • Movement of transposons significantly affects genome sequence change.

• Retrotransposon:

  • A DNA element that mobilizes via RNA, transcribed into RNA, reverse-transcribed into DNA, and inserted elsewhere in the genome.

• LTR & Non-LTR Retrotransposons:

  • Retrotransposons with long terminal repeats (LTRs) are traditional retrotransposons; those without LTRs are termed retroposons.

Insertion Sequences as Transposition Modules

• Insertion Sequence (IS):

  • A transposon encoding enzymes for transposition, flanked by short inverted terminal repeats.

  • During insertion, the target site is duplicated, forming direct repeats (5-9 bp long).

• Transposase:

  • The enzyme responsible for the insertion of the transposon at a new genomic site.

Transposition Mechanisms

• Common Mechanism:

  • Transposons typically cause staggered nicks in target DNA to integrate by joining protruding ends, followed by gap filling.

• Replicative vs Nonreplicative:

  • Order of events and connections in integration differentiate whether transposition is replicative (duplicating the transposon) or nonreplicative (moving the transposon).

• Resolvase:

  • Enzyme facilitating site-specific recombination between duplicated transposons.

• Composite Transposons:

  • Comprise two IS elements with intervening sequences, often conferring traits like antibiotic resistance.

Transposons Rearranging DNA

• Homologous Recombination: Leads to rearrangement through transposon copies.

• Erosion Mechanism: Precise or imprecise transposon excision can occur.

Replicative Transposition via Cointegrate

• Cointegrate Formation: A fusion of donor and target DNA containing two copies of the transposon.

• Resolution Process: Recombination restores original replicons while adding a transposon copy to the recipient.

Nonreplicative Transposition: Breakage and Reunion

• Mechanism: Crossover structures can modify donor strands leading to transposon transfer.

  • Varied pathways depend on whether transposon strands are joined prior to or after cutting.

Superfamilies and Families of Transposons

• Classification: Superfamilies defined by transposase sequence; comprise autonomous and nonautonomous members.

  • Autonomous Transposons: Code for necessary proteins to transpose.

  • Nonautonomous Transposons: Need autonomous counterparts for transposition functions.

• Key Elements in Maize:

  • Ac Element: Autonomous transposable element.

  • Ds Element: Nonautonomous transposable element related to Ac.

Role in Hybrid Dysgenesis

• Hybrid Dysgenesis: Sterility in the hybrids of certain D. melanogaster strains due to transposon activity.

  • P elements in P strains trigger transposition in M female crosses, leading to gene inactivation and infertility.

Activation of P Elements in Germline

• Activation Mechanism: Tissue-specific splicing activates P elements in certain crosses.

• Maternal Inheritance: Presence of transposition repressors from the maternal side influences fertility outcomes in cross scenarios.

Retrovirus Life Cycle and Related Events

• Retrovirus Structure: Two copies of single-stranded RNA genome that integrates into double-stranded DNA.

• Provirus- integrated double stranded DNA sequence

  • a retrovirus generates it by reverse transcription of retroviral genome

• Key Enzymes:

  • Reverse Transcriptase: Synthesizes DNA from RNA template.

  • Integrase: Responsible for inserting DNA into the host genome.

Retroviral Genes and Polyproteins

• Gene Composition: Retroviruses typically express gag, pol, and env as polyproteins through unique translation processes.

  • proteases process these proteins to give multiple proteins

Viral DNA From Reverse Transcription

• Genomic Organization: DNA ends marked by direct repeats crucial for integration into the host genome.

Retrotransduction and Gene Replacement

• Transformation Events: Sometimes involve host gene replacement through recombination, generating replication-defective viruses needing helper viruses for replication.

• Plus strand virus- A virus with a single- stranded nucleic acid genome whose sequence directly codes for the protein product

• minus strand DNA – The single-stranded DNA sequence that is complementary to the viral RNA genome of a plus strand virus

Viral DNA Integrates into the Chromosome

• The organization of proviral DNA in a chromosome is the same as a transposon, with the provirus flanked by short direct repeats of a sequence at the target site.

• Linear DNA is inserted directly into the host chromosome by the retroviral integrase enzyme.

• Two base pairs of DNA are lost from each end of the retroviral sequence during the integration reaction

Retroviruses May Transduce Cellular Sequences

• Transforming retroviruses are generated by a recombination event in which a cellular RNA sequence replaces part of the retroviral RNA

• replication-defective virus – A virus that cannot perpetuate an infective cycle because some of the necessary genes are absent (replaced by host DNA in a transducing virus) or mutated.
  • A helper virus may be necessary for replication, providing essential functions that the replication-defective virus lacks, thereby enabling the transduction of cellular sequences and facilitating the integration of these sequences into the host genome.

Classifications of Retroelements

• Three Classes:

  • LTR retrotransposons, LINEs, and SINEs, with significant occupancy in the human genome.

  • Alu Elements: Short, dispersed sequences linked to the SINE family.

• Long-interspersed nuclear elements (LINEs)- class of retrotransposon that occupy 21% of human genome

Yeast Ty Elements

• Structure: Resemble endogenous retroviruses and transpose via an RNA intermediate.

Alu Family Dominance

• Composition: Major repetitive component in mammalian genomes linked to RNA polymerase III transcripts.

LINEs Endonuclease Function

• Mechanism: Nicking target DNA for reverse transcription initiation, showcasing their unique mobilization method.