06 - Pseudogenes

• non-function DNA sequences

• derived from functional genes —> degenerative mutations:

  • premature stop codon

  • frameshift

  • —> prevent expression

• Types:

  • conventional

  • processed

Genes that mutated and became non functional pseudogenes

1. duplication of A gene —> 2 equivalent gene copies

2. Selection pressure on one copy (still have original function)

3. other may have mutations —> non-functional pseudogene

—> A2 genes may have different advantageous function -> selection pressure back

• Origin:

  • arise from reverse transcription of mRNA (retrotransposed)

  • subsequent integration back into the genome

  • lack introns and regulatory elements

• Characteristics:

  • non-functional

  • often containing sequence errors or truncations

  • lack the necessary promoters for gene expression

• might interfere with experiments

  • PCR and hybridization experiments

  • transcribed pseudogenes

  • interference with disease diagnostics and treatment

• molecular record of dynamics and evolution of genomes

  • rate of nucleotide substitutions

  • rate of DNA loss

• improvement of gene prediction and annotation efforts

• true:

  1. high sequence similarity with known protein

  2. alignment with functional sequence —> no gaps longer than 60bp

  3. covers >70% of the protein-coding sequence (CDS)

  4. contains frame disruptions such as frameshifts or in-frame stop codons

• putative

  • only true 1-3

  • —> probably young processed pseudogenes that were inserted into the genome so recently that they have not accumulated frame disruptions yet

• disrupted

  • true 2 not fulfilled

At least 8000

• measure for natural selection of genes/proteins

• Ka = # asynchronous base mutation —> different AA

• Ks = # synchronous base mutation —> same AA

• if Ka bigger than Ks —> positive selection

  • e.g. genes in host immune system coevolve with pathogen proteins

• pseudogenes: non-functional -> no selection pressure -> Ka/Ks ~ 1