PSEUDOGENES: Are They "Junk" or Functional DNA?

Pseudogenes have been defined as nonfunctional sequences of genomic DNA originally derived from functional genes. It is therefore assumed that all pseudogene mutations are selectively neutral and have equal probability to become fixed in the population. Rather, pseudogenes that have been suitably in...

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Bibliographic Details
Published in:Annual review of genetics 2003-01, Vol.37 (1), p.123-151
Main Authors: Balakirev, Evgeniy S, Ayala, Francisco J
Format: Article
Language:English
Subjects:
Animals
Base Sequence
Deoxyribonucleic acid
DNA
DNA polymorphism
Drosophila
Drosophila melanogaster
Drosophila melanogaster - genetics
Esterases - genetics
Evolution, Molecular
evolutionary rate
Gene expression
Gene Expression Regulation - physiology
Genes
Genetic Variation
Genomics
Mutation
neutral evolution
potogene
potogenes
Pseudogenes - physiology
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Summary:Pseudogenes have been defined as nonfunctional sequences of genomic DNA originally derived from functional genes. It is therefore assumed that all pseudogene mutations are selectively neutral and have equal probability to become fixed in the population. Rather, pseudogenes that have been suitably investigated often exhibit functional roles, such as gene expression, gene regulation, generation of genetic (antibody, antigenic, and other) diversity. Pseudogenes are involved in gene conversion or recombination with functional genes. Pseudogenes exhibit evolutionary conservation of gene sequence, reduced nucleotide variability, excess synonymous over nonsynonymous nucleotide polymorphism, and other features that are expected in genes or DNA sequences that have functional roles. We first review the Drosophila literature and then extend the discussion to the various functional features identified in the pseudogenes of other organisms. A pseudogene that has arisen by duplication or retroposition may, at first, not be subject to natural selection if the source gene remains functional. Mutant alleles that incorporate new functions may, nevertheless, be favored by natural selection and will have enhanced probability of becoming fixed in the population. We agree with the proposal that pseudogenes be considered as poto genes, i.e., DNA sequences with a pot entiality for becoming new genes.
ISSN:0066-4197
1545-2948
DOI:10.1146/annurev.genet.37.040103.103949