Bioinformatics Vol. 19 Suppl. 2 2003
page ii35
© 2003 Oxford University Press
How significant is 98.5% ‘junk’ in mammalian genomes?
Institute of Experimental Pathology, University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
Received on March 17, 2003
; accepted on June 9, 2003
Conversion of genetic information from RNA into DNA by
reverse transcription is ancient and was instrumental for the
transition from the RNP world to modern cells (Brosius, 1999a,
Nat. Genet. , 22, 8–9; Brosius, 2003, J.
Struct. Funct. Genom. , 3, 1–17). Surprisingly, in
many eukaryotic lineages, the process of retroposition is still very
active. All types of RNAs (Brosius, 1999b, Gene ,
238, 115–134) can be reverse transcribed and their cDNA
copies reintegrated into genomes as retronuons (a nuon is any
discrete segment of nucleic acid (Brosius and Gould, 1992, Proc.
Natl Acad. Sci. USA , 89, 10706–10710)). About 38%
or 42% of the mouse and human genomes, respectively, consist of
discernible retronuons (excluding mRNA-derived retroposons). Only
1.5% of the human genome consists of exons coding for proteins. Even
considering DNA transposons (
1–3% discernible),
slippage during replication and a relatively large fraction derived
from segmental duplications it is conceivable that the remainder of
mammalian genomes is probably derived from ancient, today
non-discernible retronuons. Hence, the vast majority of mammalian
genomes have been contributed by retroposition. Retroposition
predominantly leads to ‘junk DNA’. However, mRNA-derived
retronuons are known to give rise to active genes, often with
different expression patterns than their respective founder genes
(Brosius and Gould, 1992, Proc. Natl Acad. Sci. USA ,
89, 10706–10710; Brosius, 1991, Science ,
251, 753). Retronuons derived from small non-messenger RNAs
(snmRNAs) generate novel snmRNA genes (such as the neuron-specific
BC1 and BC200 RNAs) (Brosius, 1999b, Gene , 238,
115–134; Brosius and Gould, 1992, Proc. Natl Acad. Sci.
USA , 89, 10706–10710). Frequently, retronuons are
exapted (co-opted) as regulatory elements that may alter expression
or processing of targeted genes (Brosius and Gould, 1992, Proc.
Natl Acad. Sci. USA , 89, 10706–10710) (for
compilations see http://www-ifi.uni-muenster.de/exapted-retrogenes/tables.html).
Consequently, retronuons are a major driving force of evolution and
perhaps even speciation. Comparison of the human genome with that of
other mammals such as mouse or, in particular, chimpanzee reveals
that neither contains numerous additional genes. Instead, one
observes exaptation of novel exons (often involving alternative
splicing) from previously nonaptive intronic (as predicted by
Gilbert, 1978, Nature , 271, 501) or flanking
sequences originally generated by retroposition. Furthermore, the
differential expression of shared genes with respect to developmental
onset and/or cell-type specificity, that is triggered by de
novo insertions of retronuons, will turn out to be a recurrent
theme in species differences at the genomic level.
Contact: RNA.world{at}uni-muenster.de
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  C. Knibbe, A. Coulon, O. Mazet, J.-M. Fayard, and G. Beslon A Long-Term Evolutionary Pressure on the Amount of Noncoding DNA Mol. Biol. Evol., October 1, 2007; 24(10): 2344 - 2353. [Abstract] [Full Text] [PDF]
|
|