Both selective and neutral processes drive GC content evolution in the human genome.
BACKGROUND
Mammalian genomes consist of regions differing in GC content, referred to as isochores or GC-content domains. The scientific debate is still open as to whether such compositional heterogeneity is a selected or neutral trait.


RESULTS
Here we analyze SNP allele frequencies, retrotransposon insertion polymorphisms (RIPs), as well as fixed substitutions accumulated in the human lineage since its divergence from chimpanzee to indicate that biased gene conversion (BGC) has been playing a role in within-genome GC content variation. Yet, a distinct contribution to GC content evolution is accounted for by a selective process. Accordingly, we searched for independent evidences that GC content distribution does not conform to neutral expectations. Indeed, after correcting for possible biases, we show that intron GC content and size display isochore-specific correlations.


CONCLUSIONS
We consider that the more parsimonious explanation for our results is that GC content is subjected to the action of both weak selection and BGC in the human genome with features such as nucleosome positioning or chromatin conformation possibly representing the final target of selective processes. This view might reconcile previous contrasting findings and add some theoretical background to recent evidences suggesting that GC content domains display different behaviors with respect to highly regulated biological processes such as developmentally-stage related gene expression and programmed replication timing during neural stem cell differentiation.
Pozzoli
Uberto
U
Scientific Institute IRCCS E, Medea, Bioinformatic Lab, Via don L, Monza 20, 23842 Bosisio Parini (LC), Italy. uberto.pozzoli@bp.lnf.it
Menozzi
Giorgia
G
Fumagalli
Matteo
M
Cereda
Matteo
M
Comi
Giacomo P
GP
Cagliani
Rachele
R
Bresolin
Nereo
N
Sironi
Manuela
M
D000818:Animals; D019143:Evolution, Molecular; D020862:GC Rich Sequence; D005787:Gene Frequency; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D032085:Isochores; D002679:Pan troglodytes / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D016415:Sequence Alignment
D032085:Isochores