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. CONCLUSION: 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.

Both selective and neutral processes drive GC content evolution in the human genome / U. Pozzoli, G. Menozzi, M. Fumagalli, M. Cereda, G.P. Comi, R.A. Cagliani, N. Bresolin, M. Sironi. - In: BMC EVOLUTIONARY BIOLOGY. - ISSN 1471-2148. - 8:1(2008 Mar 27), pp. 99.1-99.12. [10.1186/1471-2148-8-99]

Both selective and neutral processes drive GC content evolution in the human genome

M. Cereda;G.P. Comi;R.A. Cagliani;N. Bresolin;M. Sironi
2008

Abstract

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. CONCLUSION: 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.
biased gene conversion; warm-blooded vertebrates; mammalian genomes; noncoding DNA; isochores; recombination; ALU; expression; sequences; database
Settore MED/26 - Neurologia
27-mar-2008
Article (author)
File in questo prodotto:
File Dimensione Formato  
1471-2148-8-99.pdf

accesso aperto

Tipologia: Publisher's version/PDF
Dimensione 917.03 kB
Formato Adobe PDF
917.03 kB Adobe PDF Visualizza/Apri
Pubblicazioni consigliate

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/57479
Citazioni
  • ???jsp.display-item.citation.pmc??? 28
  • Scopus 50
  • ???jsp.display-item.citation.isi??? 44
social impact