Genetic differences that specify unique aspects of human evolution have typically been identified by comparative analyses between the genomes of humans and closely related primates, including more recently the genomes of archaic hominins. Not all regions of the genome, however, are equally amenable to such study. Recurrent copy number variation (CNV) at chromosome 16p11.2 accounts for approximately 1% of cases of autism and is mediated by a complex set of segmental duplications, many of which arose recently during human evolution. Here we reconstruct the evolutionary history of the locus and identify bolA family member 2 (BOLA2) as a gene duplicated exclusively in Homo sapiens. We estimate that a 95-kilobase-pair segment containing BOLA2 duplicated across the critical region approximately 282 thousand years ago (ka), one of the latest among a series of genomic changes that dramatically restructured the locus during hominid evolution. All humans examined carried one or more copies of the duplication, which nearly fixed early in the human lineage-a pattern unlikely to have arisen so rapidly in the absence of selection (P < 0.0097). We show that the duplication of BOLA2 led to a novel, human-specific in-frame fusion transcript and that BOLA2 copy number correlates with both RNA expression (r = 0.36) and protein level (r = 0.65), with the greatest expression difference between human and chimpanzee in experimentally derived stem cells. Analyses of 152 patients carrying a chromosome 16p11.2 rearrangement show that more than 96% of breakpoints occur within the H. sapiens-specific duplication. In summary, the duplicative transposition of BOLA2 at the root of the H. sapiens lineage about 282 ka simultaneously increased copy number of a gene associated with iron homeostasis and predisposed our species to recurrent rearrangements associated with disease.

Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility / X. Nuttle, G. Giannuzzi, M.H. Duyzend, J.G. Schraiber, I. Narvaiza, P.H. Sudmant, O. Penn, G. Chiatante, M. Malig, J. Huddleston, C. Benner, F. Camponeschi, S. Ciofi Baffoni, H.A.F. Stessman, M.C.N. Marchetto, L. Denman, L. Harshman, C. Baker, A. Raja, K. Penewit, N. Janke, W. Joyce Tang, M. Ventura, L. Banci, F. Antonacci, J.M. Akey, C.T. Amemiya, F.H. Gage, A. Reymond, E.E. Eichler. - In: NATURE. - ISSN 0028-0836. - 536:7615(2016), pp. 205-209. [10.1038/nature19075]

Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility

G. Giannuzzi;
2016

Abstract

Genetic differences that specify unique aspects of human evolution have typically been identified by comparative analyses between the genomes of humans and closely related primates, including more recently the genomes of archaic hominins. Not all regions of the genome, however, are equally amenable to such study. Recurrent copy number variation (CNV) at chromosome 16p11.2 accounts for approximately 1% of cases of autism and is mediated by a complex set of segmental duplications, many of which arose recently during human evolution. Here we reconstruct the evolutionary history of the locus and identify bolA family member 2 (BOLA2) as a gene duplicated exclusively in Homo sapiens. We estimate that a 95-kilobase-pair segment containing BOLA2 duplicated across the critical region approximately 282 thousand years ago (ka), one of the latest among a series of genomic changes that dramatically restructured the locus during hominid evolution. All humans examined carried one or more copies of the duplication, which nearly fixed early in the human lineage-a pattern unlikely to have arisen so rapidly in the absence of selection (P < 0.0097). We show that the duplication of BOLA2 led to a novel, human-specific in-frame fusion transcript and that BOLA2 copy number correlates with both RNA expression (r = 0.36) and protein level (r = 0.65), with the greatest expression difference between human and chimpanzee in experimentally derived stem cells. Analyses of 152 patients carrying a chromosome 16p11.2 rearrangement show that more than 96% of breakpoints occur within the H. sapiens-specific duplication. In summary, the duplicative transposition of BOLA2 at the root of the H. sapiens lineage about 282 ka simultaneously increased copy number of a gene associated with iron homeostasis and predisposed our species to recurrent rearrangements associated with disease.
Animals; Autistic Disorder; Chromosome Breakage; Chromosomes; Human; Pair 16; DNA Copy Number Variations; Gene Duplication; Homeostasis; Humans; Iron; Pan troglodytes; Pongo; Proteins; Recombination; Genetic; Species Specificity; Time Factors; Evolution; Molecular; Genetic Predisposition to Disease; Medicine (all); Multidisciplinary
Settore BIO/18 - Genetica
Article (author)
File in questo prodotto:
File Dimensione Formato  
2016 Nuttle.pdf

accesso aperto

Tipologia: Publisher's version/PDF
Dimensione 3.39 MB
Formato Adobe PDF
3.39 MB Adobe PDF Visualizza/Apri
Pubblicazioni consigliate

Caricamento 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: http://hdl.handle.net/2434/863072
Citazioni
  • ???jsp.display-item.citation.pmc??? 46
  • Scopus 68
  • ???jsp.display-item.citation.isi??? 67
social impact