IDCHPRIMATESDS

Identification and characterization of primate-specific duplications and an assessment of intra-specific patterns of selection and copy-number variation

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 Obiettivo del progetto (Objective)

'Segmental Duplications (SDs) can be defined as blocks of DNA ranging from 1-400kb in length with copies found in multiple sites and typically share high sequence similarity (>90%). Studies based in both experimental and computational analyses show that ~5% of the human genome is composed of duplicated sequences. More generally, primate genomes have been found enriched for this complex patterns of interspersed segmental duplications.This 5% of euchromatin differs in structure and content between closely related primates and is not easily resolved by whole-genome shotgun sequence assembly methods.This proposal focuses on this 5% of the genome that historically has been the most difficult for sequence and assembly.The aim of this research is to reconstruct the evolutionary history of all primate segmental duplications in 6 species of primates (Human, Chimpanzee, Orangutan, Gibbon and Macaque and Marmoset) and to understand gene innovations that have emerged within these dynamic genomic regions. The Main goals of the proposal are: 1.SDs detection and analysis of non-human primate genomes. 2.SDs validation (by means of FISH and CGH arrays hybridizations) 3.Analyze species-specific functional elements and their polymorphism and divergence patterns The proposed work not only can assist/direct efforts in these regions but serve as a benchmark of the quality of the final sequenced genomes, and, as such, benefit the genomics/evolutionary/genetics community as a whole. The long-term goal is to create an integrated view of the evolution of primate segmental duplications by studying changes in the composition, frequency, size and location at the major branchpoints in the primate phylogeny. This work has the ancillary benefit that it will provide inssight the origin of SD structure associated with genomic disease and characterize lineage-specific genes relevant to realization of these primates as models of human disease and to the adaptation of these species.'

Introduzione (Teaser)

The genetic link between human beings and other primates has been investigated by European researchers to gain greater understanding of among other things the human genome.

Descrizione progetto (Article)

Segmental duplications (SDs) are sections of DNA with almost identical sequences which are believed to have played a role in creating new primate genes. This can be witnessed in human genetic variation. Experimental and computer analysis shows that around 5% of the humane genome, which contains all of a person's hereditary information, consists of SDs.

The EU-funded IDCHPRIMATESDS project is reconstructing the evolutionary history of all primate SDs in six primate species, including humans, chimpanzees, orangutans, gibbons, macaques and marmosets. The aim of the project is to shed light on the genetic innovations that have emerged from within these dynamic genomic regions.

Molecular biologists are using fluorescence in situ hybridisation (FISH) and comparative genomic hybridisation technology (CGH) to identify and study non-human primate genomes. The primate genetic material is examined for unique features, such as polymorphism which involves different forms of the same species, together with patterns of genetic divergence.

Researchers have addressed the question of polymorphism within primates, by determining how different regions of the genome behave compared to other forms of mutations. The results have shown that with regards to SDs humans are less polymorphic than the chimpanzees and orangutans.

A structural map can be created for each non-human primate species which indicates those regions that show variation when compared to the organisation of the human genome. This work can help scientists to better understand the evolutionary origin and selection on these regions.

Regions of the genome enriched for SD can contribute to disease, the emergence of novel genes and significant genetic differences between and within species. Therefore, the work carried out by the project can help provide greater insight into the human genome and genetic disorders and possible treatments.