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Inter-population Differences in Retrogene Loss and Expression in Humans.

Kabza M, Kubiak MR, Danek A, Rosikiewicz W, Deorowicz S, Polański A, Makałowska I - PLoS Genet. (2015)

Bottom Line: Most of these RDVs resulted from recent retroduplications.In this study, we used the results of Phase 1 from the 1000 Genomes Project to investigate the variation in loss of ancestral (i.e. shared with other primates) retrocopies among different human populations.Altogether, we were able to detect 193 RDVs; the majority resulted from retrocopy deletion.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland.

ABSTRACT
Gene retroposition leads to considerable genetic variation between individuals. Recent studies revealed the presence of at least 208 retroduplication variations (RDVs), a class of polymorphisms, in which a retrocopy is present or absent from individual genomes. Most of these RDVs resulted from recent retroduplications. In this study, we used the results of Phase 1 from the 1000 Genomes Project to investigate the variation in loss of ancestral (i.e. shared with other primates) retrocopies among different human populations. In addition, we examined retrocopy expression levels using RNA-Seq data derived from the Ilumina BodyMap project, as well as data from lymphoblastoid cell lines provided by the Geuvadis Consortium. We also developed a new approach to detect novel retrocopies absent from the reference human genome. We experimentally confirmed the existence of the detected retrocopies and determined their presence or absence in the human genomes of 17 different populations. Altogether, we were able to detect 193 RDVs; the majority resulted from retrocopy deletion. Most of these RDVs had not been previously reported. We experimentally confirmed the expression of 11 ancestral retrogenes that underwent deletion in certain individuals. The frequency of their deletion, with the exception of one retrogene, is very low. The expression, conservation and low rate of deletion of the remaining 10 retrocopies may suggest some functionality. Aside from the presence or absence of expressed retrocopies, we also searched for differences in retrocopy expression levels between populations, finding 9 retrogenes that undergo statistically significant differential expression.

No MeSH data available.


Related in: MedlinePlus

Detection of novel retrocopy deletion sites, example of retrocopy rdn3.(A) Contig and BAC containing its sequence. (B) Alignment with chimpanzee genome. (C) Identification of indel site. F and R refer to forward and reverse primers designed for examined indel site in human genome, respectively.
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pgen.1005579.g007: Detection of novel retrocopy deletion sites, example of retrocopy rdn3.(A) Contig and BAC containing its sequence. (B) Alignment with chimpanzee genome. (C) Identification of indel site. F and R refer to forward and reverse primers designed for examined indel site in human genome, respectively.

Mentions: Detected retrocopies show significant divergence between their sequences and sequences of their parental genes, indicating old retroposition events. We were able to find the orthologs of discovered retrocopies in the chimpanzee and/or gorilla genomes, confirming that they are indeed, ancestral retroduplications that were subsequently lost during human evolution. This analysis also allowed us to determine exact locations and sizes of deletions for retrocopies rdn1, rdn2 and rdn3 (Table 3 and Fig 7).


Inter-population Differences in Retrogene Loss and Expression in Humans.

Kabza M, Kubiak MR, Danek A, Rosikiewicz W, Deorowicz S, Polański A, Makałowska I - PLoS Genet. (2015)

Detection of novel retrocopy deletion sites, example of retrocopy rdn3.(A) Contig and BAC containing its sequence. (B) Alignment with chimpanzee genome. (C) Identification of indel site. F and R refer to forward and reverse primers designed for examined indel site in human genome, respectively.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4608704&req=5

pgen.1005579.g007: Detection of novel retrocopy deletion sites, example of retrocopy rdn3.(A) Contig and BAC containing its sequence. (B) Alignment with chimpanzee genome. (C) Identification of indel site. F and R refer to forward and reverse primers designed for examined indel site in human genome, respectively.
Mentions: Detected retrocopies show significant divergence between their sequences and sequences of their parental genes, indicating old retroposition events. We were able to find the orthologs of discovered retrocopies in the chimpanzee and/or gorilla genomes, confirming that they are indeed, ancestral retroduplications that were subsequently lost during human evolution. This analysis also allowed us to determine exact locations and sizes of deletions for retrocopies rdn1, rdn2 and rdn3 (Table 3 and Fig 7).

Bottom Line: Most of these RDVs resulted from recent retroduplications.In this study, we used the results of Phase 1 from the 1000 Genomes Project to investigate the variation in loss of ancestral (i.e. shared with other primates) retrocopies among different human populations.Altogether, we were able to detect 193 RDVs; the majority resulted from retrocopy deletion.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland.

ABSTRACT
Gene retroposition leads to considerable genetic variation between individuals. Recent studies revealed the presence of at least 208 retroduplication variations (RDVs), a class of polymorphisms, in which a retrocopy is present or absent from individual genomes. Most of these RDVs resulted from recent retroduplications. In this study, we used the results of Phase 1 from the 1000 Genomes Project to investigate the variation in loss of ancestral (i.e. shared with other primates) retrocopies among different human populations. In addition, we examined retrocopy expression levels using RNA-Seq data derived from the Ilumina BodyMap project, as well as data from lymphoblastoid cell lines provided by the Geuvadis Consortium. We also developed a new approach to detect novel retrocopies absent from the reference human genome. We experimentally confirmed the existence of the detected retrocopies and determined their presence or absence in the human genomes of 17 different populations. Altogether, we were able to detect 193 RDVs; the majority resulted from retrocopy deletion. Most of these RDVs had not been previously reported. We experimentally confirmed the expression of 11 ancestral retrogenes that underwent deletion in certain individuals. The frequency of their deletion, with the exception of one retrogene, is very low. The expression, conservation and low rate of deletion of the remaining 10 retrocopies may suggest some functionality. Aside from the presence or absence of expressed retrocopies, we also searched for differences in retrocopy expression levels between populations, finding 9 retrogenes that undergo statistically significant differential expression.

No MeSH data available.


Related in: MedlinePlus