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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

Retroposition events in Eutheria.Left boxes show number of retrocopies originated in a given lineage ancestors’ genome; right boxes show number of retrocopies detected in the human genome.
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pgen.1005579.g002: Retroposition events in Eutheria.Left boxes show number of retrocopies originated in a given lineage ancestors’ genome; right boxes show number of retrocopies detected in the human genome.

Mentions: In the case of retroposition, a reciprocal sequence similarity search is not sufficient to establish orthology, since many genes undergo independent retroduplication in different species [20]. Hence, in order to pinpoint orthologous retrocopies we used information concerning the location of retrocopies identified by us in mammalian genomes [19] and mapped them on the genomic sequences alignments using Ensembl release 73. First, we checked for orthologous genes in major mammalian lineages. We classified a retrocopy as common for a lineage if it was observed in any two species from this lineage. The requirement of retrocopy presence in a minimum of two but not necessarily all genomes is based on the assumption that the probability of independent retroposition of the same gene at the same location is close to zero. Using this approach, we identified as many as 1,282 retroposition events that took place in the Hominidae ancestor genome. As many as 510 retropositions are common to Catarrhini, and 360 to primates. In comparison, we did not detect any retrocopies common to Glires and only 84 shared by mouse and rat (Fig 2). This analysis confirms a burst of retroposition in Primates and shows that it was especially intensive in Hominidae [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)

Retroposition events in Eutheria.Left boxes show number of retrocopies originated in a given lineage ancestors’ genome; right boxes show number of retrocopies detected in the human genome.
© Copyright Policy
Related In: Results  -  Collection

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

pgen.1005579.g002: Retroposition events in Eutheria.Left boxes show number of retrocopies originated in a given lineage ancestors’ genome; right boxes show number of retrocopies detected in the human genome.
Mentions: In the case of retroposition, a reciprocal sequence similarity search is not sufficient to establish orthology, since many genes undergo independent retroduplication in different species [20]. Hence, in order to pinpoint orthologous retrocopies we used information concerning the location of retrocopies identified by us in mammalian genomes [19] and mapped them on the genomic sequences alignments using Ensembl release 73. First, we checked for orthologous genes in major mammalian lineages. We classified a retrocopy as common for a lineage if it was observed in any two species from this lineage. The requirement of retrocopy presence in a minimum of two but not necessarily all genomes is based on the assumption that the probability of independent retroposition of the same gene at the same location is close to zero. Using this approach, we identified as many as 1,282 retroposition events that took place in the Hominidae ancestor genome. As many as 510 retropositions are common to Catarrhini, and 360 to primates. In comparison, we did not detect any retrocopies common to Glires and only 84 shared by mouse and rat (Fig 2). This analysis confirms a burst of retroposition in Primates and shows that it was especially intensive in Hominidae [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