Limits...
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

Frequencies of retro_hsap_1441 absence in different human populations.Maps for all retrocopies are available at http://rhesus.amu.edu.pl/RetrogeneMaps/.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4608704&req=5

pgen.1005579.g001: Frequencies of retro_hsap_1441 absence in different human populations.Maps for all retrocopies are available at http://rhesus.amu.edu.pl/RetrogeneMaps/.

Mentions: Indels that were detected only rarely in populations have, with some exceptions, low frequencies and are observed in 0.5%–2% of alleles. This may suggest that these indels represent either relatively new deletions or deleterious deletions, and thus, were subjected to negative selective pressure. The highest rate of absence was observed in the case of retrogene retro_hsap_1441 (Fig 1). This retrogene is present in about 20% of alleles in Asian populations, in about 50% of the alleles in European and American populations, and in about 70% in populations with African ancestry. The most likely explanation for this phenomenon is the emergence of a new retroposition in Africa, which spread to other continents, or alternatively, a deletion that originated in Asia. However, based on available data we cannot distinguish between these two scenarios.


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)

Frequencies of retro_hsap_1441 absence in different human populations.Maps for all retrocopies are available at http://rhesus.amu.edu.pl/RetrogeneMaps/.
© Copyright Policy
Related In: Results  -  Collection

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

pgen.1005579.g001: Frequencies of retro_hsap_1441 absence in different human populations.Maps for all retrocopies are available at http://rhesus.amu.edu.pl/RetrogeneMaps/.
Mentions: Indels that were detected only rarely in populations have, with some exceptions, low frequencies and are observed in 0.5%–2% of alleles. This may suggest that these indels represent either relatively new deletions or deleterious deletions, and thus, were subjected to negative selective pressure. The highest rate of absence was observed in the case of retrogene retro_hsap_1441 (Fig 1). This retrogene is present in about 20% of alleles in Asian populations, in about 50% of the alleles in European and American populations, and in about 70% in populations with African ancestry. The most likely explanation for this phenomenon is the emergence of a new retroposition in Africa, which spread to other continents, or alternatively, a deletion that originated in Asia. However, based on available data we cannot distinguish between these two scenarios.

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