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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

Agarose gel results for novel retrogenes.Left side of figure (column 1) represents presence or absence of novel retrogenes in 17 examined genomes. Agarose gels on the right side of figure (column 2) show PCR products corresponding to the region of deletion. This indicates homo- or heterozygotic character of 17 studied individuals. Lane 1 –GeneRuler 100 bp Plus DNA Ladder or GeneRuler 1 kb DNA Ladder (Thermo Scientific); lanes 2–18 –genomic DNA templates (see S1 Table for details), lane 19 –negative control (water instead of DNA).
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pgen.1005579.g008: Agarose gel results for novel retrogenes.Left side of figure (column 1) represents presence or absence of novel retrogenes in 17 examined genomes. Agarose gels on the right side of figure (column 2) show PCR products corresponding to the region of deletion. This indicates homo- or heterozygotic character of 17 studied individuals. Lane 1 –GeneRuler 100 bp Plus DNA Ladder or GeneRuler 1 kb DNA Ladder (Thermo Scientific); lanes 2–18 –genomic DNA templates (see S1 Table for details), lane 19 –negative control (water instead of DNA).

Mentions: To confirm the identified retrocopies and their deletions in some individuals, we performed PCR on 17 human genomes supplied by the 1000 Genome Project (Coriell Cell Repositories). Individuals were selected based on previous bioinformatic analyses, and each originated from a different population. Using primers from identified retrocopy sequences, we confirmed the existence of four retrocopies (rdn1–rdn4). Retrocopy rdn5 contains a large number of repetitive sequences. Therefore, we could not obtain a product specific enough to confirm the presence of this particular retrocopy: it was excluded from further studies. However, we were able to prove the deletions of retrocopies rdn1 to 3 in some individuals. Apparently, retrocopy rdn4 was present in all investigated genomes. In addition, utilizing primers designed from the flanking regions of the deletion, we confirmed the size of the deleted regions (Table 3), as well as the homo- and heterozygosity of the studied individuals (Fig 8).


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)

Agarose gel results for novel retrogenes.Left side of figure (column 1) represents presence or absence of novel retrogenes in 17 examined genomes. Agarose gels on the right side of figure (column 2) show PCR products corresponding to the region of deletion. This indicates homo- or heterozygotic character of 17 studied individuals. Lane 1 –GeneRuler 100 bp Plus DNA Ladder or GeneRuler 1 kb DNA Ladder (Thermo Scientific); lanes 2–18 –genomic DNA templates (see S1 Table for details), lane 19 –negative control (water instead of DNA).
© Copyright Policy
Related In: Results  -  Collection

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

pgen.1005579.g008: Agarose gel results for novel retrogenes.Left side of figure (column 1) represents presence or absence of novel retrogenes in 17 examined genomes. Agarose gels on the right side of figure (column 2) show PCR products corresponding to the region of deletion. This indicates homo- or heterozygotic character of 17 studied individuals. Lane 1 –GeneRuler 100 bp Plus DNA Ladder or GeneRuler 1 kb DNA Ladder (Thermo Scientific); lanes 2–18 –genomic DNA templates (see S1 Table for details), lane 19 –negative control (water instead of DNA).
Mentions: To confirm the identified retrocopies and their deletions in some individuals, we performed PCR on 17 human genomes supplied by the 1000 Genome Project (Coriell Cell Repositories). Individuals were selected based on previous bioinformatic analyses, and each originated from a different population. Using primers from identified retrocopy sequences, we confirmed the existence of four retrocopies (rdn1–rdn4). Retrocopy rdn5 contains a large number of repetitive sequences. Therefore, we could not obtain a product specific enough to confirm the presence of this particular retrocopy: it was excluded from further studies. However, we were able to prove the deletions of retrocopies rdn1 to 3 in some individuals. Apparently, retrocopy rdn4 was present in all investigated genomes. In addition, utilizing primers designed from the flanking regions of the deletion, we confirmed the size of the deleted regions (Table 3), as well as the homo- and heterozygosity of the studied individuals (Fig 8).

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