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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.


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Expression and conservation of retrocopies deleted relative to the reference genome.
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pgen.1005579.g003: Expression and conservation of retrocopies deleted relative to the reference genome.

Mentions: Most retrocopies are non functional and therefore, their loss is in most cases neutral. However, many retrocopies are expressed and this, together with conservation may indicate some functionality. To assess retrocopy expression, we used RNA-Seq samples from ten individuals selected from five different populations (CEU, GBR, FIN, TSI, YRI) derived from the Geuvadis RNA sequencing project [18], as well as data for 16 human tissues from the Illumina Bodymap 2.0 project. To distinguish between parental gene and the retrocopy, only uniquely mapped reads were considered. As expressed we considered a retrocopy with a normalized expression value of at least 1 RPM (reads per million mapped reads) in at least one sample, either one library from the Body Map project or one individual from the Geuvadis RNA sequencing project. These criteria were met by 588 retrocopies, and 11 of them were also ancestral and absent in some individuals (Fig 3).


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)

Expression and conservation of retrocopies deleted relative to the reference genome.
© Copyright Policy
Related In: Results  -  Collection

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

pgen.1005579.g003: Expression and conservation of retrocopies deleted relative to the reference genome.
Mentions: Most retrocopies are non functional and therefore, their loss is in most cases neutral. However, many retrocopies are expressed and this, together with conservation may indicate some functionality. To assess retrocopy expression, we used RNA-Seq samples from ten individuals selected from five different populations (CEU, GBR, FIN, TSI, YRI) derived from the Geuvadis RNA sequencing project [18], as well as data for 16 human tissues from the Illumina Bodymap 2.0 project. To distinguish between parental gene and the retrocopy, only uniquely mapped reads were considered. As expressed we considered a retrocopy with a normalized expression value of at least 1 RPM (reads per million mapped reads) in at least one sample, either one library from the Body Map project or one individual from the Geuvadis RNA sequencing project. These criteria were met by 588 retrocopies, and 11 of them were also ancestral and absent in some individuals (Fig 3).

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