You will be presented with the abstract, introduction, and discussion section from a biomedical research article. Your task is to create a summary that a layperson can understand, capturing the essence of the research article. Keep essential scientific terms, but ensure that the language remains clear and the concepts are explained in an uncomplicated manner.

Title: Inter-population Differences in Retrogene Loss and Expression in Humans}
Article:
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.
Introduction:
Retro( pseudo) genes are gene copies that originate through the process of reverse transcription of mRNAs and their subsequent insertion into the genome. This process, called retroposition is usually mediated by enzymes provided by retrotransposable elements and creates intronless copies of existing genes[1]. Due to the lack of promoter sequence of their parental genes, retrocopies were long assumed to be nonfunctional and simply “junk DNA”. However, multiple findings challenged that view and a few mechanisms were proposed for retrogene transcription[2]. Functional retrocopies( retrogenes) may have an intact open reading frame and thus be protein-coding, but can also act as long noncoding RNAs[3], sources of short interfering RNAs[4] and microRNA sponges[5]. The loss of parental regulatory sequences and potential replacement with those recruited from the new locus of integration is believed to be the most possible reason that retrogenes are able to undergo neofunctionalization more often than other types of gene copies[6] and take part in the shaping of lineage- and species-specific features[7]. As recently shown, retrogenes can also replace their parental genes[8]. Apart from their functionality, retrocopies are also useful phylogenetic markers, providing insight into such evolutionary processes as sex chromosome origination[9] or changes in retrotransposable element activity and germ line gene expression[2]. In recent years, numerous studies have shown that many retrogenes are vitally important and a number of them are involved in diseases. A good example is the RHOB gene( ras homolog gene family member B[MIM: 165370]), a tumor suppressor that belongs to the Rho GTPases family[10]. A mutation in another retrogene, RNF113A( ring finger protein 113A[MIM: 300951]), results in trichothiodystrophy[11]. On the other hand, insertion of the PPIA cDNA( peptidyl-prolyl isomerase A[MIM: 123840]) into the TRIM5 gene( tripartite motif-containing protein 5[MIM: 608487]) confers resistance to HIV in owl monkeys[12]. Retroposition gives rise to considerable genetic variation between individuals. Recent developments in sequencing technology allow researchers to move beyond the analysis of individual genomes from model organisms to the study of retrocopies within a population. Large-scale sequencing projects, such as the 1000 Genomes Project[13] enable the exploration of differences in copy-number variation within human populations. Three recent studies[14–16] on the retrocopy repertoire in human populations revealed a total of 208 polymorphic retrocopies[17] called retroduplication variations( RDVs). In addition, two of them[14, 15] aided in reconstructing the phylogenetic tree of human populations. Thus, proving the value of RDV polymorphisms as genomic markers for population history. Despite these advances, many questions remained unanswered. Current methods of discovering novel retropositions,( i. e. not annotated on the reference genome), utilize paired-end reads and require at least one read from the pair to map to the parental gene of the retrocopy. As a result, this approach allows only for the detection of retrocopies that originated relatively recently in evolutionary history and show little sequence divergence compared to their parental genes. Evolutionary events that happened earlier in the human lineage and resulted in currently observed RDVs have been less explored. Moreover, we know surprisingly little about the functional aspects of different kinds of retrogene polymorphisms. Single nucleotide polymorphisms located in retrogene promoters and regulatory sequences might result in different levels of retrogene expression between individuals and populations. Presence or absence of a functional retrocopy might have far reaching biological implications. Due to lack of reliable experimental data, these issues have thus far been ignored; yet, this will most certainly change in the near future. In this study, we focused on aspects not covered by aforementioned publications. We used the results of Phase 1 from the 1000 Genomes Project to investigate variation in loss of ancient( i. e. shared with other primates) retrocopies among human populations. In addition, we utilized RNA-Seq data from the Ilumina BodyMap project as well as data from the lymphoblastoid cell lines of 50 individuals provided by the Geuvadis Consortium[18] to examine variation in the expression level of retrocopies.
Discussion:
Retroduplication variations( RDVs) are a class of genomic sequence polymorphisms associated with the presence or absence of retrocopies in individual genomes. Until recently, our knowledge of the prevalence and significance of this phenomenon was limited. The advent of large-scale sequencing projects, such as The 1000 Genomes Project, allowed researchers to detect such polymorphisms on a massive scale, including both known and novel( not present in the reference genome) retrocopies. Particularly the latter class has drawn much attention, as their discovery is much more challenging than determining the presence or absence of an annotated retrocopy. Previous studies[14–16] focused on relatively recent retroduplication events, which is hardly surprising given that they are very informative on the history of human populations. Two of these studies were indeed able to reconstruct population phylogenetic trees from detected retroduplication variations. Identifying these novel retrocopies required mapping short reads to the genomic sequences spanning splice sites of their parental genes. However, not every novel human retroduplication polymorphism can be discovered in that way. For example, retrocopies that originated very early in the human lineage might have diverged too much from their parental genes to be mapped to their sequences. Similarly, some ancestral retrocopies may have been lost from some of the ancient genomes and are thus, very infrequent in contemporary human populations. As a result, they were not included in the human reference genome. Finally, some retrocopies may not be included in the reference genome, simply due to genome misassembly. Using our two approaches, we were able to detect 193 RDVs( 190 RDVs affecting annotated retrogenes and 3 RDVs of retrocopies absent from the reference genome). This is slightly less than the sum of all previous studies, but significantly more than in any of these studies individually( 176[15], 58[14], and 91[16]). However, due to a different approach, our results complement rather than overlap previous studies. While previous studies mainly focused on RDVs from recent retroposition events, our dataset revealed RDVs resulting from retrocopy deletion. We found orthologs for only 56 retrocopies missing in some human genomes. Nevertheless, we are confident that indels resulting from a deletion dominate in this set, since frequency of retrocopy absence is low for the majority of them; absence in more than 50% of individuals was observed in only a few of the retrogenes. For new retropositions, we would expect absence to be close to 100% of alleles in at least some populations. In this study we developed an approach to detect and characterize hitherto undiscovered retroduplication variations in the human genome. To accomplish this, we de novo assembled the unmapped reads from 500 individuals whose genomes were sequenced in the 1000 Genomes Project. Contigs from different individuals were subsequently combined and assembled into novel genomic regions. Finally, genomic regions were filtered to exclude cross-species contaminations and sequences from alternative human genome assemblies( HuRef) and reference genome patches( GRCh37. p10). These filtered sequences were searched for retrocopies using the RetrogeneDB pipeline[19]. Using this strategy, we were able to discover 5 novel retrocopies, none of which were previously detected[14–16]. We experimentally confirmed the existence of the detected retrocopies and checked for their presence and absence in the human genomes from 17 different populations. The profile of retrocopy presence varied greatly between retrocopies, with some of them being ubiquitous and some detected in only few populations. Detected retrocopies showed significant divergence between their sequences and sequences of their parental genes, indicating an old retroposition event. For all of these retrocopies, we were able to find the orthologs in the chimpanzee or gorilla genome, confirming that they are, in fact ancestral retroduplications that were subsequently lost during human evolution. The number of discovered novel retrocopies( i. e. not annotated on the reference genome) is much lower than in previous studies[14–16]. This is mostly due to the fact that the current human reference genome is of very high quality. As a result, most polymorphic retroduplications with sequences clearly distinguishable from their parental genes are simply present in the reference genome. Our results suggest that we have reached the limit where the reference genome contains almost the entire human retrogene repertoire, with the exception of recent retroduplications, for which obtaining the exact sequence from the genome sequencing data is not trivial, as they are extremely similar to their parental genes. This is certainly not the case for most sequenced genomes, and our approach can be used to complement the retrogene set in many low-coverage, draft euakryotic genomes, for which resequencing data is available. Our pipeline can also be potentially applied to detect retrocopies specific to genomes of ancient, extinct organisms, such as neanderthal[24] or woolly mammoth[25]. The role of retrocopy polymorphisms as markers for human population history is clearly established, but our findings suggest that they can also provide great insight into ongoing evolutionary processes. The availability of population RNA-Seq data from the Geuvadis Consortium[18] allowed us not only to study changes in retrocopy sequences and repertoire, but also consider their potential functional implications. We particularly focused on expressed retrogenes that are absent in the genomes of some individuals. RDVs seem to affect both expressed and non-expressed retrocopies indiscriminately, but their allele frequency for most deletions of expressed retrocopies is relatively low( < 2%), suggesting that they are new or slightly deleterious. We experimentally confirmed the expression of 11 ancestral transcriptionally active retrogenes undergoing deletions. The frequency of their deletion is very low with the exception of retrogene retro_hsap_4873, which is absent in over 10% of alleles in African populations. The expression, ancient origin and low rate of deletion of the remaining 10 retrocopies may suggest some functionality, but further studies would be required to establish their function and the possible consequences of their deletion. Numerous studies revealed a tendency of retrogenes to be expressed in the testis[9, 26]. It has been hypothesized that this specific transcription may be the result of the hypertranscription state observed in meiotic and postmeiotic spermatogenic cells[27]. Alternatively, retrocopies could be preferentially inserted into actively transcribed, and therefore open chromatin[28]. Since the retroposition occurs in the germ line, retrocopies may be primarily inserted into, or near to genes expressed in the germ line, which may enable or enhance their expression in testis. Another hypothesis links this testis-specific expression with an escape from the male meiotic sex chromosome inactivation[29]. To verify the tendency of retrocopies to be expressed in testis, we performed expression analysis on 16 cDNA libraries from various human organs. Our findings confirmed testis-specific expression of only one retrogene. This supports results from our previous studies, showing that many retrogenes have broad expression patterns[8]. However, the set of analyzed retrogenes is relatively small and may not be fully representative. Apart from the presence or absence of expressed retrocopies, we also searched for more subtle differences in retrocopy expression levels between populations. Overall, we detected 9 retrogenes that undergo statistically significant differential expression. Similar to inter-population differences in RDVs frequencies, retrogene expression differences tend to coincide with geographical locations, with most differences occurring between African and European populations. Observed differences most likely arise from different frequencies of short sequence variants( SNPs and indels) in the regulatory sequences of the retrogenes studied, but we cannot exclude more complicated scenarios, such as variation in DNA methylation. At this point, we still know very little concerning the functional implications of discovered expression differences, and this will require further study.
Many retrogenes , long considered to be genomic “junk” , were recently revealed as vitally important . Retroposition plays an important role in shaping differences between species , populations and individuals . Variation may result either from new retroposition events and/or retrocopy loss , as well as from differences in retrocopy expression . Genome analysis of 1092 individuals from various populations and transcriptomes from 50 individuals , revealed differences between populations in the frequency of transcriptionally active ancient retrocopy loss , as well as differences in retrocopy expression levels . Overall , these results provide new insights into the genomic events of inter-population variation , which has not been evaluated much with respect to gene loss .