Burst of Young Retrogenes and Independent Retrogene Formation in Mammals

Pan, Deng; Zhang, Liqing

doi:10.1371/journal.pone.0005040

Cited by 45 publications

(46 citation statements)

References 48 publications

(88 reference statements)

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“…Most of these show low divergence at synonymous sites compared with their parental gene (d S ∼ 0.1) (Supplemental Fig. S1; Supplemental Table S1), suggesting that they emerged relatively recently during mammalian evolution (Marques et al 2005;Pan and Zhang 2009). In contrast, we found fewer retrocopies in the genomes of platypus and chicken, consistent with the lack of LINE-1 activity in these lineages (Hillier et al 2004;Warren et al 2008;Kaessmann et al 2009).…”

Section: Annotation and Transcriptional Profiling Of Retrocopies In 1mentioning

confidence: 99%

The life history of retrocopies illuminates the evolution of new mammalian genes

et al. 2016

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New genes contribute substantially to adaptive evolutionary innovation, but the functional evolution of new mammalian genes has been little explored at a broad scale. Previous work established mRNA-derived gene duplicates, known as retrocopies, as models for the study of new gene origination. Here we combine mammalian transcriptomic and epigenomic data to unveil the processes underlying the evolution of stripped-down retrocopies into complex new genes. We show that although some robustly expressed retrocopies are transcribed from preexisting promoters, most evolved new promoters from scratch or recruited proto-promoters in their genomic vicinity. In particular, many retrocopy promoters emerged from ancestral enhancers (or bivalent regulatory elements) or are located in CpG islands not associated with other genes. We detected 88–280 selectively preserved retrocopies per mammalian species, illustrating that these mechanisms facilitated the birth of many functional retrogenes during mammalian evolution. The regulatory evolution of originally monoexonic retrocopies was frequently accompanied by exon gain, which facilitated co-option of distant promoters and allowed expression of alternative isoforms. While young retrogenes are often initially expressed in the testis, increased regulatory and structural complexities allowed retrogenes to functionally diversify and evolve somatic organ functions, sometimes as complex as those of their parents. Thus, some retrogenes evolved the capacity to temporarily substitute for their parents during the process of male meiotic X inactivation, while others rendered parental functions superfluous, allowing for parental gene loss. Overall, our reconstruction of the “life history” of mammalian retrogenes highlights retroposition as a general model for understanding new gene birth and functional evolution.

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Section: Annotation and Transcriptional Profiling Of Retrocopies In 1mentioning

confidence: 99%

The life history of retrocopies illuminates the evolution of new mammalian genes

et al. 2016

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“…Other studies have also shown that there is an excess of X-linked parental genes (genes which give rise to retrocopies) in both mammals and flies [13,14,22], a possible result of meiotic X chromosome inactivation (XCI) [27]. However, it is still at the early stage to compare the evolutionary pattern of retrocopies among primates at a genome-wide scale [16,28], therefore a systematic comparative study is desirable to leverage our knowledge on primate genome evolution, lineage-specific adaptations, and fine time scales of genomic changes [29,30]. Thus, I exploited four fully sequenced primate genomes, human (Homo sapiens) [31], chimpanzee (Pan troglodytes) [32], orangutan (Pongo pygmaeus) [33], and macaque (Macaca mulatta) [34]) to study the evolutionary pattern of retropositions in primates.…”

Section: Introductionmentioning

confidence: 99%

The role of mRNA‐based duplication in the evolution of the primate genome

2013

FEBS Letters

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a b s t r a c tAnalysis of the human genome suggests novel genes created by retroposition may play an important role in primate evolution. However, data from non-human primates is still scarce. A comprehensive comparison was thus performed among four primate genomes (human, chimpanzee, orangutan, and macaque), which detects elevated rates of retroposition in both the common ancestor of hominoids and macaques. Further analysis shows approximately 10% of intact retrocopies may be under positive selection and at least 4% of retrocopies become functional copies eventually. Moreover, human intact retrocopies were found enriched in transcription-related functions. Collectively, these findings emphasize the important contribution of retroposition to primate genome evolution.

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“…As a copy mechanism to generate new genes (Brosius, 1991;Kaessmann et al, 2009), retroposition is widely observed in animals, such as in mammals or Drosophila (Drosophila melanogaster; Betrán et al, 2002;Emerson et al, 2004;Pan and Zhang, 2009). In contrast, knowledge of retrogenes in plants is so far limited.…”

mentioning

confidence: 99%

Extensive Structural Renovation of Retrogenes in the Evolution of the Populus Genome

2009

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Retroposition, as an important copy mechanism for generating new genes, was believed to play a negligible role in plants. As a representative dicot, the genomic sequences of Populus (poplar; Populus trichocarpa) provide an opportunity to investigate this issue. We identified 106 retrogenes and found the majority (89%) of them are associated with functional signatures in sequence evolution, transcription, and (or) translation. Remarkably, examination of gene structures revealed extensive structural renovation of these retrogenes: we identified 18 (17%) of them undergoing either chimerization to form new chimerical genes and (or) intronization (transformation into intron sequences of previously exonic sequences) to generate new intron-containing genes. Such a change might occur at a high speed, considering eight out of 18 such cases occurred recently after divergence between Arabidopsis (Arabidopsis thaliana) and Populus. This pattern also exists in Arabidopsis, with 15 intronized retrogenes occurring after the divergence between Arabidopsis and papaya (Carica papaya). Thus, the frequency of intronization in dicots revealed its importance as a mechanism in the evolution of exon-intron structure. In addition, we also examined the potential impact of the Populus nascent sex determination system on the chromosomal distribution of retrogenes and did not observe any significant effects of the extremely young sex chromosomes.

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Burst of Young Retrogenes and Independent Retrogene Formation in Mammals

Cited by 45 publications

References 48 publications

The life history of retrocopies illuminates the evolution of new mammalian genes

The life history of retrocopies illuminates the evolution of new mammalian genes

The role of mRNA‐based duplication in the evolution of the primate genome

Extensive Structural Renovation of Retrogenes in the Evolution of the Populus Genome

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