Downloaded from genome. cshlporg on June 20, 2011-Published by Cold Spring Harbor Laboratory Press Evolution of new genes Thus, it now seems clear that the many mammalian retrogenes be depauperate in terms of retroposition activity, such as plants, that stem from the X have been fixed during evolution and shaped have recently unveiled a surprisingly large number of apparentl by natural selection to compensate for the transcriptional silenc. selectively constrained retrogenes (wang et ing of their parental (often housekeeping) genes during male 2009). Thus, retroduplication has contributed to the phenotypic germline silencing of the X(Bradley et al. 2004; Rohozinski and evolution of many multicellular eukaryotes, ranging from mam- Bishop 2004; Potrzebowski et al. 2008). Indeed, systematic analy. mals and insects to plants, by giving rise to many functional new ses of chromosomal positions of parental genes and their daughter genes, although this contribution has been more variable than retrocopies revealed that a larger than expected number of auto- that of the more common and widespread DNA-mediated dupli- somal retrogenes are derived from parental genes located on cation mechanisms the X in various mammals (emerson et al. 2004; Potrzebowskiet al. during and after meiosis, when their parental genes are silenced Formation of new gene structures (Potrzebowski et al. 2008). Consequently, testis functions of pa- by retrotransposon-mediated transduction rental genes can be considered to have spread or"moved"to the An alternative mode by which retrotrans could contribute autosomes, a process that was facilitated by the fact that the ret- to the formation of new gene structures was identified in the late roposition process readily transfers genes between chromosomes 1990s(Moran et al. 1999 ). The investigators showed that, in ad- (more readily so than segmental duplication, which often occurs dition to the process of retroposition, in which the retrotransposon on the same chromosome). Notably, recent work (Vibranovski derived enzymes generate copies of mature mRNAS(see section et al. 2009)indicates that meiotic sex chromosome inactivation above), Ll retrotransposon transcripts can also directly carry may also underlie the export of retrogenes from the X in Drosophila downstream flanking genomic sequences with them. In this pro- (Betran et al. 2002) ess,termed 3 transduction, the RNA transcription machinery nowing the functional basis for this so called"out of X" reads through the weak retrotransposon polyadenylation signal onset of mammalian meiotic sex chromosome silencing through stream in the 3'flanking sequence(for review, see Cordaux and assessments of the age of X-derived retrogenes. This work revealed Batzer 2009). Subsequent studies showed that many Ll and SVA that not only the mechanisms of meiotic sex chromosome si- retrotransposon insertions (-10%)are associated with 3'trans lencing but also the sex chromosomes themselves originated in the duction events, copying various genic elements into new genomic common ancestor of placental mammals and marsupials (i. e, after locations( Cordaux and Batzer 2009 and references therein).An the divergence from lineage of egg-laying monotremes), and hence interesting recent study provided initial evidence that 3'trans are younger than previously thought(Potrzebowski et al. 2008). duction may have led to the formation of new genes in primates Notably, tracing the evolutionary origin of individual X-derived (Xing et al. 2006). As part of a genome-wide analysis of SvA retrogenes also identified striking cases of independent parallel mediated transduction, Xing and colleagues identified 143 events exports of key housekeeping genes in eutherians and marsupials, that transduced sequences of various sizes. Notably, three separate which illustrates the strong selective pressures that drove genes out events transduced the entire amacil3 gene into three new ge- of the x upon the emergence of sex chromosomes. Curiously, nomic locations -7-14 million yr ago in the human/African ape a recent study revealed that the X chromosome not only exported ancestor. The novel gene copies were shown to be transcribed, but many genes but also preferentially accumulated new retrogenes it was unclear whether they have been preserved by natural se. upon therian(eutherian and marsupial) sex chromosome differ- lection(Xing et al. 2006). Thus, while the functional relevance of entiation, apparently owing to the emerging sex-related (poten- this new gene family in African apes remains unclear, this study tially antagonistic) selective forces(Potrzebowski et al. 2010) provides initial evidence that 3 transduction may represent yet another way by which retrotransposons have contributed to the Retroduplication in different evolutionary lineage functional evolution of the genome Together, these examples illustrate that new retrogenes have been conducive to the evolution of new genome functions and phe- Gene fusion-the origin of new chimeric genes notypic innovation. However, it should be noted that retro- The process of gene fusion is defined as the fusion of two pre-. position has contributed to the evolution of different eukaryotic viously separate source genes into a single transcription unit-the lineages to highly varying degrees, because of fundamental dif- so-called fusion or chimeric gene(long et al. 2003).Gene fusion is ferences related to the machinery responsible for this process. For example, the rate of retroduplication has been overall high in bound to give rise to new functions given its combinatorial nature therian mammals because of the high activity of LI retrotrans- assuming that the fusion gene is beneficial and selectively pre- posons, which provide the enzymes(reverse transcriptase and served). In agreement with this notion, a number of chimeric endonuclease)necessary for this process(Kaessmann et al. 2009). genes with important functions have been described (Long et al Thus, thousands of retrocopies and over 100 functional retrogenes 2003; Zhou and Wang 2008; Kaessmann et al. 2009). The various e ve been identified in the human genome(Vinckenbosch et al. mechanisms underlying the formation of new chimeric gene unctional retrogenes(Betran et al. 2002; Baiet al. 2007; Zhou et al. following sections using representative examples 2008). In contrast, genomes from monotreme mammals and birds propriate retroposition machinery(Hillier et al. 2004; Kaessmann A common theme underlying several of the different gene fusion et al. 2009). However, eukaryotic lineages previously thought to mechanisms is gene duplication, which provides the necessary raw Genome Research 131Thus, it now seems clear that the many mammalian retrogenes that stem from the X have been fixed during evolution and shaped by natural selection to compensate for the transcriptional silenc￾ing of their parental (often housekeeping) genes during male germline silencing of the X (Bradley et al. 2004; Rohozinski and Bishop 2004; Potrzebowski et al. 2008). Indeed, systematic analy￾ses of chromosomal positions of parental genes and their daughter retrocopies revealed that a larger than expected number of auto￾somal retrogenes are derived from parental genes located on the X in various mammals (Emerson et al. 2004; Potrzebowski et al. 2008) and that these retrogenes are specifically expressed during and after meiosis, when their parental genes are silenced (Potrzebowski et al. 2008). Consequently, testis functions of pa￾rental genes can be considered to have spread or ‘‘moved’’ to the autosomes, a process that was facilitated by the fact that the ret￾roposition process readily transfers genes between chromosomes (more readily so than segmental duplication, which often occurs on the same chromosome). Notably, recent work (Vibranovski et al. 2009) indicates that meiotic sex chromosome inactivation may also underlie the export of retrogenes from the X in Drosophila (Betran et al. 2002). Knowing the functional basis for this so called ‘‘out of X’’ movement of genes then also allowed dating of the evolutionary onset of mammalian meiotic sex chromosome silencing through assessments of the age of X-derived retrogenes. This work revealed that not only the mechanisms of meiotic sex chromosome si￾lencing but also the sex chromosomes themselves originated in the common ancestor of placental mammals and marsupials (i.e., after the divergence from lineage of egg-laying monotremes), and hence are younger than previously thought (Potrzebowski et al. 2008). Notably, tracing the evolutionary origin of individual X-derived retrogenes also identified striking cases of independent parallel exports of key housekeeping genes in eutherians and marsupials, which illustrates the strong selective pressures that drove genes out of the X upon the emergence of sex chromosomes. Curiously, a recent study revealed that the X chromosome not only exported many genes but also preferentially accumulated new retrogenes upon therian (eutherian and marsupial) sex chromosome differ￾entiation, apparently owing to the emerging sex-related (poten￾tially antagonistic) selective forces (Potrzebowski et al. 2010). Retroduplication in different evolutionary lineages Together, these examples illustrate that new retrogenes have been conducive to the evolution of new genome functions and phe￾notypic innovation. However, it should be noted that retro￾position has contributed to the evolution of different eukaryotic lineages to highly varying degrees, because of fundamental dif￾ferences related to the machinery responsible for this process. For example, the rate of retroduplication has been overall high in therian mammals because of the high activity of L1 retrotrans￾posons, which provide the enzymes (reverse transcriptase and endonuclease) necessary for this process (Kaessmann et al. 2009). Thus, thousands of retrocopies and over 100 functional retrogenes have been identified in the human genome (Vinckenbosch et al. 2006). Fruit fly genomes have also been found to contain many functional retrogenes (Betran et al. 2002; Bai et al. 2007; Zhou et al. 2008). In contrast, genomes from monotreme mammals and birds only contain very few retrocopies and lack functional retrogenes, due to the absence of retrotransposons that could provide the ap￾propriate retroposition machinery (Hillier et al. 2004; Kaessmann et al. 2009). However, eukaryotic lineages previously thought to be depauperate in terms of retroposition activity, such as plants, have recently unveiled a surprisingly large number of apparently selectively constrained retrogenes (Wang et al. 2006; Zhu et al. 2009). Thus, retroduplication has contributed to the phenotypic evolution of many multicellular eukaryotes, ranging from mam￾mals and insects to plants, by giving rise to many functional new genes, although this contribution has been more variable than that of the more common and widespread DNA-mediated dupli￾cation mechanisms. Formation of new gene structures by retrotransposon-mediated transduction An alternative mode by which retrotransposons could contribute to the formation of new gene structures was identified in the late 1990s (Moran et al. 1999). The investigators showed that, in ad￾dition to the process of retroposition, in which the retrotransposon￾derived enzymes generate copies of mature mRNAs (see section above), L1 retrotransposon transcripts can also directly carry downstream flanking genomic sequences with them. In this pro￾cess, termed 39 transduction, the RNA transcription machinery reads through the weak retrotransposon polyadenylation signal and terminates transcription by using an alternative signal down￾stream in the 39 flanking sequence (for review, see Cordaux and Batzer 2009). Subsequent studies showed that many L1 and SVA retrotransposon insertions (;10%) are associated with 39 trans￾duction events, copying various genic elements into new genomic locations (Cordaux and Batzer 2009 and references therein). An interesting recent study provided initial evidence that 39 trans￾duction may have led to the formation of new genes in primates (Xing et al. 2006). As part of a genome-wide analysis of SVA￾mediated transduction, Xing and colleagues identified 143 events that transduced sequences of various sizes. Notably, three separate events transduced the entire AMAC1L3 gene into three new ge￾nomic locations ;7–14 million yr ago in the human/African ape ancestor. The novel gene copies were shown to be transcribed, but it was unclear whether they have been preserved by natural se￾lection (Xing et al. 2006). Thus, while the functional relevance of this new gene family in African apes remains unclear, this study provides initial evidence that 39 transduction may represent yet another way by which retrotransposons have contributed to the functional evolution of the genome. Gene fusion—the origin of new chimeric genes The process of gene fusion is defined as the fusion of two pre￾viously separate source genes into a single transcription unit—the so-called fusion or chimeric gene (Long et al. 2003). Gene fusion is a fascinating mechanism of new gene origination that is almost bound to give rise to new functions given its combinatorial nature (assuming that the fusion gene is beneficial and selectively pre￾served). In agreement with this notion, a number of chimeric genes with important functions have been described (Long et al. 2003; Zhou and Wang 2008; Kaessmann et al. 2009). The various mechanisms underlying the formation of new chimeric gene structures and their evolutionary relevance are discussed in the following sections using representative examples. DNA-mediated gene fusions A common theme underlying several of the different gene fusion mechanisms is gene duplication, which provides the necessary raw Evolution of new genes Genome Research 1317 www.genome.org Downloaded from genome.cshlp.org on June 20, 2011 - Published by Cold Spring Harbor Laboratory Press