Downloaded from genome. cshlporg on June 20, 2011-Published by Cold Spring Harbor Laboratory Press Kaessmann expressed in testes. This suggests that de novo gene formation may nome and the fact that useable proto-promoters (or promoters that have contributed an unexpectedly large proportion of new genes can be co-opted from other genes)and cryptic splice sites abound n this genus. Other studies have reported new genes that evolved in the genome(as also evidenced by the emergence of multi-exonic McLysaght 2009: Toll-Rieraet al 2009).For example, Knowles and of noncoding RNA(Hg. ty, Boog; see above), de novo emergence McLysaght(2009)recently identified three genes that seem to have turn out to be a rather frequent phenomenon. However, the reg. arisen from scratch on the human lineage. Detailed analyses of ulatory, sequence, and structural requirements for the function lese human-specific genes, which involved comparisons with ality of long noncoding RNAs are so far poorly understood and corresponding noncoding sequences from closely related primate hence the probability of such gene formation events is hard to relatives, revealed that a few mutational events after the separation predict. of the human and chimpanzee lineages abolished"disabling reading frame precursors (Fig 3), Protein-coding genes transformed into RNA genes allowing relatively long coding sequences to emanate in humans. The origin of a classic IncRNA gene suggests an important alter- mportantly, the functionality of these new human genes is sup- ported by evidence for translation of their coding sequences native trajectory for the origin of new IncRNAs(Fig. 4B). The Xist Together, these studies suggest that the de novo emergence of gene, well known for its crucial role in x chromosome dosage new protein-coding genes is more likely than previously thought, compensation in eutherian mammals(where it triggers transcrip- although more work is required to elucidate the functional rele. vance and potential phenotypicimplications of the reported cases. the remnants of a former protein-coding gene(Duret et al. 2006). the two ke This metamorphosis involved the loss of protein-coding capacity that must precede the birth and fixation of a new protein-coding of the precursor gene's exons and subsequent reuse of several of gene from an ancestrally noncoding DNA region(Fig 3):(1)The these exons and original promoter elements in the newly minted DNA must become transcriptionally active, and(2)it must also Xist RNA gene. But the origin of IncRNA genes from protein-coding evolve a translatable open reading frame that encodes a potentially antecedents is not confined to mammals. An intriguing example beneficial protein. The former may be readily achieved, given the from Drosophila is the spx gene, which represents a fusion of an ATP synthase gene to functionally uncharacterized exons near the in high transcriptional activity of the genome and the various sertion site(Wang et al. 2002). Remarkably, the spx ancestor lost its mechanisms that allow new genes to recruit regulatory sequences (see above). A more global assessment of the probability for the coding capacity and evolved into an RNA gene with a function in atter will have to await future studies. These will also further male courtship behavior, a process that was shaped by positive ur understanding of the evolutionary importance of de novo selection Dai et aL. 2008). These cases illustrate that the formation protein-coding gene birth relative to other mechanisms of ne gene formation. structure information and regulatory capacity. Given the constant generation of new protein-coding gene copies through gene plication and the frequent(often associated) gene death processes Origins of noncoding RNa genes during evolution, the origin of Xist and spx might exemplify Recent transcriptome studies have unveiled an unexpectedly rich a potentially common mechanism repertoire of noncoding RNA species, which, in mammals, are derived from hundreds of small and thousands of IncRNA loci Small RNAs Carthew and Sontheimer 2009; Ponting et al. 2009). As already The birth of small RNAs also seems to have benefited from erst- noted above, it is known that at least miRNA and piRNA genes while protein-coding gene material. For example, two primate proliferated and diversified via gene duplication (for lncRNAs mirNa genes were shown to have arisen from retropseudogenes, there is so far little evidence). But how did the original noncoding a process that apparently profited from the fact that the pseud RNA genes arise? what are their ancestral precursors? Could th also have evolved de novo from previously nonfunctional geno- genes provided sequences of the potential target genes(the retro- mic sequence, akin to the protein-coding genes described above? eudogenes' parental genes)and regulatory elements (Devor 2006). Similarly, but on a larger scale, it was found that mamma- Recent work has started to provide some pertinent answers to these lian retropseudogenes seem to frequently encode small interfering RNAs that may play important roles in the regulation of their pa Long noncoding RNa origination from scratch rental source genes in the germline(Tam et al. 2008; Watanabe et al. 2008). A recent pioneering study dissected the origin and functional im- plications of a multi-exonic lncRNA in mice(Heinen et al. 2009). to have arisen throu he transcriptional activation of a region containing preexisting Parasitic elements of the genome, such as transposons and en- cryptic splice sites in post-meiotic testis cells(spermatidsand was dogenous retroviruses, have indirectly contributed to the func. fixed by a selective sweep in Mus musculus musculus populations. tional evolution of genomes in many ways. For example, given Remarkably, knocking out Pldi led to reduced sperm motility and that transposable elements are key mediators of segmental dupl reduced testis weight, suggesting that Pldi contributed to enhanced cation(by stimulating various recombination events; Fig. 1A; fertility of the mice carrying it. Gene expression analyses indicate Marques-Bonet et al. 2009a)and provide the core machinery that the molecular basis of this phenotype is related to regulatory underlying retroduplication(see above), they represent primary changes at the chromatin level induced by this new RNa gene, in promoters of new gene birth. But, interestingly, genomic parasites line with the notion that lncRNA often exert regulatory functions have also more directly contributed to the evolution of new genes (Ponting et al. 2009). Given the pervasive transcription of the ge in their host genomes, as summarized in the following sections. 1320 Genomeexpressed in testes. This suggests that de novo gene formation may have contributed an unexpectedly large proportion of new genes in this genus. Other studies have reported new genes that evolved de novo in yeast and primates (Cai et al. 2008; Knowles and McLysaght 2009; Toll-Riera et al. 2009). For example, Knowles and McLysaght (2009) recently identified three genes that seem to have arisen from scratch on the human lineage. Detailed analyses of these human-specific genes, which involved comparisons with corresponding noncoding sequences from closely related primate relatives, revealed that a few mutational events after the separation of the human and chimpanzee lineages abolished ‘‘disabling’’ nucleotides in the ancestral open reading frame precursors (Fig. 3), allowing relatively long coding sequences to emanate in humans. Importantly, the functionality of these new human genes is sup￾ported by evidence for translation of their coding sequences. Together, these studies suggest that the de novo emergence of new protein-coding genes is more likely than previously thought, although more work is required to elucidate the functional rele￾vance and potential phenotypic implications of the reported cases. More generally, the available studies illustrate the two key events that must precede the birth and fixation of a new protein-coding gene from an ancestrally noncoding DNA region (Fig. 3): (1) The DNA must become transcriptionally active, and (2) it must also evolve a translatable open reading frame that encodes a potentially beneficial protein. The former may be readily achieved, given the high transcriptional activity of the genome and the various mechanisms that allow new genes to recruit regulatory sequences (see above). A more global assessment of the probability for the latter will have to await future studies. These will also further our understanding of the evolutionary importance of de novo protein-coding gene birth relative to other mechanisms of new gene formation. Origins of noncoding RNA genes Recent transcriptome studies have unveiled an unexpectedly rich repertoire of noncoding RNA species, which, in mammals, are derived from hundreds of small and thousands of lncRNA loci (Carthew and Sontheimer 2009; Ponting et al. 2009). As already noted above, it is known that at least miRNA and piRNA genes proliferated and diversified via gene duplication (for lncRNAs, there is so far little evidence). But how did the original noncoding RNA genes arise? What are their ancestral precursors? Could they also have evolved de novo from previously nonfunctional geno￾mic sequence, akin to the protein-coding genes described above? Recent work has started to provide some pertinent answers to these questions. Long noncoding RNA origination from scratch A recent pioneering study dissected the origin and functional im￾plications of a multi-exonic lncRNA in mice (Heinen et al. 2009). The gene expressing this RNA, Pldi, seems to have arisen through the transcriptional activation of a region containing preexisting cryptic splice sites in post-meiotic testis cells (spermatids) and was fixed by a selective sweep in Mus musculus musculus populations. Remarkably, knocking out Pldi led to reduced sperm motility and reduced testis weight, suggesting that Pldi contributed to enhanced fertility of the mice carrying it. Gene expression analyses indicate that the molecular basis of this phenotype is related to regulatory changes at the chromatin level induced by this new RNA gene, in line with the notion that lncRNA often exert regulatory functions (Ponting et al. 2009). Given the pervasive transcription of the ge￾nome and the fact that useable proto-promoters (or promoters that can be co-opted from other genes) and cryptic splice sites abound in the genome (as also evidenced by the emergence of multi-exonic retrogenes; Kaessmann et al. 2009; see above), de novo emergence of noncoding RNA (Fig. 4A) genes as exemplified by Pldi might turn out to be a rather frequent phenomenon. However, the reg￾ulatory, sequence, and structural requirements for the function￾ality of long noncoding RNAs are so far poorly understood and hence the probability of such gene formation events is hard to predict. Protein-coding genes transformed into RNA genes The origin of a classic lncRNA gene suggests an important alter￾native trajectory for the origin of new lncRNAs (Fig. 4B). The Xist gene, well known for its crucial role in X chromosome dosage compensation in eutherian mammals (where it triggers transcrip￾tional inactivation of one female X chromosome), emanated from the remnants of a former protein-coding gene (Duret et al. 2006). This metamorphosis involved the loss of protein-coding capacity of the precursor gene’s exons and subsequent reuse of several of these exons and original promoter elements in the newly minted Xist RNA gene. But the origin of lncRNA genes from protein-coding antecedents is not confined to mammals. An intriguing example from Drosophila is the spx gene, which represents a fusion of an ATP synthase gene to functionally uncharacterized exons near the in￾sertion site (Wang et al. 2002). Remarkably, the spx ancestor lost its coding capacity and evolved into an RNA gene with a function in male courtship behavior, a process that was shaped by positive selection (Dai et al. 2008). These cases illustrate that the formation of new lncRNA genes may directly draw from previous gene structure information and regulatory capacity. Given the constant generation of new protein-coding gene copies through gene du￾plication and the frequent (often associated) gene death processes during evolution, the origin of Xist and spx might exemplify a potentially common mechanism. Small RNAs The birth of small RNAs also seems to have benefited from erst￾while protein-coding gene material. For example, two primate miRNA genes were shown to have arisen from retropseudogenes, a process that apparently profited from the fact that the pseudo￾genes provided sequences of the potential target genes (the retro￾pseudogenes’ parental genes) and regulatory elements (Devor 2006). Similarly, but on a larger scale, it was found that mamma￾lian retropseudogenes seem to frequently encode small interfering RNAs that may play important roles in the regulation of their pa￾rental source genes in the germline (Tam et al. 2008; Watanabe et al. 2008). New genes from domesticated genomic parasites Parasitic elements of the genome, such as transposons and en￾dogenous retroviruses, have indirectly contributed to the func￾tional evolution of genomes in many ways. For example, given that transposable elements are key mediators of segmental dupli￾cation (by stimulating various recombination events; Fig. 1A; Marques-Bonet et al. 2009a) and provide the core machinery underlying retroduplication (see above), they represent primary promoters of new gene birth. But, interestingly, genomic parasites have also more directly contributed to the evolution of new genes in their host genomes, as summarized in the following sections. Kaessmann 1320 Genome Research www.genome.org Downloaded from genome.cshlp.org on June 20, 2011 - Published by Cold Spring Harbor Laboratory Press