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... be.oxfordjournals.org/ D ow nloaded froms7 RNA-seq data, one can identify exons and predict transcript structures de novo even insthe absence of prior transcriptome annotations (Guttman et al. 2010; =-=Trapnell et al. 2010-=-).sHere we used deep RNA-seq data of human and nonhuman primate tissues to reconstructsand compare transcript structures across the primate phylogeny. By identifying exonssabsent in human RNAs but pre...

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... mouse genes (seesdetails in Materials and Methods). For each tissue and species, we consolidated RNA-seqsreads from all biological replicates and mapped reads to the respective genomes usingsTopHat (=-=Trapnell et al. 2009-=-). We then used Cufflinks (Trapnell et al. 2010) to performsde novo reconstruction of transcript structures. To compare transcript structures acrosssspecies, we matched genomic regions between chimpan...

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...l.s2011), exaptation of non-functional sequences including transposable elementss(Feschotte 2008; Muotri et al. 2007), and small-scale sequence changes that alter genesregulation or protein function (=-=Enard et al. 2002-=-; Haygood et al. 2007; Maricic et al.s2013; Wang et al. 2007). Additionally, lineage-specific loss of functional geneticsmaterials can play a role in adaptive evolution (McLean et al. 2011; Wang et al...

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...te tissues (Table S4). Moreover, for these 27 events, we reanalyzed the corresponding gene expression levels of 17 events that had normalizedsRNA-seq RPKM values provided in the original publication (=-=Brawand et al. 2011-=-). Mostsat Pennsylvania State U niversity on M ay 11, 2016 http://m be.oxfordjournals.org/ D ow nloaded froms20 of these 17 genes were broadly and highly expressed. In human, chimpanzee, and rhesussma...

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...king advantage of RNA-seq as a powerful technology for exon discovery andsannotation. RNA-seq enables accurate characterization and comparison of transcriptsstructures across closely related species (=-=Blekhman et al. 2010-=-; Perry et al. 2012). Usingsat Pennsylvania State U niversity on M ay 11, 2016 http://m be.oxfordjournals.org/ D ow nloaded froms7 RNA-seq data, one can identify exons and predict transcript structure...

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...ion of exon-intron structures and gene splicing patterns hassemerged as an important mechanism for the evolution of gene functions and speciesspecific regulatory networks (Barbosa-Morais et al. 2012; =-=Merkin et al. 2012-=-; Xing andsLee 2006). The vast majority of genes in multicellular eukaryotes have multiple exons,sand alternative splicing of multi-exon genes can produce distinct mRNA and proteinsisoforms from a sin...

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...n of non-functional sequences including transposable elementss(Feschotte 2008; Muotri et al. 2007), and small-scale sequence changes that alter genesregulation or protein function (Enard et al. 2002; =-=Haygood et al. 2007-=-; Maricic et al.s2013; Wang et al. 2007). Additionally, lineage-specific loss of functional geneticsmaterials can play a role in adaptive evolution (McLean et al. 2011; Wang et al. 2006).sFor example,...

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...ity on M ay 11, 2016 http://m be.oxfordjournals.org/ D ow nloaded froms19 to strong purifying selection and could provide evolutionary intermediates for subsequentsadaptive changes (Boue et al. 2003; =-=Xing and Lee 2006-=-). By contrast, the definition ofshuman-specific exon loss events requires an exon to be detected (and conserved) inschimpanzee and other nonhuman primate species but absent only in human RNAs. Suchse...

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...ne, whichsencodes a hydroxylase responsible for the biosynthesis of N-glycolylneuraminic acids(Neu5Gc) from N-acetylneuraminic acid (Neu5Ac) (Chou et al. 2002; Chou et al. 1998;sHayakawa et al. 2001; =-=Irie et al. 1998-=-). Neu5Ac and Neu5Gc are sialic acids that playsimportant roles in cell-cell and cell-pathogen interactions (Schauer 2009). A 92-bp exonsof CMAH was deleted from the human genome via Alu mediated repl...

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... human evolution (Zhang and Chasin 2006). Sela and colleagues identified over 1,500shuman exons derived from primate-specific Alu retrotransposons, and these exons are bysdefinition primate-specific (=-=Sela et al. 2007-=-). Through subsequent evolution, some ofsthese new exons can acquire functional roles. For example, a primate-specific new exonsof the RNA editing enzyme ADARB1 (also known as ADAR2), created through ...

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... a human-specific exon loss event in SLC7A6.sSLC7A6 encodes an amino acid transporter involved in the uptake of arginine, leucine,sand glutamine and the release of arginine in exchange for glutamine (=-=Broer et al. 2000-=-). Itsat Pennsylvania State U niversity on M ay 11, 2016 http://m be.oxfordjournals.org/ D ow nloaded froms22 plays a role in the trafficking of amino acids between brain cells (Broer et al. 2000). It...

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...). During evolution, newsexons can be added to existing functional genes through exonization of non-exonicssequences or duplication of existing exons (Kondrashov and Koonin 2001; Letunic et al.s2002; =-=Wang et al. 2005-=-; Zhang and Chasin 2006). A series of studies have systematicallysanalyzed exon creation in higher eukaryotes using transcriptome data generated byscDNA/EST sequencing (Alekseyenko et al. 2007; Corvel...

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...and proteinsisoforms from a single gene locus (Nilsen and Graveley 2010). These alternativesisoforms can be viewed as “internal paralogs” of a gene to allow for an accelerated rate ofsgene evolution (=-=Boue et al. 2003-=-; Modrek and Lee 2003). The most well-studied type ofsat Pennsylvania State U niversity on M ay 11, 2016 http://m be.oxfordjournals.org/ D ow nloaded froms4 splicing evolution is the creation of new e...

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...t al. 2002; Haygood et al. 2007; Maricic et al.s2013; Wang et al. 2007). Additionally, lineage-specific loss of functional geneticsmaterials can play a role in adaptive evolution (McLean et al. 2011; =-=Wang et al. 2006-=-).sFor example, a number of genes were inactivated in humans after the divergence fromschimpanzees, and these gene loss events were thought to play an active role in thesevolution of human-specific tr...

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... transcriptome data generated byscDNA/EST sequencing (Alekseyenko et al. 2007; Corvelo and Eyras 2008; Modrek andsLee 2003; Wang et al. 2005; Zhang and Chasin 2006), exon microarray (Lin et al. 2009;s=-=Lin et al. 2008-=-), and RNA sequencing (RNA-seq) (Shen et al. 2011). Collectively thesesstudies demonstrate that exon creation is widespread during recent primate and humansevolution, and provides an important means f...

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.... 2005; Zhang and Chasin 2006). A series of studies have systematicallysanalyzed exon creation in higher eukaryotes using transcriptome data generated byscDNA/EST sequencing (Alekseyenko et al. 2007; =-=Corvelo and Eyras 2008-=-; Modrek andsLee 2003; Wang et al. 2005; Zhang and Chasin 2006), exon microarray (Lin et al. 2009;sLin et al. 2008), and RNA sequencing (RNA-seq) (Shen et al. 2011). Collectively thesesstudies demonst...

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...y on M ay 11, 2016 http://m be.oxfordjournals.org/ D ow nloaded froms21 generating mRNA isoforms with distinct regulatory properties such as mRNA decay orstranslational efficiency (Lewis et al. 2003; =-=Sterne-Weiler et al. 2013-=-). For all 6 humanspecific exon loss events validated in this study, the effects appear to regulatory rathersthan protein-coding. For example, in CMAH, the exon loss event disrupted the opensreading f...

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...udies used the human-chimpanzeesgenome alignment to identify chimpanzee genomic regions that match exons inschimpanzee gene models or non-primate vertebrate mRNAs but are deleted in the humansgenome (=-=Hahn et al. 2007-=-; Sen et al. 2006). This strategy identified several putativeshuman-specific exon loss events. However, there was no direct evidence to support thessplicing of these exons in nonhuman primates, and al...

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...mes, wesanalyzed independent human RNA-seq data covering 19 tissues, including 16 tissues insthe Human Body Map 2.0 dataset and 3 tissues from different anatomical compartmentssof the human placenta (=-=Kim et al. 2012-=-) (see Materials and Methods). We used Cufflinkssto reconstruct transcript structures for this expanded set of human tissues and searchedschimpanzee exons against the Cufflinks-reconstructed human exo...

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...C) in the human sequence. Previous studies show that the replacement of rarescodons by common codons in the uORF can increase translation of the downstreamsprotein-coding ORF (Meijer and Thomas 2003; =-=Qiao et al. 2011-=-). We obtained similarsresults when we repeated the luciferase reporter assays in the JEG-3 cell lines(supplementary fig. S6, Supplementary Material online). To confirm that the observedstranslational...