Evolution of Retrogenes in the Mouse Genome

本研究主要分為兩大部分。第一部分我們以老鼠體內兩份胰島素基因為模式，探討重複基因及其母基因如何共同演化。第二部分探討X染色體關聯反轉錄基因(X-related retrogenes)的演化。 在先前的研究中發現，不同於其他哺乳類動物，小家鼠(Mus musculus)及溝鼠(Rattus norvegicus)基因體中有兩份胰島素基因。胰島素重複基因(Ins1)經由不完全反轉錄胰島素母基因(Ins2)而產生，因此重複基因只有一個內含子(intron)。這兩份胰島素基因除了基因結構不同外，他們擁有高度相似的蛋白質轉錄序列，並在胰島素調控路徑中扮演相似的角色。此外，兩份胰島素基因被認為具有不同的表現功能: 只表現胰島素重複基因會加速糖尿病的症狀，而過量表現胰島素母基因卻能抑制糖尿病的進程。結合本研究及本實驗室先前的結果，我們發現胰島素重複基因只存在於鼠亞科動物(Murinae)的基因體。並且經由Ka/Ks檢驗結果顯示，兩份胰島素基因在我們檢測的鼠亞科動物基因體中都是有功能的。此外，我們還發現小家鼠體內的兩份胰島素基因都顯著受到正向選汰的影響。換句話說，擁有兩份基因對小家鼠個體有必然的優勢。因此，我們提出一個小家鼠胰島素基因演化的假說。大約在10,000年前，小家鼠的祖先仍未開始依賴人類生存的生活模式。因此，擁有重複基因的個體因為能有效儲存醣類而佔有優勢。當小家鼠能從人類的穀倉獲得充足的糧食之後，胰島素母基因能防止糖尿病的發生。然而，小家鼠仍然是人類趕盡殺絕的對象，使得牠們的食物來源並沒有辦法獲得百分之百保證。因此，我們在現今的小家鼠野外族群中，仍然可以發現正向選汰同時作用於兩份胰島素基因的證據。 在第二部分的研究中，我們探討與X染色體相關的反轉錄基因的演化。由我們先前的研究中發現，反轉錄基因在基因體中並不是隨機分布。果蠅及哺乳動物的基因體中，在X染色體與體染色體之間跳躍的反轉錄基因，顯著多於在體染色體之間跳躍的基因。一般相信，造成反轉錄基因不隨機分布的原因，是由於雄性的X染色體會在精子發生(spermatogenesis)的晚期被去活化(inactivated)，使得X染色體上的基因無法正常表達。因此，X染色體上的基因會傾向於獲得在體染色體上的替補。根據檢測結果，我們判斷正向選汰主導了反轉錄基因的不隨機分布。然而，目前的研究僅止於基因體層次的分析，並無針對單一反轉錄基因及其母基因做深入的探討。因此在第二部分的研究中，我們廣泛的搜索小家鼠整個基因體內年輕的反轉錄新基因，進而研究這些反轉錄基因與其母基因之間功能的分化，以及選汰對基因體保有兩份序列相似基因的機制。我們的研究發現，不同於母基因，反轉錄新基因不只是雄性專一，而且都在精子發生的晚期表達。這個結果證實了我們的假說：反轉錄新基因成為X染色體上母基因的替補。更進一步分析小家鼠族群的族群序列，發現正向選汰扮演重要的角色。因此，我們推論，X關聯基因在體染色體擁有一份序列相似的基因，並且演化出新的雄性功能有利於生物體的演化。除此之外，幾乎所有的反轉錄基因都從相鄰的基因體序列獲得新的非轉錄區域(untranslated regions, UTRs)。顯示非轉錄區域在新基因獲得新功能上扮演重要的角色。The mechanisms of how duplicate genes are retained in genomes remain an important question. Retrogenes are those intronless duplicate genes originated from reverse transcriptions of mRNA and integrated into genomic locations which are different from parental genes. More and more retrogenes are identified as being responsible for novel functions in mammals, particularly those involving in male fertilities. In my dissertation, I used insulin genes in rodent as a model for studying evolution of mammalian retrogenes and also identified several X chromosome related novel retrogenes in the mouse genome. In Chapter 2, we show the first case of the retention of a retrogene by co-adaptive evolution with its parental copy in the mouse genome. Unlike human, preproinsulins previously were identified as a two-gene system with a duplicate retrogene in mouse and rat. Preproinsulin 1 (Ins1) was found to be retroposed from the partial processed mRNA of preproinsulin 2 (Ins2). Here we further demonstrate that Ins1 only exists within the subfamily Murinae, indicating its specificity to the rodent species, and both Ins2 and Ins1 are under strong functional constraints in these species. Interestingly, by examining spectra of nucleotide polymorphisms, we detect positive selection acting on both Ins2 and Ins1 gene regions in the mouse natural population. The analyses of gene flanking regions and substitutions further indicate that the positive Darwinian selection is unique to the gene surrounding regions. The existence of Ins1 was posited to accelerate diabetes in non obese diabetic mice in the previous literatures. Our studies demonstrate the first case of the fixation and adaptation of a retrogene in association with a harmful phenotype, Type 1 Diabetes. Moreover, several amino acid sites were also identified as evolving under positive Darwinian selection in both insulin coding regions. In conclusion, our data suggests a rapid adaptive divergence in the mouse insulin two-gene system and cast the new insight into the mechanisms that retain new gene duplicates in the genomes. In Chapter 3, we integrated genome-wide investigations and expression analyses to elucidate the evolution of X-related retrogene pairs in rodents. Directional movements of male-related retrogenes have been identified in mammals and flies. Several selection-based mechanisms have been proposed. Testing these selection-based hypotheses requires examinations of evolutionary genetics and expression-related biological properties of these new retrogenes. We demonstrate that all the X-derived autosomal retrogenes evolved a more restricted male function: they are expressed exclusively or predominantly in the testis, particularly, during the late stages of spermatogenesis. In contrast, parental genes are expressed in various tissues and all the spermatogenetic stages. We further observed that positive selection is only targeting on X-derived autosomal retrogenes with new male functions, suggesting that retrogenes may have evolved new testis functions complementary to the parental genes without male specific functions. In the two cases we observed in this study, not only retrogenes but also parental counterparts evolve adaptively, indicating a tendency of increasing in diversity selectively by gene duplication. Furthermore, most retrogenes we identified to have recruited novel sequences as the untranslated regions (UTRs), suggesting evolution of new regulatory elements in these UTRs.致謝................................................................................................................................I 中文摘要.....................................................................................................................III ABSTRACT.................................................................................................................V LIST OF TABLES.....................................................................................................IV LIST OF FIGURES.....................................................................................................X LIST OF APPENDIXES...........................................................................................XI CHAPTER I GENERAL INTRODUCTION............................................................................................1 General Introduction…………………………………………………………………….1 Mechanisms of new gene initiation...................................................................................5 Gene duplication..........................................................................................................................5 Exon shuffling..............................................................................................................................6 Retroposition................................................................................................................................7 Mobile elements...........................................................................................................................8 Horizontal transfer......................................................................................................................9 Gene fission and fusion..............................................................................................................10 Mixture of duplication mechanisms..........................................................................................10 Evolution forces that drive changes in new genes.........................................................10 The role of retroposition in the genomes........................................................................12 Structure of Thesis……………………………………………………………………...13 References.........................................................................................................................15 CHAPTER II THE CO-ADAPTIVE EVOLUTION OF INSULIN TWO-GENE SYSTEM IN MOUSE.........20 Introduction......................................................................................................................21 Materials and methods.....................................................................................................23 Result and discussions......................................................................................................26 Origination of duplicate retrogene, Ins1...................................................................................26 Functionality of Ins2 and Ins1 in Rodent Species.....................................................................27 Co-adaptive Evolution of Insulin Two-gene System.................................................................28 Scenario of Evolution of Insulin Two-gene System..................................................................30 Conclusion.........................................................................................................................32 References.........................................................................................................................33 CHAPTER III EVOLUTION OF X-RELATED RETROGENES IN MOUSE..............................................47 Introduction......................................................................................................................48 Evolution of sex chromosomes in mammals..............................................................................48 Evolution of X-related retrogenes.............................................................................................50 Materials and methods.....................................................................................................53 Selection of retrogene candidates..............................................................................................53 Ka/Ks ratios estimation of young retrogenes in rodent.............................................................54 Expression analyses...................................................................................................................56 DNA sequence analyses.............................................................................................................56 Gene structure identification.....................................................................................................57 Results................................................................................................................................58 X-related young retrogenes evolved more restricted male functions........................................58 Selection is targeting on gene pairs with novel male functions.................................................60 Retrogenes acquire untranslated regions (UTRs) de novo....................................................... 63 Discussions.........................................................................................................................65 Selection-based mechanisms in driving genes out of X.............................................................65 Restricted male expression pattern of X-derived autosomal retrogenes...................................66 Co-adaptive evolution of gene pairs with novel male functions................................................67 The de novo acquisition of UTRs may play an important role in functional novelties.............69 Conclusions.......................................................................................................................71 References.........................................................................................................................72 CHAPTER IV PROSPECTS..................................................................................................................8