Retroviruses and Primate Genome Evolution PDF

PREFACE

Three famous questions: "Who we are?" "Where are we from?" and "Where are we going?" together with a more general one "What is life?" were asked by people of every culture. When it became clear that certain genes are responsible for certain phenotypic traits, one more question was added to these four: "Which genes make us human?". One could hope to find the answers by studying primates, their communities and differences from humans, as well as their evolutionary rdations, succession of appearance and accumulation of differences afrer the divergence of the human lineage from lineages of the extant human close rdatives, great apes (chimpanzees, gorillas, and orangutans). Humans and our closest living relatives, the apes, including both "great apes" and "lesser apes" (gibbons and siamangs) form the Hominoidea superfamily. These Hominoidea are remarkably similar and at the same time dramatically different. They are different not only in their appearance but also in such characteristics as behavior and resistance to various diseases, including cancer and AIDS. Many lines of evidence indicate that all of them originated from a common ancestor about 17 Mya (million years ago), and that the last common ancestor of human and great apes, i.e., of human and chimpanzee, extincted about 5 Mya. It is a great challenge to reconstruct its genetic architecture and then to understand the ways of its transformation into two closely rdated, but different architectures ofhuman and chimpanzee. What events caused their divergence in evolution? What genes and regulatory systems were involved in branching hominids off from their closest rdatives, chimpanzees and bonobo and then in their proceeding to the Homo genus crowned with extant Homo sapiens, that is humans with their brain size of at least 600 cubic centimeters, extended period of childhood growth and devdopment, possession of language and many other human specific traits? And what processes step by step shaped the modern human, Homo sapiens sapiens during 5 Myr (million years) of its progress afrer the divergence from chimpanzee?

It is widdy believed that the evolutionary history of a species is reflected in its genome sequence, and therefore the most straightforward way to study primates is sequence comparisons of various primate genomes. The sequencing of the human genome has already contributed a great deal to such an analysis, and as soon as the sequencing of the chimpanzee genome is finished, we will have enormous information to work on. Multiple differences of various kinds that can be envisioned between the two genomes will inevitably puzzle researchers trying to find the genetic reasons for human speciation and rapid phenotypic evolution. How can one single out a rdativdy small number of the differences that have been actually or most possibly involved in speciation from the multitude of just random neutral mutations accumulated during millions of years?

One way is to try to identifY the regions positively selected in evolution. In the case of coding stretches of the genome, an enhanced rate of nonsynonymous substitutions compared to synonymous ones is a widely accepted indication of positive selection. However, the situation with regulatory regions or regions which encode noncoding RNAs is much more tangled. Their conservation indicates that these regions were important for a sufficiently long period(s) of evolution, but generally speaking could be of no importance in other periods. Clearly, this criterion may not be applicable to the regulatory units that appeared afrer the human-chimp lineages divergence. But precisely these units might be the acquisitions that played a major role in shaping our human phenotype.

Therefore, it seems inevitable to resort to rather traditional hypothesis-driven approaches, when the research starts from the hypotheses aimed at explaining why and how the most significant human features, such as language or cognitive capacities, could emerge. In this approach, only particular loci will be taken for interspecies comparison. This "last line of research" will undoubtedly be stimulated by new information on genome-wide comparisons.

Obviously, the chances to reconstruct the succession of the genetic events which had occurred during millions of years of evolution are negligible. But what we can hope to gain as a result of such a comparative research is a deeper understanding of the mechanisms governing the modern genome and the role of particular elements in the networks responsible for the functional integrity of the genome. We will also certainly be able to reveal differences in spatial-temporal networks of the events determining the development of different species and thus to form a basis for the second order hypotheses related to the genetic basis of differences in the phenotypes of extant species. The achievement of this goal will be a great step towards the understanding of what life is in general, and what its peculiarities are regarding our presently prospering, but still endangered, species as well as how these peculiarities could evolve.

What kind of differences might promote speciation? Since a classical work of King and Wilson, who in 1975 undertook a thorough comparison of the molecular data available on chimpanzee (Pan troglodytes) and human (Homo sapiens), it is widely accepted that, as put by the authors: " ... a relatively small number of genetic changes in systems controlling the expression of genes may account for major organizational differences between human and chimpanzees". It is now known as the regulatory hypothesis. Later, it became a major constituent of the Evo-Devo concept suggesting that evolution depends on heritable changes in the development and, according to Duboule and Wilkins (l998), " ... the primary source of developmental differences ... will prove to be not unique gene products but rather the way that comparable, or the same, gene functions are differentially deployed in their development .... Many so called heterochronic shifts altering developmental programs and morphologies involve no more than alteration in the times and cellular site at which particular regulatory molecules are expressed rather than alteration in those molecules themselves". In metazoan evolution, these processes have been brought under intercellular control regarding the time, place, and conditions of functioning. It seems logical to propose that such developmental functional shifts could be caused by changes in gene regulation, which in turn could result from addition of a new regulatory module(s) to the pre-existing gene regulatory system.

The title of this volume, Retroviruses and Primate Genome Evolution, reflects its goal to conceive the role of the obligate inhabitants of all vertebrate genomesendogenous retroviruses, especially those emerged in genomes rather recently, during primate evolution. Although a special focus in the volume is put on human endogenous retroviruses (HERVs), some attention is also paid to other retroelements (REs), like LINEs and Alu to give a more comprehensive view of the evolutionary potential of these perpetually mobile entities now occupying almost a half of the human genome.

Keeping in mind that REs are jumping carriers of the regulatory cis-elements adapted for RNA-polymerase II or III transcription regulation, it is quite reasonable to put them on the list  of highly probable candidates for evolutionarily significant changes, capable of affecting the regulation of the genes in the vicinity of which they were inserted. Such changes could quite possibly occur in the developmental regulatory machinery thus causing the above mentioned developmental shifts.

Indeed, the data obtained for different species clearly demonstrate that REs insertions can change not only the structure of genes, and hence their products, but also their regulation. Moreover, transposable elements can have their own genes and thus entich the genome with new genetic information, like genes of reverse transcriptase or viral resistance. Although the newly inserted elements are known to mostly cause deleterious effects including hereditary diseases, the host cells sometimes exploit the ability of REs to generate variations for their own benefit. Among other REs, HERVs are considered to be the most sophisticated. ERV-related sequences are believed to represent footprints of ancient germ-cell retroviral infections which now occupy up to 8% of the human genome. They have excitingly diverse tools of affecting the human genome functioning originated from exogenous retrovirus systems of successful life cycle. They can change the host genome function through expression of retroviral genes, human genome loci rearrangements due to retropositions of HERVs, or by the ability of their long terminal repeats (LTRs) to regulate nearby genes. A multitude of solitary LTRs comprise a variety of transcription regulatory elements, such as promoters, enhancers, hormone-responsive elements, and polyadenylation signals. This feature makes LTRs potentially able to strongly affect the expression patterns of neighboring genes. It can be imagined that the appearance of such invaders in the genome can change some functions relevant to development and thus provide new traits for subsequent natural selection. They can therefore be considered prime suspects for being a major class of causative agents in speciation.

Individual chapters in this book are devoted to specific areas of research into human genome evolution and possible involvement of REs in the processes related to evolution and includes REs own evolution which was prime interdependent with the host genome evolution.

The book opens with four chapters giving a general insight into human genome structure and function analysis and ideas on the genome evolution. Chapter 1, ''A glance at evolution through the genomic window" (by E. Sverdlov), describes the status of whole genome sequence comparisons which, for the first time, opened a possibility to analyze evolutionary changes at a whole genome level. The intraand interspecies comparisons of the sequenced genomes demonstrated that the genome complexities did not directly correlate with the number of genes and suggested the importance of combinatorial interactions in the cells and organisms as a major player in the complexity of live systems. The whole genome comparisons allowed one to elucidate the role of gene duplications, gross genome rearrangements, transposable elements and other genomic changes in divergence of genomes, thus forming a solid basis for understanding genetic mechanisms of evolution. The whole genome analyses developed in parallel and interdependently with the development of new concepts of evolution, such as evolutionary developmental biology (Evo-Devo), aimed at explaining how developmental processes and mechanisms become modified in evolution, and how these modifications produce changes in animal morphology. This review considers new data and trends and supports the idea that transposable elements playa role of a major pacemaker in evolution being a "depot" of evolvability factors.

Chapter 2 entitled "Complex Genome Comparisons: Problems and Approaches" by N. Broude and myself provides a brief outline of the experimental approaches to genome-wide interindividual, interpopulation, and interspecies comparisons. Such comparisons form a unique background for deciphering spatial and temporal genomic regulatory networks and their changes during evolution. They are also indispensable for understanding genetic and environmental contributions to complex diseases afflicting modern society. The chapter describes also a range of modern approaches to genome-wide complex genome comparisons with their advantages and disadvantages.

Chapter 3 by H. Zischler and his colleagues is devoted to primate evolution. Information on evolutionary events and relations of different primate extant species is indispensable for understanding the role of particular genomic elements in evolution. The authors review the modern status of investigations on primate phylogeny with all its problems and contradictions. An emphasis is made on the divergence of nonhuman primates, relevant interpretations of the fossil record and molecular evidence, including retropositional evidence. Whereas a congruent view is emerging concerning phylogenetic relationships among primate taxa at a higher taxonomic level, e.g., primate infraorders, there is still considerable debate on primate origins or very recent splits in primate evolution. Obtaining more clarity about primate origins is to a large degree hampered by the sparseness of the critical fossil record. If both molecular and fossil evidence is available for a certain splitting, many interpretations based on these two completely different approaches seem to be remarkably compatible. Attention is also paid to problems of modern human evolution.

Chapter 4 "How different is the human genome from genomes of the great apes?" by E. Nadezdin and E. Sverdlov gives an account on sequence and chromosomal organization differences between highly related genomes of humans and the African great apes that were accumulated during Hominoid evolution. Some of them certainly form a genetic basis for recently evolved, specifically human traits. Human genome sequencing revealed its characteristic features, and the ongoing sequencing of the chimpanzee genome continuously widens the possibilities oflargescale systematic comparison of the two genomes. Now it is more and more apparent that most probably hundreds and thousands of genes were involved in the divergence of even the most closely related species of human and chimpanzee. The divergence might be caused by changes in gene regulation and by modifications of protein biochemical functions, gene duplications, losses and acquisitions. A great challenge will be to single out functionally significant differences from the mess of all changes accumulated during evolution.

These four general chapters are followed by reviews devoted to various aspects of evolution, interactions with the host genome, and involvement of REs in various human diseases. This series opens with a very brief introduction, Chapter 5, "Endogenous Retroviruses and other retroinsiders", which I wrote to give general information about retroviruses, their endogenous counterparts, and other retroelements in the human genome. I hope it will make the reading of the following more specialized reviews easier.

The next two chapters, by Dixie Mager et al (Chapter 6, "Genomic Distributions of Human Retroelements") and by Christine Leib-Mosch et al (Chapter 7, "Influence of human endogenous retroviruses on cellular gene expression") focus on distribution and function of REs in the human genome. Chapter 6 reviews the studies performed in the last 20 years on chromosomal arrangements of human retroelements including endogenous retroviruses. Biological mechanisms or evolutionary forces that might influence their modern distribution patterns are also discussed. Chapter 7 discusses a variety of effects of newly inserted REs on adjacent genes. These effects include not only impairment of gene function, but also enhancement of transcription, changes in tissue specificity of gene expression, and creation of new gene products with modified functions, e.g., via alternative splicing. The conclusion is that retrotransposable elements may have served as catalysts of genomic evolution and possibly played a role in primate speciation and adaptation.

The reviews by Yu. Lebedev, "Genome-wide search for human specific retroelements" (Chapter 8), and Tatyana Vinogradova, ''Approaches to genome wide analysis of human gene expression: application to analysis of expression of human endogenous retroviruses in normal and cancerous tissues" (Chapter 9), provide an insight into experimental techniques used for revealing species specific REs and analysis of their functional status.

Chapter 10 by A. Katzourakis and M. Tristem, "Phylogeny of human endogenous and exogenous retroviruses", is somewhat different in its style from other reviews in this book. And although it is rather a research article than a review, this chapter successfully demonstrates the state-of-the art for attempts to reconstruct the correct phylogeny of endogenous retroviruses with all their problems and difficulties. Quite a number of assumptions made to smooth evident contradictions of grouping based on just the level of sequence identity make the resulting tree appreciably dependent on the researcher's intuition and prejudice. Similarly, the results obtained with even more sophisticated tools of modern computer-based phylogeny analysis are by no means final or indisputable. Unfortunately, our past seems to be almost as cloudy as our future. With all their assumptions, Tristem and his colleagues found 31 HERV families in the human genome. Currently, it is probably the most extensive survey of HERVs diversity. I think that sequencing of other primate genomes will reveal even more HERV families.

Finally, the title of the last chapter by J. Blomberg et al, "Evolutionary aspects of human endogenous retroviral sequences (HERVs) and diseases", precisely reflects its content. Also discussed is the impact of retroviruses on a variety of human diseases.

Taken together, these partially overlapping chapters hopefully provide a balanced and accurate overview of our current knowledge of the complex interplay of the human genome with its mobile inhabitants, retrotransposons.

To conclude the Preface, I would like to stress that hardly a particular genomic constituent or even a numerous group of constituents like REs has caused such a pronounced phenotypic difference berween human and chimpanzee. Undoubtedly, hundreds or even thousands of changes occurred during 5 million years after the rwo species diverged, and that eventually made us humans. However, the chain of events leading to human might well be initiated by some very first genomic perturbations, and this initiation could be caused by retroviral integration(s) and/or by other RE retropositions into a critical site of the ancestor genome.

Exact dating of RE integrations and comparative functional analysis of the genes in the species which sustained the integrations and those retaining the same but native genes will help us to better understand our own evolution.

Author: Eugene D. Sverdlov