Retroviruses And Primate Genome Evolution

This book describes the role of the obligate inhabitants of all vertebrate genomes—endogenous retroviruses, especially those emerged in genomes rather recently, during primate evolution. It specially focuses on human endogenous retroviruses as well as other retroelements.

In 2001, first reports of the human draft genome were published. Since then, genomes of many other organisms have been sequenced, including several primate species: the chimpanzee, rhesus macaque, gorilla, orangutan, gibbon, baboon, marmoset, tarsier, galago, lemur, and more recently Neanderthals. In a new era of "post-genome biology", scientists now have the vast amount of information revealed by genome research to confront one of the most challenging, fundamental questions in primatology and anthropology: What makes us human? This volume comprises a collection of articles on a variety of topics relevant to primate genomes, including evolution, human origins, genome structure, chromosome genomics, and bioinformatics. The book covers the cutting-edge research in molecular primatology and provides great insights into the functional diversity of primates. This valuable collection will benefit researchers and students, including primatologists, anthropologists, molecular biologists, evolutionary biologists, and animal behaviorists.

Controversy over human evolution remains widespread. However, the human genome project and genetic sequencing of many other species have provided myriad precise and unambiguous genetic markers that establish our evolutionary relationships with other mammals. Human Evolution: Genes, Genealogies and Phylogenies identifies and explains these identifiable, rare and complex markers including endogenous retroviruses, genome-modifying transposable elements, gene-disabling mutations, segmental duplications and gene-enabling mutations. The new genetic tools also provide fascinating insights into when and how many features of human biology arose: from aspects of placental structure, vitamin C dependence and trichromatic vision, to tendencies to gout, cardiovascular disease and cancer. Bringing together a decade's worth of research and tying it together to provide an overwhelming argument for the mammalian ancestry of the human species, the book will be of interest to professional scientists and students in both the biological and biomedical sciences.

Brings together new research demonstrating how evidence based on genetic phenomena should end any lingering controversy over human evolution.

Approximately eight percent of our DNA contains retroviral sequences that are millions of years old. Through engaging stories of scientific discovery, Anna Marie Skalka explains our evolving knowledge of these ancient denizens of the biosphere and how this understanding has significantly advanced research in genetic engineering, gene delivery systems, and precision medicine. Discovering Retroviruses begins with the pioneer scientists who first encountered these RNA-containing viruses and solved the mystery of their reproduction. Like other viruses, retroviruses invade the cells of a host organism to reproduce. What makes them “retro” is a unique process of genetic information transfer. Instead of transcribing DNA into RNA as all living cells do, they transcribe their RNA into DNA. This viral DNA is then spliced into the host’s genome, where the cell’s synthetic machinery is co-opted to make new virus particles. The 100,000 pieces of retroviral DNA in the human genome are remnants from multiple invasions of our ancestors’ “germline” cells—the cells that allow a host organism to reproduce. Most of these bits of retroviral DNA are degenerated fossils, but some have been exploited during evolution, with profound effects on our physiology. Some present-day circulating retroviruses cause cancers in humans and other animals. Others, like HIV, cause severe immunodeficiencies. But retroviruses also hold clues to innovative approaches that can prevent and treat these diseases. In laboratories around the world, retroviruses continue to shed light on future possibilities that are anything but “retro.”

Human retroviruses, HIV and HTLV have been recognized as important pathogens because of their association with lethal diseases such as AIDS and ATL. Considerable resources and efforts have been directed at understanding the interaction between these retroviruses and their host which may provide clues as to how the infection can be controlled or prevented. Among the key scientific successes is the identification of intracellular “restriction factors” that have evolved as obstacles to the replication of pathogens including infectious retroviruses. The discovery of APOBEC, which are strong mutagens of retroviral genomes and intracellular retroelements, began a new era of intense research activities into the spectrum of intrinsic anti-HIV activity, leading to the identification of TRIM5a, BST2/Tetherin, and SAMHD1. In response, HIV has evolved several accessory genes as weaponries to evade these intracellular restriction activities. The intracellular antiretroviral defenses evolved in response to endogenous retroelements that make up more than 40% of the entire mammalian genome, and which are regarded as ancestors of infectious retroviruses. LTR-type retroelements are present in all higher eukaryotes, representing about 8% of the human genome. Non-LTR retroelements can be found at extremely high copy numbers also, with a significant portion of mammalin genomes consisting of LINEs. Mammalian genomes are modified by LINEs through insertions, but also by the indirect replication of non-autonomous retrotransposons such as SINEs. LINEs insertion was shown to have played, and continue to play important roles in genomic evolution and somatic genome mosaicism-mediated physiology. And, because retrotransposition can confer genetic diversity that is beneficial to the host, the vertebrate intrinsic immunity has evolved to support a balance between retroelement insertions that confer beneficial and those that cause deleterious gene disruptions. The articles published in this Research Topic should serve not only as valuable references for the field, but provide future topics of research for investigators that should further our understanding of the retrovirus, retroelements and their restrictions.