Genomics

Alternative splicing: conservation and function (Genomics)

At least half of human genes seem to be alternatively spliced (Lander et al., 2001). This estimate is mainly based on the comparison of genomic DNA with EST (expressed sequence tag, see Article 78, What is an EST?, Volume 4) sequences (Mironov et al., 1999; Brett et al., 2000), and thus is subject to uncertainty […]

Overlapping genes in the human genome (Genomics)

Viruses have very compact genomes. Yet, the discovery of the overlapping genes in bacteriophage phiX174 in1976 (Barrell et al., 1976) came as a surprise. It took another decade before similar phenomena were noticed in higher eukaryotes. In 1998, in the same issue of Nature, Spencer et al. (Spencer et al., 1986) published two overlapping genes […]

Comparisons with primate genomes (Genomics)

The complete sequence of human, mouse, and rat genomes is now available, and sequence comparison has started to unveil the forces that shaped mammalian genomes. Whole-genome comparison among these three genomes is very interesting, but almost fruitless if used to delineate the recent evolutionary history of the human genome. Comparison of our genome with those […]

Transcriptional promoters (Genomics)

1. Introduction Transcription, the first step in the flow of genetic information from DNA to RNA to protein, acts as the gatekeeper controlling the influence of genes upon the phenotype of cells. When the three-dimensional structure of chromatin and the presence of appropriate catalytic proteins are permissive, biochemical protein machinery is assembled within regions of […]

Human microRNAs (Genomics)

1. Introduction In 2001, three groups published independent reports of the discovery of a large class of tiny noncoding RNAs (ncRNAs, see Article 27, Noncoding RNAs in mammals, Volume 3) in worm, fly, and human (Lagos-Quintana, 2001; Lee, 2001; Lau, 2001). The ncRNAs were named microRNAs (miRNAs) and the reports generated widespread interest. The founder […]

Genome archaeology (Genomics)

1. Introduction The availability of substantially sequenced animal genomes in the last 5 years has served as the framework not only for studies of individual genes, but has allowed much greater insight into the evolution of content and structure. Also at a very practical level, the availability of completed genomes has transformed the speed at […]

Endogenous retroviruses (Genomics)

Vertebrate genomes harbor considerable sequence portions of retroviral origin that are stably inherited genome components. Retroviruses typically infect somatic cells of a host organism. They reverse transcribe their RNA genome to double-stranded DNA, and integrate the DNA into the host cell genome, forming a so-called provirus, that serves to produce RNA transcripts and retroviral proteins […]

Functional analysis of genes (Genomics)

1. Introduction The Human Genome Project started a revolution in biology. The initial effort to sequence the genomes of humans and many model organisms is now essentially complete (see Article 43, Functional genomics in Saccharomyces cerevisiae, Volume 3, Article 44, The C. elegans genome, Volume 3, Article 45, The Drosophila genome(s), Volume 3, Article 46, […]

Mouse models (Genomics)

1. Introduction 1.1. Why use the mouse as a model system? The mouse has very well-defined genetics, with genetically homogenous inbred strains and a completed genome sequence. In addition, mice have a short breeding time that allows easy generation of sufficient numbers of individuals for an experiment, defined housing conditions including diet and health status, […]

The rat as a model physiological system (Genomics)

  1. Introduction Much of our current understanding of integrative physiology is based on studies in the laboratory rat, and the body of physiological and pathophysiological data, as well as toxicological and pharmacological data, that are available for the rat is unparalleled in other species (Jacob and Kwitek, 2001). The rat has been the favored […]

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