Origen De Los Fenotipos

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Origin of phenotypes: Genes and transcripts

Thomas R. Gingeras

Genome Res. 2007 17: 682-690
Access the most recent version at doi:.1101/gr.6525007



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Perspective

Origin of phenotypes: Genes and transcripts

Thomas R. Gingeras
Affymetrix, Inc., Santa Clara, California 95051, USA


While the concept of a gene has been helpful in defining the relationship of a portion of a genome to a phenotype, this traditional term may not be as useful as it once was.Currently, “gene” has come to refer principally to a genomic region producing a polyadenylated mRNA that encodes a protein. However, the recent emergence of a large collection of unannotated transcripts with apparently little protein coding capacity, collectively called transcripts of unknown function (TUFs), has begun to blur the physicalboundaries and genomic organization of genic regions with noncoding transcripts often overlapping protein-coding genes on the same (sense) and opposite strand (antisense). Moreover, they are often located in intergenic regions, making the genic portions of the human genome an interleaved network of both annotated polyadenylated and nonpolyadenylated transcripts, includingsplice variants with novel 5 ends extending hundreds of kilobases. This complex transcriptional organization and other recently observed features of genomes argue for the reconsideration of the term “gene” and suggests that transcripts may be used to define the operational unit of a genome.



New technical and conceptual insights have often prompted re-considerations of what constitutes fundamental functional ele- ments in a genome. In 1909, influenced by the writings of Hugo de Vries, Wilhelm Johannsen coined the term “gene” (Churchill
1974; Stamhuis et al. 1999). It was an attempt to provide a term that would represent an element that connected an inherited physical entity to an observable phenotype (Fig. 1A). Empirical findings andconceptual proposals made in the mid-20th century focused on the structural entities composing a gene. Notably, the elucidation of the structure of DNA (Watson and Crick 1953) and the subsequent unraveling of the processes of DNA replication and RNA transcription led to the identification of new elements in the genome, which, in turn, helped to sharpen an understand- ing of both thephysical properties and definition of the term “gene” (Fig. 1B). Not long after the first description of the double helical structure of DNA, Francis Crick published a Central Dogma proposition as an operational framework describing how information stored in the sequence of DNA was transferred from the genome into functional protein products (Crick 1958). Two unstated implications...