Genetics: what is a gene?

 

Nature. 2006 May 25;441(7092):469-74.

 

The idea of genes as beads on a DNA string is fast fading. Protein-coding sequences have no clear beginning or end and RNAi is a key part of information package, reports Helen Pearson

 

Genetics: what is a gene?

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Genetic information: codes and enigmas.

 

Nature. 2006 Nov 16;444(7117):259-61.

 

There’s more than one way to read a stretch of DNA, finds Helen Pearson - and we need to understand them all.

  

Genetic information: codes and enigmas.

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Between the cross and the sword: the crisis of the gene concept

 

Charbel Niño El-Hani. Between the cross and the sword: the crisis of the gene concept. Genet. Mol. Biol. 2007 vol.30 no.2 São Paulo Mar. 

 

Challenges to the gene concept have shown the difficulty of preserving the classical molecular concept, according to which a gene is a stretch of DNA encoding a functional product (polypeptide or RNA). The main difficulties are related to the overlaying of the Mendelian idea of the gene as a unit: the interpretation of genes as structural and/or functional units in the genome is challenged by evidence showing the complexity and diversity of genomic organization. This paper discusses the difficulties faced by the classical molecular concept and addresses alternatives to it. Among the alternatives, it considers distinctions between different gene concepts, such as that between the molecular and the evolutionary gene, or between gene-P (the gene as determinant of phenotypic differences) and gene-D (the gene as developmental resource). It also addresses the process molecular gene concept, according to which genes are understood as the whole molecular process underlying the capacity to express a particular product, rather than as entities in bare DNA; a treatment of genes as sets of domains (exons, introns, promoters, enhancers, etc.) in DNA; and a systemic understanding of genes as combinations of nucleic acid sequences corresponding to a product specified or demarcated by the cellular system. In all these cases, possible contributions to the advancement of our understanding of the architecture and dynamics of the genetic material are emphasized.

  

 Between the cross and the sword-the crisis of the

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Origin of phenotypes: genes and transcripts.

 

Gingeras TR. Origin of phenotypes: genes and transcripts. Genome Res., 2007 Jun;17(6):682-90.

 

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 physical boundaries 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, including splice 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.

 Origin of phenotypes-genes and transcripts

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What is a gene, post ENCODE? History and updated definition

 

Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M. What is a gene, post ENCODE? History and updated definition. Genome Res., 2007 Jun; 17 (6): 669-81.

 

While sequencing of the human genome surprised us with how many protein-coding genes there are, it did not fundamentally change our perspective on what a gene is. In contrast, the complex patterns of dispersed regulation and pervasive transcription uncovered by the ENCODE project, together with non-genic conservation and the abundance of noncoding RNA genes, have challenged the notion of the gene. To illustrate this, we review the evolution of operational definitions of a gene over the past century--from the abstract elements of heredity of Mendel and Morgan to the present-day ORFs enumerated in the sequence databanks. We then summarize the current ENCODE findings and provide a computational metaphor for the complexity. Finally, we propose a tentative update to the definition of a gene: A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products. Our definition side-steps the complexities of regulation and transcription by removing the former altogether from the definition and arguing that final, functional gene products (rather than intermediate transcripts) should be used to group together entities associated with a single gene. It also manifests how integral the concept of biological function is in defining genes.

  

What is a gene, post ENCODE

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