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Related Experiment Videos

Origin of phenotypes: genes and transcripts.

Thomas R Gingeras1

  • 1Affymetrix, Inc., Santa Clara, California 95051, USA. tom_gingeras@affymetrix.com

Genome Research
|June 15, 2007
PubMed
Summary
This summary is machine-generated.

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The traditional gene concept is challenged by numerous unannotated transcripts. These findings suggest that transcripts, not genes, may better define the genome's operational unit.

Area of Science:

  • Genomics
  • Molecular Biology
  • Transcriptomics

Background:

  • The traditional definition of a gene as a genomic region encoding a protein via polyadenylated mRNA is becoming insufficient.
  • The discovery of transcripts of unknown function (TUFs) complicates the understanding of genic regions and genomic organization.

Purpose of the Study:

  • To evaluate the utility of the traditional gene concept in light of new transcriptomic data.
  • To propose an alternative operational unit for the genome based on transcript characteristics.

Main Methods:

  • Analysis of large-scale transcriptomic datasets, including annotated and unannotated transcripts.
  • Examination of transcript overlap, including sense and antisense transcripts, and splice variants.
  • Assessment of transcript location within both genic and intergenic regions.

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Main Results:

  • A complex network of annotated and non-annotated transcripts, including noncoding and polyadenylated RNAs, has been identified.
  • Transcripts exhibit extensive overlap, with novel splice variants extending over large genomic distances.
  • Transcripts of unknown function (TUFs) blur the defined boundaries of traditional genic regions.

Conclusions:

  • The traditional definition of a gene is inadequate to describe the complexity of the human genome's transcriptional landscape.
  • The operational unit of the genome may be better represented by transcripts rather than the traditional gene model.
  • Reconsideration of the term 'gene' is necessary given the intricate organization of genomic information.