Empirical analysis of transcriptional activity in the Arabidopsis genome

Science. 2003 Oct 31;302(5646):842-6. doi: 10.1126/science.1088305.


Functional analysis of a genome requires accurate gene structure information and a complete gene inventory. A dual experimental strategy was used to verify and correct the initial genome sequence annotation of the reference plant Arabidopsis. Sequencing full-length cDNAs and hybridizations using RNA populations from various tissues to a set of high-density oligonucleotide arrays spanning the entire genome allowed the accurate annotation of thousands of gene structures. We identified 5817 novel transcription units, including a substantial amount of antisense gene transcription, and 40 genes within the genetically defined centromeres. This approach resulted in completion of approximately 30% of the Arabidopsis ORFeome as a resource for global functional experimentation of the plant proteome.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Arabidopsis / genetics*
  • Chromosome Mapping
  • Chromosomes, Plant / genetics
  • Cloning, Molecular
  • Computational Biology
  • DNA, Complementary / genetics
  • DNA, Intergenic
  • Expressed Sequence Tags
  • Gene Expression Profiling
  • Genes, Plant
  • Genome, Plant*
  • Genomics
  • Nucleic Acid Hybridization
  • Oligonucleotide Array Sequence Analysis
  • Open Reading Frames
  • RNA, Messenger / genetics*
  • RNA, Plant / genetics*
  • Reverse Transcriptase Polymerase Chain Reaction
  • Transcription, Genetic*


  • DNA, Complementary
  • DNA, Intergenic
  • RNA, Messenger
  • RNA, Plant