Landscape of transcription in human cells

Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233.


Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.

Publication types

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

MeSH terms

  • Alleles
  • Cell Line
  • DNA / genetics*
  • DNA, Intergenic / genetics
  • Encyclopedias as Topic*
  • Enhancer Elements, Genetic
  • Exons / genetics
  • Gene Expression Profiling
  • Genes / genetics
  • Genome, Human / genetics*
  • Genomics
  • Humans
  • Molecular Sequence Annotation*
  • Polyadenylation / genetics
  • Protein Isoforms / genetics
  • RNA / biosynthesis
  • RNA / genetics
  • RNA Editing / genetics
  • RNA Splicing / genetics
  • Regulatory Sequences, Nucleic Acid / genetics*
  • Repetitive Sequences, Nucleic Acid / genetics
  • Sequence Analysis, RNA
  • Transcription, Genetic / genetics*
  • Transcriptome / genetics*


  • DNA, Intergenic
  • Protein Isoforms
  • RNA
  • DNA

Associated data

  • GEO/GSE24565
  • GEO/GSE26284
  • GEO/GSE33480
  • GEO/GSE33600
  • GEO/GSE34448