The Human Transcriptome Map Reveals Extremes in Gene Density, Intron Length, GC Content, and Repeat Pattern for Domains of Highly and Weakly Expressed Genes

  1. Rogier Versteeg,1,6,
  2. Barbera D.C. van Schaik1,2,
  3. Marinus F. van Batenburg4,5,
  4. Marco Roos1,
  5. Ramin Monajemi2,
  6. Huib Caron1,3,
  7. Harmen J. Bussemaker5, and
  8. Antoine H.C. van Kampen2
  1. 1 Department of Human Genetics, Academic Medical Center, University of Amsterdam, 1100DE Amsterdam, The Netherlands
  2. 2 Department of Bioinformatics, Academic Medical Center, University of Amsterdam, 1100DE Amsterdam, The Netherlands
  3. 3 Department of Paediatric Oncology/EKZ, Academic Medical Center, University of Amsterdam, 1100DE Amsterdam, The Netherlands
  4. 4 Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
  5. 5 Department of Biological Sciences and Center for Computational Biology and Bioinformatics, Columbia University, New York 10027, USA

Abstract

The chromosomal gene expression profiles established by the Human Transcriptome Map (HTM) revealed a clustering of highly expressed genes in about 30 domains, called ridges. To physically characterize ridges, we constructed a new HTM based on the draft human genome sequence (HTMseq). Expression of 25,003 genes can be analyzed online in a multitude of tissues (http://bioinfo.amc.uva.nl/HTMseq). Ridges are found to be very gene-dense domains with a high GC content, a high SINE repeat density, and a low LINE repeat density. Genes in ridges have significantly shorter introns than genes outside of ridges. The HTMseq also identifies a significant clustering of weakly expressed genes in domains with fully opposite characteristics (antiridges). Both types of domains are open to tissue-specific expression regulation, but the maximal expression levels in ridges are considerably higher than in antiridges. Ridges are therefore an integral part of a higher order structure in the genome related to transcriptional regulation.

Footnotes

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1649303. Article published online before print in August 2003.

  • [Supplemental material is available online at www.genome.org. The HTMseq application is available online at http://bioinfo.amc.uva.nl/HTMseq].

  • 6 Corresponding author. E-MAIL R.Versteeg{at}AMC.UVA.NL; FAX 0031-20-6918626.

    • Accepted June 16, 2003.
    • Received March 12, 2003.
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