Letter | Published:

Megabase deletions of gene deserts result in viable mice

Nature volume 431, pages 988993 (21 October 2004) | Download Citation



The functional importance of the roughly 98% of mammalian genomes not corresponding to protein coding sequences remains largely undetermined1. Here we show that some large-scale deletions of the non-coding DNA referred to as gene deserts2,3,4 can be well tolerated by an organism. We deleted two large non-coding intervals, 1,511 kilobases and 845 kilobases in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis. Further detailed analysis of the expression of multiple genes bracketing the deletions revealed only minor expression differences in homozygous deletion and wild-type mice. Together, the two deleted segments harbour 1,243 non-coding sequences conserved between humans and rodents (more than 100 base pairs, 70% identity). Some of the deleted sequences might encode for functions unidentified in our screen; nonetheless, these studies further support the existence of potentially ‘disposable DNA’ in the genomes of mammals.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


  1. 1.

    Genomes for medicine. Nature 429, 440–445 (2004)

  2. 2.

    et al. The DNA sequence and analysis of human chromosome 13. Nature 428, 522–528 (2004)

  3. 3.

    et al. Human chromosome 7: DNA sequence and biology. Science 300, 767–772 (2003)

  4. 4.

    et al. The sequence of the human genome. Science 291, 1304–1351 (2001)

  5. 5.

    & The human genome. Science 291, 1153 (2001)

  6. 6.

    et al. Role of duplicate genes in genetic robustness against null mutations. Nature 421, 63–66 (2003)

  7. 7.

    et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901–906 (1999)

  8. 8.

    , & The regulatory content of intergenic DNA shapes genome architecture. Genome Biol. 5, R25.1–R25.15 (2004)

  9. 9.

    et al. Ultraconserved elements in the human genome. Science 304, 1321–1325 (2004)

  10. 10.

    , & Chromosome engineering in mice. Nature 378, 720–724 (1995)

  11. 11.

    & Engineering chromosomal rearrangements in mice. Nature Rev. Genet. 2, 780–790 (2001)

  12. 12.

    et al. Genomic interval engineering of mice identifies a novel modulator of triglyceride production. Proc. Natl Acad. Sci. USA 97, 1137–1142 (2000)

  13. 13.

    , , & Scanning human gene deserts for long-range enhancers. Science 302, 413 (2003)

  14. 14.

    et al. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum. Mol. Genet. 12, 1725–1735 (2003)

  15. 15.

    et al. Characterization of the pufferfish Otx2 cis-regulators reveals evolutionarily conserved genetic mechanisms for vertebrate head specification. Development 131, 57–71 (2004)

  16. 16.

    , & Interpreting mammalian evolution using Fugu genome comparisons. Genomics (in the press)

  17. 17.

    et al. Inducible expression of an hsp68–lacZ hybrid gene in transgenic mice. Development 105, 707–714 (1989)

  18. 18.

    , & Comparative genomics at the vertebrate extremes. Nature Rev. Genet. 5, 456–465 (2004)

  19. 19.

    et al. A highly conserved enhancer in the Dlx5/Dlx6 intergenic region is the site of cross-regulatory interactions between Dlx genes in the embryonic forebrain. J. Neurosci. 20, 709–721 (2000)

  20. 20.

    et al. Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are frequently functional. Genome Res. 14, 367–372 (2004)

  21. 21.

    et al. Detection of large-scale variation in the human genome. Nature Genet. 36, 949–951 (2004)

  22. 22.

    et al. Large-scale copy number polymorphism in the human genome. Science 305, 525–528 (2004)

  23. 23.

    & Targeted insertion of exogenous DNA into the eukaryotic genome by the Cre recombinase. New Biol. 2, 441–449 (1990)

  24. 24.

    & Manipulating the Mouse Embryo: A Laboratory Manual (Cold Spring Harbor Laboratory Press, Plainview, New York, 1994)

  25. 25.

    . Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428, 493–521 (2004)

  26. 26.

    . Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002)

  27. 27.

    et al. HRC is a direct transcriptional target of MEF2 during cardiac, skeletal, and arterial smooth muscle development in vivo. Mol. Cell. Biol. 24, 3757–3768 (2004)

  28. 28.

    , & mef2c is activated directly by myogenic basic helix–loop–helix proteins during skeletal muscle development in vivo. Mech. Dev. 120, 1021–1032 (2003)

Download references


We thank I. Ovcharenko, G. Loots and J. Schwartz for help with the identification and annotation of the gene deserts; D. Boffelli, L. Pennacchio, N. Ahituv, J. Bristow and other Rubin laboratory members for suggestions and criticisms on the manuscript; and H. Jacob for providing the clinical chemistry assays. Research was conducted at the E. O. Lawrence Berkeley National Laboratory and at the Joint Genome Institute, with support by grants from the Programs for Genomic Application, the NHLBI and the DOE.

Author information

Author notes

    • Marcelo A. Nóbrega
    •  & Yiwen Zhu

    These authors contributed equally to this work


  1. DOE Joint Genome Institute Walnut Creek, California 94598, USA, and Genomics Division Lawrence Berkeley National Laboratory Berkeley, California 94720, USA


  1. Search for Marcelo A. Nóbrega in:

  2. Search for Yiwen Zhu in:

  3. Search for Ingrid Plajzer-Frick in:

  4. Search for Veena Afzal in:

  5. Search for Edward M. Rubin in:

Competing interests

The authors declare that they have no competing financial interests.

Corresponding author

Correspondence to Edward M. Rubin.

Supplementary information

Word documents

  1. 1.

    Supplementary Methods

    Methods used to generate and screen the animals generated in this study, as well as details of the annotation of the genomic intervals targeted for deletion.

  2. 2.

    Supplementary Tables

    A total of seven tables listing all relevant primer sequences used in the protocols, and results from functional analysis of the ice concerning general fitness, survival and reproduction.

Image files

  1. 1.

    Supplementary Figure 1

    Results from the clinical chemistry assays tested in the various strains of mice.

  2. 2.

    Supplementary Figure 2

    Results from macroscopic pathology in 12 organs analysed.

About this article

Publication history






Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.