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Megabase deletions of gene deserts result in viable mice


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.

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Figure 1: Design of genomic deletions in gene deserts MMU3 and MMU19, displaying a wild-type (WT) and a deletion (DEL) allele for each desert.
Figure 2: Survival and growth curves of mice carrying the MMU3 and MMU19 deletions.
Figure 3: Expression of genes bracketing the chromosomal deletions in a panel of 12 tissues.
Figure 4: Conservation profile between human, mouse, rat and chicken.


  1. Bentley, D. R. Genomes for medicine. Nature 429, 440–445 (2004)

    Article  ADS  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  5. Jasny, B. R. & Kennedy, D. The human genome. Science 291, 1153 (2001)

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  8. Nelson, C. E., Hersh, B. M. & Carroll, S. B. The regulatory content of intergenic DNA shapes genome architecture. Genome Biol. 5, R25.1–R25.15 (2004)

    Article  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  10. Ramirez-Solis, R., Liu, P. & Bradley, A. Chromosome engineering in mice. Nature 378, 720–724 (1995)

    Article  ADS  CAS  Google Scholar 

  11. Yu, Y. & Bradley, A. Engineering chromosomal rearrangements in mice. Nature Rev. Genet. 2, 780–790 (2001)

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  13. Nobrega, M. A., Ovcharenko, I., Afzal, V. & Rubin, E. M. Scanning human gene deserts for long-range enhancers. Science 302, 413 (2003)

    Article  CAS  Google Scholar 

  14. Lettice, L. A. 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)

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  16. Ovcharenko, I., Loots, G. G. & Stubbs, L. Interpreting mammalian evolution using Fugu genome comparisons. Genomics (in the press)

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

    CAS  PubMed  Google Scholar 

  18. Boffelli, D., Nobrega, M. A. & Rubin, E. M. Comparative genomics at the vertebrate extremes. Nature Rev. Genet. 5, 456–465 (2004)

    Article  CAS  Google Scholar 

  19. Zerucha, T. 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)

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  24. Hogan, B. C. B. & Lacy, E. Manipulating the Mouse Embryo: A Laboratory Manual (Cold Spring Harbor Laboratory Press, Plainview, New York, 1994)

    Google Scholar 

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

    Article  Google Scholar 

  26. Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002)

    Article  Google Scholar 

  27. Anderson, J. P. 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)

    Article  CAS  Google Scholar 

  28. Dodou, E., Xu, S. M. & Black, B. L. mef2c is activated directly by myogenic basic helix–loop–helix proteins during skeletal muscle development in vivo. Mech. Dev. 120, 1021–1032 (2003)

    Article  CAS  Google Scholar 

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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.

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Correspondence to Edward M. Rubin.

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Supplementary information

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. (DOC 36 kb)

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. (DOC 91 kb)

Supplementary Figure 1

Results from the clinical chemistry assays tested in the various strains of mice. (JPG 53 kb)

Supplementary Figure 2

Results from macroscopic pathology in 12 organs analysed. (JPG 38 kb)

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Nóbrega, M., Zhu, Y., Plajzer-Frick, I. et al. Megabase deletions of gene deserts result in viable mice. Nature 431, 988–993 (2004).

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