Protocol | Published:

Computational screening of conserved genomic DNA in search of functional noncoding elements

Nature Methods volume 2, pages 535545 (2005) | Download Citation

Subjects

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1.

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

  2. 2.

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

  3. 3.

    , & Interpreting mammalian evolution using Fugu genome comparisons. Genomics 84, 890–895 (2004).

  4. 4.

    et al. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3, e7 (2004).

  5. 5.

    , & Into the heart of darkness: large-scale clustering of human non-coding DNA. Bioinformatics 20 (suppl. 1), I40–I48 (2004).

  6. 6.

    , & Conserved non-genic sequences—an unexpected feature of mammalian genomes. Nat. Rev. Genet. 6, 151–157 (2005).

  7. 7.

    , , , & Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. Genome Res. (in the press).

  8. 8.

    et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002).

  9. 9.

    & Computational identification of regulatory DNAs underlying animal development. Nat. Methods 2, 529–534 (2005).

  10. 10.

    et al. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 32, 493–496 (2004).

  11. 11.

    , , , & Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl. Acad. Sci. 100, 11484–11489 (2003).

  12. 12.

    BLAT—the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002).

  13. 13.

    et al. Exploring relationships and mining data with the UCSC Gene Sorter. Genome Res. 15, 737–741 (2005).

  14. 14.

    & BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 32, 20–25 (2004).

  15. 15.

    et al. The EMBL Nucleotide Sequence Database. Nucleic Acids Res. 33, D29–D33 (2005).

  16. 16.

    et al. Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol. 23, 137–144 (2005).

  17. 17.

    & A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 5, 140 (2004).

  18. 18.

    , , & A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions. Trends Genet. 19, 119–124 (2003).

  19. 19.

    et al. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299, 1391–1394 (2003).

  20. 20.

    , & Exploiting human–fish genome comparisons for deciphering gene regulation. Hum. Mol. Genet. 13 (special issue 2), 261–266 (2004).

  21. 21.

    & Long-range control of gene expression: emerging mechanisms and disruption in disease. Am. J. Hum. Genet. 76, 8–32 (2005).

  22. 22.

    , , & Identification and characterization of multi-species conserved sequences. Genome Res. 13, 2507–2518 (2003).

  23. 23.

    et al. Characterization of evolutionary rates and constraints in three Mammalian genomes. Genome Res. 14, 539–548 (2004).

  24. 24.

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

  25. 25.

    & Transcription regulation and animal diversity. Nature 424, 147–151 (2003).

  26. 26.

    , , & Communication over a large distance: enhancers and insulators. Biochem. Cell Biol. 81, 241–251 (2003).

Download references

Acknowledgements

The authors are grateful to the UCSC Genome Browser staff for continuously developing and maintaining the infrastructure on which this protocol relies. We also thank N. Ahituv for critically reading the manuscript and M. Nobrega for advice. A.C.S. is supported by the Graduate Research and Education in Adaptive bio-Technology (GREAT) Training Program of the UC Systemwide Biotechnology Research and Education Program, grant #2004-33. D.H. and G.B. are supported by a US National Human Genome Research Institute grant P41 HG002371. D.H. is also supported by a Howard Hughes Medical Institute grant.

Author information

Affiliations

  1. Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA.

    • Gill Bejerano
    • , Adam C Siepel
    • , W James Kent
    •  & David Haussler
  2. Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California 95064, USA.

    • David Haussler

Authors

  1. Search for Gill Bejerano in:

  2. Search for Adam C Siepel in:

  3. Search for W James Kent in:

  4. Search for David Haussler in:

Corresponding author

Correspondence to Gill Bejerano.

About this article

Publication history

Published

DOI

https://doi.org/10.1038/nmeth0705-535

Further reading