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In vivo enhancer analysis of human conserved non-coding sequences

Author

Listed:
  • Len A. Pennacchio

    (US Department of Energy Joint Genome Institute
    MS 84-171, Lawrence Berkeley National Laboratory)

  • Nadav Ahituv

    (MS 84-171, Lawrence Berkeley National Laboratory)

  • Alan M. Moses

    (MS 84-171, Lawrence Berkeley National Laboratory)

  • Shyam Prabhakar

    (MS 84-171, Lawrence Berkeley National Laboratory)

  • Marcelo A. Nobrega

    (MS 84-171, Lawrence Berkeley National Laboratory
    University of Chicago)

  • Malak Shoukry

    (MS 84-171, Lawrence Berkeley National Laboratory)

  • Simon Minovitsky

    (MS 84-171, Lawrence Berkeley National Laboratory)

  • Inna Dubchak

    (US Department of Energy Joint Genome Institute
    MS 84-171, Lawrence Berkeley National Laboratory)

  • Amy Holt

    (MS 84-171, Lawrence Berkeley National Laboratory)

  • Keith D. Lewis

    (MS 84-171, Lawrence Berkeley National Laboratory)

  • Ingrid Plajzer-Frick

    (MS 84-171, Lawrence Berkeley National Laboratory)

  • Jennifer Akiyama

    (MS 84-171, Lawrence Berkeley National Laboratory)

  • Sarah De Val

    (University of California)

  • Veena Afzal

    (MS 84-171, Lawrence Berkeley National Laboratory)

  • Brian L. Black

    (University of California)

  • Olivier Couronne

    (US Department of Energy Joint Genome Institute
    MS 84-171, Lawrence Berkeley National Laboratory)

  • Michael B. Eisen

    (MS 84-171, Lawrence Berkeley National Laboratory
    University of California-Berkeley)

  • Axel Visel

    (MS 84-171, Lawrence Berkeley National Laboratory)

  • Edward M. Rubin

    (US Department of Energy Joint Genome Institute
    MS 84-171, Lawrence Berkeley National Laboratory)

Abstract

Gene regulators unmasked Identifying the non-coding DNA sequences that act at a distance to regulate patterns of gene expression is not a simple matter; one useful pointer is evolutionary sequence conservation. An in vivo analysis of 167 non-coding elements in the human genome that are extremely conserved based on comparisons with pufferfish, rat and mouse genomes, has identified 75 previously unknown tissue-specific enhancers. These are active in embryos on day 11, most of them directing expression in the developing nervous system. The success of this method suggests that the further 5,500 non-coding sequences conserved between humans and pufferfish may yield another new batch of gene enhancers.

Suggested Citation

  • Len A. Pennacchio & Nadav Ahituv & Alan M. Moses & Shyam Prabhakar & Marcelo A. Nobrega & Malak Shoukry & Simon Minovitsky & Inna Dubchak & Amy Holt & Keith D. Lewis & Ingrid Plajzer-Frick & Jennifer , 2006. "In vivo enhancer analysis of human conserved non-coding sequences," Nature, Nature, vol. 444(7118), pages 499-502, November.
    • Handle: RePEc:nat:nature:v:444:y:2006:i:7118:d:10.1038_nature05295
    DOI: 10.1038/nature05295
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    Citations

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    Cited by:

    1. Victor Lopez Soriano & Alfredo Dueñas Rey & Rajarshi Mukherjee & Frauke Coppieters & Miriam Bauwens & Andy Willaert & Elfride De Baere, 2024. "Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    2. Mukta Kundu & Alexander Kuzin & Tzu-Yang Lin & Chi-Hon Lee & Thomas Brody & Ward F Odenwald, 2013. "cis-Regulatory Complexity within a Large Non-Coding Region in the Drosophila Genome," PLOS ONE, Public Library of Science, vol. 8(4), pages 1-14, April.
    3. Iksoo Huh & Isabel Mendizabal & Taesung Park & Soojin V Yi, 2018. "Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals," PLOS Computational Biology, Public Library of Science, vol. 14(10), pages 1-21, October.
    4. Buki Kwon & Mervin M. Fansler & Neil D. Patel & Jihye Lee & Weirui Ma & Christine Mayr, 2022. "Enhancers regulate 3′ end processing activity to control expression of alternative 3′UTR isoforms," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    5. Andrew T Kwon & Alice Yi Chou & David J Arenillas & Wyeth W Wasserman, 2011. "Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers," PLOS Computational Biology, Public Library of Science, vol. 7(12), pages 1-15, December.
    6. Jin Woo Oh & Michael A. Beer, 2024. "Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    7. Timothy H-C Hsiau & Claudiu Diaconu & Connie A Myers & Jongwoo Lee & Constance L Cepko & Joseph C Corbo, 2007. "The Cis-regulatory Logic of the Mammalian Photoreceptor Transcriptional Network," PLOS ONE, Public Library of Science, vol. 2(7), pages 1-16, July.

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