Brief Communications Arising | Published:

Universality of core promoter elements?

Nature volume 511, pages E11E12 (24 July 2014) | Download Citation

Abstract

Arising from B. J. Venters & B. F. Pugh Nature 502, 53–58 (2013); doi:10.1038/nature12535

How cells locate the regions to initiate transcription is an open question, because core promoter elements (CPEs) are found in only a small fraction of core promoters1,2,3,4. A recent study5 measured 159,117 DNA binding regions of transcription factor IIB (TFIIB) by ChIP-exo (chromatin immunoprecipitation with lambda exonuclease digestion followed by high-throughput sequencing) in human cells, found four degenerate CPEs—upstream and downstream TFIIB recognition elements (BREu and BREd), TATA and initiator element (INR)in nearly all of them, and concluded that these regions represent sites of transcription initiation marked by universal CPEs. We show that the claimed universality of CPEs is explained by the low specificities of the patterns used and that the same match frequencies are obtained with two negative controls (randomized sequences and scrambled patterns). Our analyses also cast doubt on the biological significance of most of the 150,753 non-messenger-RNA-associated ChIP-exo peaks, 72% of which lie within repetitive regions. There is a Retraction accompanying this Brief Communication Arising by Venters, B. J. & Pugh, B. F. Nature 511, http://dx.doi.org/10.1038/nature13588 (2014).

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References

  1. 1.

    , , & Computational analysis of core promoters in the Drosophila genome. Genome Biol. 3, RESEARCH0087 (2002)

  2. 2.

    Perspectives on the RNA polymerase II core promoter. Wiley Interdiscip. Rev. Dev. Biol. 1, 40–51 (2012)

  3. 3.

    , & Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nature Rev. Genet. 13, 233–245 (2012)

  4. 4.

    , , , & P-value-based regulatory motif discovery using positional weight matrices. Genome Res. 23, 181–194 (2013)

  5. 5.

    & Genomic organization of human transcription initiation complexes. Nature 502, 53–58 (2013)

  6. 6.

    & Mammalian retroelements. Genome Res. 12, 1455–1465 (2002)

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Author information

Affiliations

  1. *Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany

    • Matthias Siebert
    •  & Johannes Söding
  2. †Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany

    • Johannes Söding

Authors

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Contributions

M.S. performed research and J.S. guided research; both M.S. and J.S. wrote the manuscript.

Competing interests

Declared none.

Corresponding author

Correspondence to Johannes Söding.

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DOI

https://doi.org/10.1038/nature13587

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