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Prior related work

Posted by PLOS_CompBiol on 26 Feb 2008 at 14:54 GMT

Originally submitted as a Reader Response on 12th November 2007

We wish to correct a claim made in the abstract of this paper that this is the "first demonstration that nucleosome occupancy information can be used to improve motif discovery". In point of fact, information on nucleosome occupancy was used by us and our colleagues in 2006, in a paper cited by the authors in a different context (Reference 15; Liu et al, Whole genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome Research 16 1517 (2006)). Specifically, in a section of that paper entitled "Use of nucleosome occupancy for improvement of ChIP-chip-based motif identification", we showed that motif discovery could be dramatically improved by weighting the input sequences based on a histone ChIP-chip experiment. Details can also be found in the Methods section of that paper. We ask readers who have occasion to cite Narlikar et al to also examine the Genome Research paper (PMID: 17053089) and make their own judgment as to whether citation of that paper is also appropriate.

Neil D. Clarke (Genome Institute of Singapore) and Jason D. Lieb (University of North Carolina)

Submitted by: Neil Clarke
E-mail: clarken@gis.a-star.edu.sg
Occupation: Deputy Director
Genome Insitute of Singapore

Additional authors: Jason Lieb

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Authors respond

PLOS_CompBiol replied to PLOS_CompBiol on 26 Feb 2008 at 14:56 GMT

Originally submitted as a Reader Response on 7th December 2007

Hello Neil and Jason,

Thanks for your posted message. I wanted the PLoS readership to know that the three of us have now had a chance to discuss offline the issue that you raised in your post to our collective satisfaction. To achieve closure, I thought it would be helpful to readers for me to post a message sharing some of what we have discussed.

The paper in which you and your co-authors examine the average nucleosome occupancy of yeast promoters bound by Leu3 is nice work, and my co-authors and I agree that readers interested in the results of our paper should also read yours. Since we were aware of your paper (cited as ref. 15), we chose the wording of our abstract carefully. In particular, we used the word demonstration in the sense of its first definition listed at http://dictionary.referen...

1. the act or circumstance of proving or being proved conclusively, as by reasoning or a show of evidence.

With this conclusive sense in mind, we think the sentence in our abstract is accurate. At the same time, we recognize that the word demonstration is sometimes used in a less stringent sense, as reflected in the third and fourth definitions listed at the same site. As a result, our intended meaning was ambiguous; we appreciate you bringing this to our attention. The sentence would have been clearer had we added "systematic", "comprehensive", or "conclusive" to specify our intended meaning.

From a scientific point of view, it is intriguing to note that you reported a stronger Leu3 motif by giving more weight to highly occupied promoters, while our approach is based on giving more weight to positions less likely to be occupied. It will be interesting to learn more about when these alternative strategies work, and more generally, how to best make use of the wealth of epigenetic data that is now being generated. It is an exciting time to be working in this area.

Thanks again for your note.

Warm regards,
Alex

Submitted by: Alexander Hartemink
E-mail: amink@cs.duke.edu
Occupation: Professor
Duke University

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