Publishing with eLife: “make positive impacts by contributing to such nourishing culture”

Our lab has previously shown that CDCA7, a protein with a unique zinc finger domain (zf-4CXXC_R1), is a critical activator of the nucleosome remodelling ATPase HELLS. DDM1, the plant homolog of HELLS, is famous for its importance in maintaining genomic DNA methylation, and mutations of human CDCA7 and HELLS cause immunodeficiency, centromeric instability, facial anomalies (ICF) syndrome, which is associated with DNA hypomethylation. Although it was predicted that nucleosome remodelling activity will help DNA methyltransferases access nucleosomal DNA, it was not clear if/why HELLS/DDM1, among several other nucleosome remodelling ATPases, plays a unique role in DNA methylation. We hypothesized that if the role of CDCA7 and HELLS is tightly coupled to DNA methylation, they would readily become dispensable during evolution in species that lost DNA methyltransferases (and DNA methylation), as seen in Drosophila and C. elegans. In this paper, through investigating the presence and absence of genes in diverse eukaryotic species, we present evidence of coevolution of CDCA7, HELLS and DNMT1, the maintenance DNA methyltransferase, supporting the hypothesis.

... constructive criticisms greatly improved our manuscript.

This manuscript was atypical for a couple of reasons; this was my first first-author original research article since I became a lab head 20 years ago, and the topic (Evolutionary Biology) of the paper was not my expertise. Yet, I believed that our finding will be informative to the epigenetics field, and I wanted to publish a good paper, i.e., matching to the rigor that I ask for publications from my lab.

For that reason, it was essential to find experts who are willing to critically review our paper manuscript. At the same time, I did not want to spend too much time on the revision process, since the core message of the paper has already inspired us to test a specific hypothesis, and we had very exciting supporting results (that we've published in a follow-up paper)! Coincidentally, I realized that the new eLife review model was going to be available about the time when my manuscript would be ready for submission. The mechanism that would allow the authors to control the “Version of Record” after review was particularly attractive to this manuscript. The fact that I was the first and corresponding author of this manuscript made it easy to make the decision; I was happy to serve as a “Guinea pig” to check out this model.

Overall, I was pleased to choose this venue. The most important point for me was to secure constructive reviewers, which I got. I really thanked the two reviewers, whose constructive criticisms greatly improved our manuscript. However, I found that the time to make editorial decisions was much slower than I wished to have, due to several of those rate limiting steps, such as decision to review and drafting the summary statements by the editor. This was understandable since the editor was an active scientist, and I did not push to accelerate the process since I was not in a hurry. In fact, one concern I had was the requirement to “publish” our responses to public comments by the editor and reviewers two weeks after we received these comments – I did not want to craft them while I was chasing the important grant due date! So, I think it would be nice to have a reasonable grace period where the authors can control the timing of publishing the reviewers’ comments, although I understand the necessity of the deadline. Overall, I found that the fee was very reasonable for what we got.

[public commentary] takes extra effort, but you can make positive impacts by contributing to such nourishing culture.

I was very fortunate to have the two reviewers who both gave constructive criticisms, which significantly improved our manuscript. eLife Assessment was also important, especially for this new model, in which the authors can control what to “publish”. One thing that I did not realize was that there were two distinct parts of the review, public comments and specific comments that were not published. I thought that it would be better to publish specific comments as well, since they revealed the quality of the reviewers.

I still believe that peer review is essential for science, but reviewers… cannot be responsible for the content of the paper.

We (the scientists) complain about the amount of data that we are expected to generate for one paper as available technologies keep expanding. We also complain that we have no time to catch up with the inflating number of publications and that data included in one paper are too massive for a reviewer to critically evaluate in a timely manner. I still believe that peer review is essential for science, but reviewers are after all free volunteers and cannot be responsible for the content of the paper. Instead, the authors must be fully responsible for the content, and it is the authors’ responsibility to decide whether and how each point raised by the reviewers should be addressed. The new eLife Model has a reasonable reconciliation to alleviate the current issues associated with publication in science. It is a good option for the scientists to have so that the authors gain the full responsibility in what to publish while keeping the curation/review process, which is also important to maintain the journal’s credibility. However, the success of the new eLife Model depends on commitment and diversity of the editors.

As the number of publications has been inflating, it has become difficult to find a good reviewer who is willing to take time to make constructive criticisms of your paper. Thankfully, most of my published papers were significantly improved during the process of responding to reviewers’ comments, though I encountered a few unconstructive reviewers once in a while. During the revision process, we often found an error that was not pointed out by any of the reviewers. In the end, you must be the most critical reviewer of your own manuscript, and you must know how to make a constructive criticism – asking if the major points are supported by data, if the major points are important/exciting, and if not, what can be done. We need to develop the culture of making constructive criticisms in the lab, in the institute, in the field, and in journals. Once you learn how to make constructive criticisms and regularly practise it, you should be able to defend your points against unreasonable comments and requests. The eLife review model encourages constructive criticisms through visualizing reviewers’ identity among them, and through asking them to write public comments. This takes extra effort, but you can make positive impacts by contributing to such nourishing culture.

“we liked the idea of having an open "conversation" with the reviewers...without the threat of rejection.” – Patrick Allard

“In this new process of publishing, authors have significant autonomy over their papers. The entire publication and review process are more transparent.” – Chunxiao Li

“... immediately clear that the paper was reviewed by experts in the field who provided great and constructive feedback.” – Meike van der Heijden

What is a Reviewed Preprint?
What is an eLife Assessment?
What happens after you submit your research?

Hiro Funabiki is a faculty member in the David Rockefeller Graduate Program, the Tri-Institutional M.D.-Ph.D. Program, and the Cell & Developmental Biology Program, Weill Cornell Medicine Graduate School of Medical Sciences.