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The physiological effect of a gene is not just determined by its DNA sequence alone. In recent years, researchers have discovered the important role of DNA methylation: A methyl group on cytosine is an epigenetic modification that affects development, transcription, and a range of other functions.

To understand how DNA methylation affects a particular phenotype, it can be useful to look at methylation of an entire genome. In a recent F1000Research paper, Michael Hackenberg (University of Granada, Spain) describes the development of a tool called MethylExtract, which makes it possible to generate whole genome methylation maps.   Below, he answers some questions about his article.

1. What is MethylExtract?

MethylExtract is a tool for the methylation profiling from previously aligned bisulfite-treated reads. Furthermore, it can detect sequence variation in the same experimental dataset, which will be important for several downstream experiments.

2. Why is whole genome methylation mapping important?

One of the final goals of epigenome research will be to understand how DNA methylation patterns are established, and the extent to which DNA methylation is involved in gene regulation, development, or differentiation. To achieve this goal, a first step will be to obtain high quality whole genome methylation maps from many different cell types and conditions. Comparisons between the individual methylomes allow the detection of differentially methylated regions (DMRs), i.e. regions characterized by changes in the methylation levels between different tissues, conditions or developmental stages. The DMRs can then be more closely analysed with a special focus on transcription factor binding and sequence variation, which might be causally related to differential methylation.

3. How have you experienced the post-publication peer review process at F1000Research?

We are very pleased with the experience publishing with F1000Research under this new post-publication peer review process. One obvious advantage is that the manuscript is available very shortly after submission (in our case approximately one week). Since it has been available online, not only could we track the number of visits and downloads, but we obtained valuable feedback shortly after publication, which allowed us to improve some aspects in parallel to the reviewing process.

Another positive aspect not related to post-publication review but to open peer review in general is the quality of the referee reports. In our case, all three reviews showed a thorough understanding of our work, helping us to notably improve the quality of the tool and the manuscript. I can imagine that this is a general trend in open peer review, as publicly available, signed reports will lower the tendency to hand in scarce and patchy reviews.

4. What did you think of our integration of your data and software into your paper?

I agree that a better support for software applications, i.e. to upload the code to a public repository, is an important step to guarantee a long-term accessibility of the software.  Furthermore, indeed, data sharing ensures the reproducibility of scientific results.

[Editor’s note: We use Github and Zenodo to make the source code of software described in F1000Research papers available and citable. See this blogpost for more information, and see the code from Michael Hackenberg’s paper on Zenodo.]