Short interview with PLoS ONE Gene Expression author

In a recent analysis of the quality articles published in PLoS ONE, Gene Expression emerged as our second most-published topic. We’re delighted to see the Gene Expression community gathering on our peer-reviewed open accesss journal and we would like to publish more work so that we become a preferred venue for those in this field.

As part of our call for Gene Expression papers during July, this article entitled High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes by Fahlgren et al had the most citations in Google Scholar for Gene Expression papers published in PLoS ONE. It also had healthy unique page views in Google Analytics and full text and PDF downloads in PubMed Central.

Curious to know more about this paper, I reached out to the corresponding author James C. Carrington, Center for Genome Research and Biocomputing, Oregon State University, USA to ask him a few questions about his experiences of publishing in PLoS ONE and the work of this group in general. Here are his replies:

Q Could you please tell us why your team chose PLoS ONE to publish this work?

A "We chose PLoS ONE for this particular paper for a few reasons. First, I have supported the PLoS concept and principles, having served on the Editorial Board of PLoS Biology since the beginning. And we have published what I consider to be some of our most important work in PLoS Biology, even before it was clear that the model would work. I believe that the community needs to support these types of initiatives through submission of quality papers. PLoS ONE sounded like an interesting concept, so we wanted to support it. And second, as is frequently the case in the small RNA community, we wanted to get the story out quickly because of "competing" papers".

Q We were wondering what your experience of publishing with us was like, and whether you’d do it again!

A "We were quite happy with the submission, review and publication process. We wanted to make it into the first issue, but could not push it quite fast enough. We will undoubtedly publish in PLoS ONE again".

Q Please comment on the science itself – why do you think this paper is so highly read and cited? Also, how has the field and your role in it moved on since then – for instance, what are you investigating now?

A “I think the paper is getting a lot of citations because of the data relating to birth and death of MIRNA genes. The data presented in the PLoS ONE paper, as well as from the labs of David Bartel, Richard Carthew and others supports the idea that new genes with the potential to form miRNAs in plants and animals are relatively easy to spawn, but that most die out over evolutionary time. We showed that new miRNA-generating loci can form from inverted duplication events from protein-coding genes. In some cases, the new miRNA retain specificity for transcripts in the family of origin. In some other cases, however, new specificities are acquired through drift. The mechanisms whereby new genes with novel functions arise during evolution will likely be an interesting topic for a long time. Since this paper, technology to sequence and profile small RNAs has advanced rapidly. With higher throughput techniques, we can investigate miRNA evolution far more broadly and with higher resolution and confidence.

We are branching out to look at small RNA functions and evolutionary patterns in species related to Arabidopsis thaliana, with the goal of understanding how regulatory specificity is generated and utilized during evolution”.