Combining molecular information on chromatin organisation with eQTLs and evolutionary conservation provides strong candidates for the evolution of gene regulation in mammalian brains
Evolutionary analysis of candidate non-coding elements regulating neurodevelopmental genes in vertebrates
In this manuscript , Francisco J. Novo proposes candidate non-coding genomic elements regulating neurodevelopmental genes.
What is very nice about this study is the way in which public molecular data, including physical interaction data, is used to leverage recent advances in our understanding to molecular mechanisms of gene regulation in an evolutionary context. More specifically, evolutionarily conserved non coding sequences are combined with enhancers from the FANTOM5 project, DNAse hypersensitive sites, chromatin segmentation, ChIP-seq of transcription factors and of p300, gene expression and eQTLs from GTEx, and physical interactions from several Hi-C datasets. The candidate regulatory regions thus identified are linked to candidate regulated genes, and the author shows their potential implication in brain development.
While the results are focused on a small number of genes, this allows to verify features of these candidates in great detail. This study shows how functional genomics is increasingly allowing us to fulfill the promises of Evo-Devo: understanding the molecular mechanisms of conservation and differences in morphology.
 Novo, FJ. 2017. Evolutionary analysis of candidate non-coding elements regulating neurodevelopmental genes in vertebrates. bioRxiv, 150482, ver. 4 of Sept 29th, 2017. doi: 10.1101/150482
Marc Robinson-Rechavi (2017) Combining molecular information on chromatin organisation with eQTLs and evolutionary conservation provides strong candidates for the evolution of gene regulation in mammalian brains. Peer Community in Evolutionary Biology, 100035. https://doi.org/10.24072/pci.evolbiol.100035
Evaluation round #1
DOI or URL of the preprint: 10.1101/150482
Version of the preprint: 2
Author's Reply, 17 Jun 2022
Decision by Marc Robinson-Rechavi, 02 Aug 2017
Dear Francisco Novo,
Thank you for submitting your manuscript for recommendation at PCI Evol Biol. We are aware that this is a very new concept, and we appreciate that you are giving it a chance. The process is also new for us, so please do not hesitate to give us feedback, our common aim must be to make the best science possible available.
As you will see, the expert reviewer I invited and myself found your approach interesting, but also that there were problems with your interpretation of the data. Thus I am not proposing at present a public recommendation of your manuscript. But I hope that the two reviews will be helpful for you to improve the work and the manuscript, to re-request a recommendation at PCI Evol Biol or to submit directly an improved manuscript to a classical journal.
Best regards Marc