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This work was supported by grants RTI2018-097749-B-100, BIO2015-68031-R and RYC-2013-14689 to P.C., and BES-2016-078939 fellowship to L.P.V. from the Spanish Ministerio de Economia y Competitividad (MINECO/FEDER, EU); and by the Severo Ochoa Program for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain, grant SEV-2016-0672 (2017-2021) to the CBGP. M.P.M. was supported by a Postdoctoral contract associated with the Severo Ochoa Program.

Analysis of institutional authors

Paya-Milans, MiriamAuthorPoza-Viejo, LauraAuthorWilkinson, Mark D.Corresponding AuthorCrevillen, PedroCorresponding Author

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January 27, 2020
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Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa

Publicated to:Gigascience. 8 (12): giz147- - 2019-12-06 8(12), DOI: 10.1093/gigascience/giz147

Authors: Paya-Milans, Miriam; Poza-Viejo, Laura; San Martin-Uriz, Patxi; Lara-Astiaso, David; Wilkinson, Mark D.; Crevillen, Pedro;

Affiliations

Univ Navarra, CIMA, Ave Pio XII 55, Pamplona 31008, Spain - Author
UPM, Inst Nacl Invest & Tecnol Agr & Alimentari INIA, CBGP, Campus Montegancedo, Pozuelo De Alarcon 28223, Madrid, Spain - Author

Abstract

Background: Genome-wide maps of histone modifications have been obtained for several plant species. However, most studies focus on model systems and do not enforce FAIR data management principles. Here we study the H3K27me3 epigenome and associated transcriptome of Brassica rapa, an important vegetable cultivated worldwide. Findings: We performed H3K27me3 chromatin immunoprecipitation followed by high-throughput sequencing and transcriptomic analysis by 3-end RNA sequencing from B. rapa leaves and inflorescences. To analyze these data we developed a Reproducible Epigenomic Analysis pipeline using Galaxy and Jupyter, packaged into Docker images to facilitate transparency and reuse. We found that H3K27me3 covers roughly one-third of all B. rapa protein-coding genes and its presence correlates with low transcript levels. The comparative analysis between leaves and inflorescences suggested that the expression of various floral regulatory genes during development depends on H3K27me3. To demonstrate the importance of H3K27me3 for B. rapa development, we characterized a mutant line deficient in the H3K27 methyltransferase activity. We found that braA.clf mutant plants presented pleiotropic alterations, e.g., curly leaves due to increased expression and reduced H3K27me3 levels at AGAMOUS-like loci. Conclusions: We characterized the epigenetic mark H3K27me3 at genome-wide levels and provide genetic evidence for its relevance in B. rapa development. Our work reveals the epigenomic landscape of H3K27me3 in B. rapa and provides novel genomics datasets and bioinformatics analytical resources. We anticipate that this work will lead the way to further epigenomic studies in the complex genome of Brassica crops.

Keywords

Brassica rapaChromatin immunoprecipitationEpigenomicsExpressionFlowersGene expression profilingGene expression regulation, plantHigh-throughput nucleotide sequencingHistone h3HistonesPlant leavesPlant proteinsPolycomb-group genesRead alignmentSelectionSequence analysis, dnaSequence analysis, rnaTrimethylation

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Gigascience due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2019, it was in position 10/71, thus managing to position itself as a Q1 (Primer Cuartil), in the category Multidisciplinary Sciences.

From a relative perspective, and based on the normalized impact indicator calculated from the Field Citation Ratio (FCR) of the Dimensions source, it yields a value of: 2.44, which indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: Dimensions Jul 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-07-09, the following number of citations:

  • WoS: 10
  • Scopus: 16
  • Europe PMC: 7

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-07-09:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 54.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 54 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 17.05.
  • The number of mentions on the social network Facebook: 2 (Altmetric).
  • The number of mentions on the social network X (formerly Twitter): 27 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (PAYA MILANS, MIRIAM) and Last Author (Crevillen Lomas, Pedro).

the authors responsible for correspondence tasks have been WILKINSON, MARK DENIS and Crevillen Lomas, Pedro.