Simon Bourdareau1, Leila Tirichine2, Bérangère Lombard3, Damarys Loew3, Delphine Scornet1, Yue Wu2, Susana M Coelho4,5, J Mark Cock6. 1. CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France. 2. Université de Nantes, CNRS, UFIP, UMR 6286, F-44000, Nantes, France. 3. Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, 75248, Paris, Cedex 05, France. 4. CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France. susana.coelho@tuebingen.mpg.de. 5. Current address: Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany. susana.coelho@tuebingen.mpg.de. 6. CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France. cock@sb-roscoff.fr.
Abstract
BACKGROUND: Brown algae evolved complex multicellularity independently of the animal and land plant lineages and are the third most developmentally complex phylogenetic group on the planet. An understanding of developmental processes in this group is expected to provide important insights into the evolutionary events necessary for the emergence of complex multicellularity. Here, we focus on mechanisms of epigenetic regulation involving post-translational modifications of histone proteins. RESULTS: A total of 47 histone post-translational modifications are identified, including a novel mark H2AZR38me1, but Ectocarpus lacks both H3K27me3 and the major polycomb complexes. ChIP-seq identifies modifications associated with transcription start sites and gene bodies of active genes and with transposons. H3K79me2 exhibits an unusual pattern, often marking large genomic regions spanning several genes. Transcription start sites of closely spaced, divergently transcribed gene pairs share a common nucleosome-depleted region and exhibit shared histone modification peaks. Overall, patterns of histone modifications are stable through the life cycle. Analysis of histone modifications at generation-biased genes identifies a correlation between the presence of specific chromatin marks and the level of gene expression. CONCLUSIONS: The overview of histone post-translational modifications in the brown alga presented here will provide a foundation for future studies aimed at understanding the role of chromatin modifications in the regulation of brown algal genomes.
BACKGROUND: Brown algae evolved complex multicellularity independently of the animal and land plant lineages and are the third most developmentally complex phylogenetic group on the planet. An understanding of developmental processes in this group is expected to provide important insights into the evolutionary events necessary for the emergence of complex multicellularity. Here, we focus on mechanisms of epigenetic regulation involving post-translational modifications of histone proteins. RESULTS: A total of 47 histone post-translational modifications are identified, including a novel mark H2AZR38me1, but Ectocarpus lacks both H3K27me3 and the major polycomb complexes. ChIP-seq identifies modifications associated with transcription start sites and gene bodies of active genes and with transposons. H3K79me2 exhibits an unusual pattern, often marking large genomic regions spanning several genes. Transcription start sites of closely spaced, divergently transcribed gene pairs share a common nucleosome-depleted region and exhibit shared histone modification peaks. Overall, patterns of histone modifications are stable through the life cycle. Analysis of histone modifications at generation-biased genes identifies a correlation between the presence of specific chromatin marks and the level of gene expression. CONCLUSIONS: The overview of histone post-translational modifications in the brown alga presented here will provide a foundation for future studies aimed at understanding the role of chromatin modifications in the regulation of brown algal genomes.
Entities:
Keywords:
Brown algae; ChIP-seq; Chromatin; Ectocarpus; Gametophyte; Histone modification; Life cycle; Multicellularity; Polycomb complex; Sporophyte
Authors: Judd C Rice; Scott D Briggs; Beatrix Ueberheide; Cynthia M Barber; Jeffrey Shabanowitz; Donald F Hunt; Yoichi Shinkai; C David Allis Journal: Mol Cell Date: 2003-12 Impact factor: 17.970
Authors: Antoine H F M Peters; Stefan Kubicek; Karl Mechtler; Roderick J O'Sullivan; Alwin A H A Derijck; Laura Perez-Burgos; Alexander Kohlmaier; Susanne Opravil; Makoto Tachibana; Yoichi Shinkai; Joost H A Martens; Thomas Jenuwein Journal: Mol Cell Date: 2003-12 Impact factor: 17.970
Authors: Sarah R Rommelfanger; Mowei Zhou; Henna Shaghasi; Shin-Cheng Tzeng; Bradley S Evans; Ljiljana Paša-Tolić; James G Umen; James J Pesavento Journal: J Am Soc Mass Spectrom Date: 2021-06-24 Impact factor: 3.262