An Efficient Chromatin Immunoprecipitation Protocol for the Analysis of Histone Modification Distributions in the Brown Alga Ectocarpus.

The brown algae are an important but understudied group of multicellular marine organisms. A number of genetic and genomic tools have been developed for the model brown alga Ectocarpus; this includes, most recently, chromatin immunoprecipitation methodology, which allows genome-wide detection and analysis of histone post-translational modifications. Post-translational modifications of histone molecules have been shown to play an important role in gene regulation in organisms from other major eukaryotic lineages, and this methodology will therefore be a very useful tool to investigate genome function in the brown algae. This article provides a detailed, step-by-step description of the Ectocarpus ChIP protocol, which effectively addresses the difficult problem of efficiently extracting chromatin from cells protected by a highly resistant cell wall. The protocol described here will be an essential tool for the future application of chromatin analysis methodologies in brown algal research.

Chromatin landscape associated with sexual differentiation in a UV sex determination system.

In many eukaryotes, such as dioicous mosses and many algae, sex is determined by UV sex chromosomes and is expressed during the haploid phase of the life cycle. In these species, the male and female developmental programs are initiated by the presence of the U- or V-specific regions of the sex chromosomes but, as in XY and ZW systems, sexual differentiation is largely driven by autosomal sex-biased gene expression. The mechanisms underlying the regulation of sex-biased expression of genes during sexual differentiation remain elusive. Here, we investigated the extent and nature of epigenomic changes associated with UV sexual differentiation in the brown alga Ectocarpus, a model UV system. Six histone modifications were quantified in near-isogenic lines, leading to the identification of 16 chromatin signatures across the genome. Chromatin signatures correlated with levels of gene expression and histone PTMs changes in males versus females occurred preferentially at genes involved in sex-specific pathways. Despite the absence of chromosome scale dosage compensation and the fact that UV sex chromosomes recombine across most of their length, the chromatin landscape of these chromosomes was remarkably different to that of autosomes. Hotspots of evolutionary young genes in the pseudoautosomal regions appear to drive the exceptional chromatin features of UV sex chromosomes.

A partially sex-reversed giant kelp sheds light into the mechanisms of sexual differentiation in a UV sexual system.

In UV sexual systems, sex is determined during the haploid phase of the life cycle and males have a V chromosome whereas females have a U chromosome. Previous work in the brown alga Ectocarpus revealed that the V chromosome has a dominant role in male sex determination and suggested that the female developmental programme may occur by 'default'. Here, we describe the identification of a genetically male giant kelp strain presenting phenotypic features typical of a female, despite lacking the U-specific region. The conversion to the female developmental programme is however incomplete, because gametes of this feminized male are unable to produce the sperm-attracting pheromone lamoxirene. We identify the transcriptomic patterns underlying the male and female specific developmental programmes, and show that the phenotypic feminization is associated with both feminization and de-masculinization of gene expression patterns. Importantly, the feminization phenotype was associated with dramatic downregulation of two V-specific genes including a candidate male-determining gene. Our results reveal the transcriptional changes associated with sexual differentiation in a UV system, and contribute to disentangling the role of sex-linked and autosomal gene expression in the initiation of sex-specific developmental programmes. Overall, the data presented here imply that the U-specific region is not required to initiate the female developmental programme, but is critical to produce fully functional eggs, arguing against the idea that female is the 'default' sex in this species.

UV Chromosomes and Haploid Sexual Systems.

The evolution of sex determination continues to pose major questions in biology. Sex-determination mechanisms control reproductive cell differentiation and development of sexual characteristics in all organisms, from algae to animals and plants. While the underlying processes defining sex (meiosis and recombination) are conserved, sex-determination mechanisms are highly labile. In particular, a flow of new discoveries has highlighted several fascinating features of the previously understudied haploid UV sex determination and related mating systems found in diverse photosynthetic taxa including green algae, bryophytes, and brown algae. Analyses integrating information from these systems and contrasting them with classical XY and ZW systems are providing exciting insights into both the universality and the diversity of sex-determining chromosomes across eukaryotes.