Native Chromatin Immunoprecipitation

Cosseau, Céline; Grunau, Christoph

doi:10.1007/978-1-61779-316-5_15

Cited by 20 publications

(11 citation statements)

References 10 publications

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“…Experiments were done in duplicate. Antibodies were carefully tested for specificity as described in [ 27 ] and saturating quantities (see [ 27 ]) were used. Further details are available at http://methdb.univ-perp.fr/epievo/…”

Section: Methodsmentioning

confidence: 99%

The Epigenome of Schistosoma mansoni Provides Insight about How Cercariae Poise Transcription until Infection

et al. 2015

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BackgroundChromatin structure can control gene expression and can define specific transcription states. For example, bivalent methylation of histone H3K4 and H3K27 is linked to poised transcription in vertebrate embryonic stem cells (ESC). It allows them to rapidly engage specific developmental pathways. We reasoned that non-vertebrate metazoans that encounter a similar developmental constraint (i.e. to quickly start development into a new phenotype) might use a similar system. Schistosomes are parasitic platyhelminthes that are characterized by passage through two hosts: a mollusk as intermediate host and humans or rodents as definitive host. During its development, the parasite undergoes drastic changes, most notable immediately after infection of the definitive host, i.e. during the transition from the free-swimming cercariae into adult worms.Methodology/Principal FindingsWe used Chromatin Immunoprecipitation followed by massive parallel sequencing (ChIP-Seq) to analyze genome-wide chromatin structure of S. mansoni on the level of histone modifications (H3K4me3, H3K27me3, H3K9me3, and H3K9ac) in cercariae, schistosomula and adults (available at http://genome.univ-perp.fr). We saw striking differences in chromatin structure between the developmental stages, but most importantly we found that cercariae possess a specific combination of marks at the transcription start sites (TSS) that has similarities to a structure found in ESC. We demonstrate that in cercariae no transcription occurs, and we provide evidences that cercariae do not possess large numbers of canonical stem cells.Conclusions/SignificanceWe describe here a broad view on the epigenome of a metazoan parasite. Most notably, we find bivalent histone H3 methylation in cercariae. Methylation of H3K27 is removed during transformation into schistosomula (and stays absent in adults) and transcription is activated. In addition, shifts of H3K9 methylation and acetylation occur towards upstream and downstream of the transcriptional start site (TSS). We conclude that specific H3 modifications are a phylogenetically older and probably more general mechanism, i.e. not restricted to stem cells, to poise transcription. Since adult couples must form to cause the disease symptoms, changes in histone modifications appear to be crucial for pathogenesis and represent therefore a therapeutic target.

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Section: Methodsmentioning

confidence: 99%

The Epigenome of Schistosoma mansoni Provides Insight about How Cercariae Poise Transcription until Infection

et al. 2015

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“…Inputs were used for normalization in all subsequent bioinformatics analyses. Antibodies were carefully tested for specificity as described in Cosseau & Grunau () and saturating quantities were used. We had earlier shown that the above‐mentioned catalogue/lot numbers for anti‐H3K4me3 and anti‐H3K27me3 can be used for ChIP‐Seq (Roquis et al .…”

Section: Methodsmentioning

confidence: 99%

“…). For H3K27ac and H4K20me1, we performed all the validation steps described by Cosseau & Grunau (), including a chromatin titration to assess specificity of the antibodies. Titrations, using increasing amount of antibodies over the same quantity of S. mansoni chromatin, proved that antibodies were indeed specific and able to immunoprecipitate all target chromatin using 4 μL of the antibody for 5000 cercariae or 20 adult female worms (Fig.…”

Section: Methodsmentioning

confidence: 99%

Frequency and mitotic heritability of epimutations in Schistosoma mansoni

et al. 2016

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Schistosoma mansoni is a parasitic platyhelminth responsible for intestinal bilharzia. It has a complex life cycle, infecting a freshwater snail of the Biomphalaria genus, and then a mammalian host. Schistosoma mansoni adapts rapidly to new (allopatric) strains of its intermediate host. To study the importance of epimutations in this process, we infected sympatric and allopatric mollusc strains with parasite clones. ChIP-Seq was carried out on four histone modifications (H3K4me3, H3K27me3, H3K27ac and H4K20me1) in parallel with genomewide DNA resequencing (i) on parasite larvae shed by the infected snails and (ii) on adult worms that had developed from the larvae. No change in single nucleotide polymorphisms and no mobilization of transposable elements were observed, but 58-105 copy number variations (CNVs) within the parasite clones in different molluscs were detected. We also observed that the allopatric environment induces three types of chromatin structure changes: (i) host-induced changes on larvae epigenomes in 51 regions of the genome that are independent of the parasites' genetic background, (ii) spontaneous changes (not related to experimental condition or genotype of the parasite) at 64 locations and (iii) 64 chromatin structure differences dependent on the parasite genotype. Up to 45% of the spontaneous, but none of the host-induced chromatin structure changes were transmitted to adults. In our model, the environment induces epigenetic changes at specific loci but only spontaneous epimutations are mitotically heritable and have therefore the potential to contribute to transgenerational inheritance. We also show that CNVs are the only source of genetic variation and occur at the same order of magnitude as epimutations.

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“…Our chromatin extraction protocol is based on (Cosseau and Grunau, 2011), but had to be adapted so that salinity, ionic strength and osmolarity of various buffers would match those of seawater. P. acuta (healthy or bleached), M. digitata, S. pistillata and E. divisa.…”

Section: Coral Nuclei Isolationmentioning

confidence: 99%

The tropical coral Pocillopora acuta has a mosaic DNA methylome, an unusual chromatin structure and shows histone H3 clipping

Roquis

Picolo

Raffalli

et al. 2019

Preprint

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Pocillopora acuta is a hermatypic coral with a worldwide distribution and a strong ecological importance. Anthropogenic disturbances and global warming threaten it. Thermal stress can induce coral bleaching, a phenomenon in which the mutualistic symbiosis between the coral polyps host and its endosymbiotic unicellular algae is disrupted, and can lead to the death of entire colonies. Previous works have shown that soma clonal colonies display different levels of survival depending on the environmental conditions they previously faced. Epigenetic mechanisms are good candidates to explain this phenomenon. The clonal nature of a colony and the possibility of generating genetically identical colonies through propagation make corals an attractive model to study the impact of the environment on the epigenome. However, until now, no work had been published on the P. acuta epigenome. One of the main problems is caused by the intracellular location of Symbiodinium, which makes it complicated to isolate coral chromatin free of contamination by endiosymbiotic biological material. Here, (i) we describe a simple method to purify P. acuta chromatin, (ii) we provide the first description of a coral methylome, with a mosaic pattern of cytosine methylation principally in a CpG context (4% of all CpG), and (iii) we show that P. acuta, but not all corals, has an unusual chromatin structure, and displays histone H3 clipping.

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Native Chromatin Immunoprecipitation

Cited by 20 publications

References 10 publications

The Epigenome of Schistosoma mansoni Provides Insight about How Cercariae Poise Transcription until Infection

The Epigenome of Schistosoma mansoni Provides Insight about How Cercariae Poise Transcription until Infection

Frequency and mitotic heritability of epimutations in Schistosoma mansoni

The tropical coral Pocillopora acuta has a mosaic DNA methylome, an unusual chromatin structure and shows histone H3 clipping

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