Techniques to Study Epigenetic Control and the Epigenome in Parasites

Nardelli, Sheila Cristina; Ting, Li Min; Kim, Kami

doi:10.1007/978-1-4939-1438-8_10

Cited by 6 publications

(6 citation statements)

References 39 publications

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“…In previous work, we applied ChIP-chip to T. gondii and showed that the distributions of epigenomic modifications on chromatin are conserved in protozoa [ 22 ]. We standardized native chromatin immunoprecipitation (N-ChIP) for T. gondii using native DNA without crosslinking digested with Micrococcal nuclease (MNase) followed by next generation sequencing [ 23 ]. The digested fragments of around 150–200 bp represent nucleosomal DNA, as verified by nucleosome mapping of input DNA.…”

Section: Resultsmentioning

confidence: 99%

Genome-wide localization of histone variants in Toxoplasma gondii implicates variant exchange in stage-specific gene expression

et al. 2022

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Background Toxoplasma gondii is a protozoan parasite that differentiates from acute tachyzoite stages to latent bradyzoite forms in response to environmental cues that modify the epigenome. We studied the distribution of the histone variants CenH3, H3.3, H2A.X, H2A.Z and H2B.Z, by genome-wide chromatin immunoprecipitation to understand the role of variant histones in developmental transitions of T. gondii parasites. Results H3.3 and H2A.X were detected in telomere and telomere associated sequences, whereas H3.3, H2A.X and CenH3 were enriched in centromeres. Histones H2A.Z and H2B.Z colocalize with the transcriptional activation mark H3K4me3 in promoter regions surrounding the nucleosome-free region upstream of the transcription start site. The H2B.Z/H2A.Z histone pair also localizes to the gene bodies of genes that are silent but poised for activation, including bradyzoite stage-specific genes. The majority of H2A.X and H2A.Z/H2B.Z loci do not overlap, consistent with variant histones demarcating specific functional regions of chromatin. The extent of enrichment of H2A.Z/H2B.Z (and H3.3 and H2A.X) within the entire gene (5’UTR and gene body) reflects the timing of gene expression during the cell cycle, suggesting that dynamic turnover of H2B.Z/H2A.Z occurs during the tachyzoite cell cycle. Thus, the distribution of the variant histone H2A.Z/H2B.Z dimer defines active and developmentally silenced regions of the T. gondii epigenome including genes that are poised for expression. Conclusions Histone variants mark functional regions of parasite genomes with the dynamic placement of the H2A.Z/H2B.Z dimer implicated as an evolutionarily conserved regulator of parasite and eukaryotic differentiation.

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Section: Resultsmentioning

confidence: 99%

Genome-wide localization of histone variants in Toxoplasma gondii implicates variant exchange in stage-specific gene expression

et al. 2022

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“…A native MNase-ChIP-seq technique was used as described previously ( 44 ). The resulting DNA fragments were aligned to the T. brucei 427 reference genome, and peaks of enrichment were identified.…”

Section: Resultsmentioning

confidence: 99%

“…Core histones were extracted using an acid extraction protocol adapted for T. brucei ( 44 ). In brief, 1 × 10 10 and 1 × 10 9 cells/sample were harvested for BF ( n = 11) and PF ( n = 9) trypanosomes, respectively.…”

Section: Methodsmentioning

confidence: 99%

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Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark Pol II transcription start regions with hyperacetylated H2A

Maree

Tvardovskiy

Ravnsborg

et al. 2022

Nucleic Acids Research

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Trypanosomes diverged from the main eukaryotic lineage about 600 million years ago, and display some unusual genomic and epigenetic properties that provide valuable insight into the early processes employed by eukaryotic ancestors to regulate chromatin-mediated functions. We analysed Trypanosoma brucei core histones by high mass accuracy middle-down mass spectrometry to map core histone post-translational modifications (PTMs) and elucidate cis-histone combinatorial PTMs (cPTMs). T. brucei histones are heavily modified and display intricate cPTMs patterns, with numerous hypermodified cPTMs that could contribute to the formation of non-repressive euchromatic states. The Trypanosoma brucei H2A C-terminal tail is hyperacetylated, containing up to five acetylated lysine residues. MNase-ChIP-seq revealed a striking enrichment of hyperacetylated H2A at Pol II transcription start regions, and showed that H2A histones that are hyperacetylated in different combinations localised to different genomic regions, suggesting distinct epigenetic functions. Our genomics and proteomics data provide insight into the complex epigenetic mechanisms used by this parasite to regulate a genome that lacks the transcriptional control mechanisms found in later-branched eukaryotes. The findings further demonstrate the complexity of epigenetic mechanisms that were probably shared with the last eukaryotic common ancestor.

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“…Such a strategy would regulate the expression of genes involved in pathogenicity, differentiation in the life cycle, and other vital aspects of the pathogen. Therefore, identifying new epigenetic targets would contribute immensely to controlling or even eradicating these diseases [4][5][6][7].…”

Section: Introductionmentioning

confidence: 99%

Advances in Protozoan Epigenetic Targets and Their Inhibitors for the Development of New Potential Drugs

et al. 2023

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Protozoan parasite diseases cause significant mortality and morbidity worldwide. Factors such as climate change, extreme poverty, migration, and a lack of life opportunities lead to the propagation of diseases classified as tropical or non-endemic. Although there are several drugs to combat parasitic diseases, strains resistant to routinely used drugs have been reported. In addition, many first-line drugs have adverse effects ranging from mild to severe, including potential carcinogenic effects. Therefore, new lead compounds are needed to combat these parasites. Although little has been studied regarding the epigenetic mechanisms in lower eukaryotes, it is believed that epigenetics plays an essential role in vital aspects of the organism, from controlling the life cycle to the expression of genes involved in pathogenicity. Therefore, using epigenetic targets to combat these parasites is foreseen as an area with great potential for development. This review summarizes the main known epigenetic mechanisms and their potential as therapeutics for a group of medically important protozoal parasites. Different epigenetic mechanisms are discussed, highlighting those that can be used for drug repositioning, such as histone post-translational modifications (HPTMs). Exclusive parasite targets are also emphasized, including the base J and DNA 6 mA. These two categories have the greatest potential for developing drugs to treat or eradicate these diseases.

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Techniques to Study Epigenetic Control and the Epigenome in Parasites

Cited by 6 publications

References 39 publications

Genome-wide localization of histone variants in Toxoplasma gondii implicates variant exchange in stage-specific gene expression

Genome-wide localization of histone variants in Toxoplasma gondii implicates variant exchange in stage-specific gene expression

Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark Pol II transcription start regions with hyperacetylated H2A

Advances in Protozoan Epigenetic Targets and Their Inhibitors for the Development of New Potential Drugs

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