Determination of the presence of 5-methylcytosine in Paramecium tetraurelia

Singh, Aditi; Vancura, Adrienne; Wóycicki, Rafał; Hogan, Daniel J.; Hendrick, Alan G.; Nowacki, Mariusz

doi:10.1371/journal.pone.0206667

“…It is interesting to note that just like early-diverging fungi (33), 5mC in T. vaginalis was nearly undetectable. Unfortunately, detection methods that rely on the use of antibodies can give false positives when 5mC levels are low (48), which could explain the low-quality reads obtained from the 5mC MeDIP-seq experiment. These results support our conclusion that 6mA, and not 5mC, is the main DNA modification in T. vaginalis genomic DNA.…”

Section: Discussionmentioning

confidence: 99%

Adenine DNA methylation, 3D genome organization, and gene expression in the parasite Trichomonas vaginalis

Lizarraga

¹

,

O’Brown

²

,

Boulias

³

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Trichomonas vaginalisis a common sexually transmitted parasite that colonizes the human urogenital tract causing infections that range from asymptomatic to highly inflammatory. Recent works have highlighted the importance of histone modifications in the regulation of transcription and parasite pathogenesis. However, the nature of DNA methylation in the parasite remains unexplored. Using a combination of immunological techniques and ultrahigh-performance liquid chromatography (UHPLC), we analyzed the abundance of DNA methylation in strains with differential pathogenicity demonstrating that N6-methyladenine (6mA), and not 5‐methylcytosine (5mC), is the main DNA methylation mark inT. vaginalis. Genome-wide distribution of 6mA reveals that this mark is enriched at intergenic regions, with a preference for certain superfamilies of DNA transposable elements. We show that 6mA inT. vaginalisis associated with silencing when present on genes. Interestingly, bioinformatics analysis revealed the presence of transcriptionally active or repressive intervals flanked by 6mA-enriched regions, and results from chromatin conformation capture (3C) experiments suggest these 6mA flanked regions are in close spatial proximity. These associations were disrupted when parasites were treated with the demethylation activator ascorbic acid. This finding revealed a role for 6mA in modulating three-dimensional (3D) chromatin structure and gene expression in this divergent member of the Excavata.

show abstract

“…It is interesting to note that just like early-diverging fungi (33), 5mC in T. vaginalis was nearly undetectable. Unfortunately, detection methods that rely on the use of antibodies can give false positives when 5mC levels are low (47), which could explain the low-quality reads obtained from the 5mC MeDIP-seq experiment. These results support our conclusion that 6mA, and not 5mC, is the main DNA modification in T. vaginalis genomic DNA.…”

Section: Discussionmentioning

confidence: 99%

Adenine DNA methylation, 3D genome organization and gene expression in the parasiteTrichomonas vaginalis

Lizarraga

¹

,

O’Brown

²

,

Roach

³

et al. 2019

Preprint

0

View full text Add to dashboard Cite

Trichomonas vaginalis is a common sexually transmitted parasite that colonizes the human urogenital tract causing infections that range from asymptomatic to highly inflammatory. Recent works have highlighted the importance of histone modifications in the regulation of transcription and parasite pathogenesis. However, the nature of DNA methylation in the parasite remains unexplored. Using a combination of immunological techniques and UHPLC, we analyzed the abundance of DNA methylation in strains with differential pathogenicity demonstrating that N6-methyladenine (6mA), and not 5-methylcytosine (5mC), is the main DNA methylation mark in T. vaginalis. Genome-wide distribution of 6mA reveals that this mark is enriched at intergenic regions, with a preference for certain super-families of DNA transposable elements. We show that 6mA in T. vaginalis is associated with silencing when present on genes. Interestingly, bioinformatics analysis revealed the presence of transcriptionally active or repressive intervals flanked by 6mA-enriched regions and results from chromatin conformation capture (3C) experiments suggest these 6mA flanked regions are in close spatial proximity. These associations were disrupted when parasites were treated with the demethylation activator ascorbic acid. This finding revealed a new role for 6mA in modulating 3D chromatin structure and gene expression in this divergent member of the Excavata.SIGNIFICANCE STATEMENTTrichomonas vaginalis causes the most common non-viral sexually transmitted infection yet little is known about the regulation of gene expression in this eukaryotic parasite. We demonstrate that N6-methyladenine (6mA) is the main methylation mark in the T. vaginalis genome. 6mA is widespread in DNA of eubacterial genera, but uncommon in genomes of most eukaryotes. Examination of the genome-wide distribution of 6mA reveals a preference for intergenic regions. Transcriptionally active or repressive intervals are found to be flanked by 6mA-enriched regions and data suggest 6mA flanked regions are in close 3D spatial proximity. Our findings describe for the first time the presence of DNA methylation in T. vaginalis and reveal a new role for 6mA in modulating 3D chromatin architecture.

show abstract

“…Moreover, 5mC in Stylonychia correlates with gene activity as well as with chromatin structure during macronuclear differentiation [129]. However, recent work in Paramecium was unable to detect any evidence for 5mC modifications, suggesting that these modifications may only be involved in the DRGRs of spirotrich ciliates [130]. While the function of 5mC DNA modifications and their phylogenetic distribution in ciliates remains unclear, the only widely conserved DNA modification is 6N-methyladenine (6 mA) [131][132][133][134][135].…”

Section: Dna Modification In Ies Eliminationmentioning

confidence: 99%

“…Moreover, 5mC in Stylonychia correlates with gene activity as well as with chromatin structure during macronuclear differentiation [ 129 ]. However, recent work in Paramecium was unable to detect any evidence for 5mC modifications, suggesting that these modifications may only be involved in the DRGRs of spirotrich ciliates [ 130 ].…”

Section: Developmentally Regulated Genome Rearrangementsmentioning

confidence: 99%

Programmed genome rearrangements in ciliates

Rzeszutek

¹

,

Maurer‐Alcalá

²

,

Nowacki

³

2020

Cell. Mol. Life Sci.

Self Cite

View full text Add to dashboard Cite

Ciliates are a highly divergent group of unicellular eukaryotes with separate somatic and germline genomes found in distinct dimorphic nuclei. This characteristic feature is tightly linked to extremely laborious developmentally regulated genome rearrangements in the development of a new somatic genome/nuclei following sex. The transformation from germline to soma genome involves massive DNA elimination mediated by non-coding RNAs, chromosome fragmentation, as well as DNA amplification. In this review, we discuss the similarities and differences in the genome reorganization processes of the model ciliates Paramecium and Tetrahymena (class Oligohymenophorea), and the distantly related Euplotes, Stylonychia, and Oxytricha (class Spirotrichea).

show abstract

Determination of the presence of 5-methylcytosine in Paramecium tetraurelia

Cited by 14 publications

References 48 publications

Adenine DNA methylation, 3D genome organization, and gene expression in the parasite Trichomonas vaginalis

Adenine DNA methylation, 3D genome organization, and gene expression in the parasite Trichomonas vaginalis

Adenine DNA methylation, 3D genome organization and gene expression in the parasiteTrichomonas vaginalis

Programmed genome rearrangements in ciliates

Contact Info

Product

Resources

About