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Extensive N4 cytosine methylation of Marchantia genes is essential for sperm function [1]

ABSTRACT: Sperm mobility in Marchantia requires global N4 cytosine methylation catalysed by two novel DNA methyltransferases.

ORGANISM(S): Marchantia polymorpha subsp. ruderalis

PROVIDER: GSE163200 | GEO | 2025/04/09

REPOSITORIES: GEO

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Extensive N4 Cytosine Methylation is Essential for Marchantia Transcriptional Programming and Sperm Function [2]

Project description:Global N4 cytosine methylation catalyzed by a novel DNA methyltransferase is important for transcriptional programming, sperm mobility, and post-fertilization in Marchantia

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Extensive N4 cytosine methylation of Marchantia genes is essential for sperm function [1]

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Extensive N4 Cytosine Methylation is Essential for Marchantia Transcriptional Programming and Sperm Function

Project description:This SuperSeries is composed of the SubSeries listed below.

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5-methyl cytosine profile of the wild type and Mpmet mutant in Marchantia polymorpha

Project description:To understand a role of MpMET in maintenance of cytpsine methylation and transposon silencing, we obtained a genome wide profile of 5-methylated cytosine from the Mpmet mutant of a model liverwort, Marchantia polymorpha.

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EVOREPRO: RNA-seq of Marchantia polymorpha Takaragaike sperm cells

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Project description:DNA methylation is a key mechanism for regulation of DNA repair, DNA replication, and gene expression. In bacteria, DNA is modified by methylation on C5-cytosine (5mC), N6-adenine (6mA) and N4-cytosine (4mC). Metazoans were thought to only use 5mC to regulate gene expression until the recent discovery of N6-adenine methylation in DNA of diverse metazoan species, including mammals. Here we show by dot blot, immunoprecipitation with 4mC-specific antibodies, and ultra-high performance liquid chromatography coupled with triple-quadrupole mass spectrometry that 4mC also occurs in most eukaryotes. We further characterize 4mC sites on a near genome-wide scale by single molecule real time (SMRT) sequencing in the nematode C. elegans. In C. elegans, 4mC is found in all chromosomes but is relatively sparse on the X chromosome. 4mC is relatively enriched on introns, depleted on exons, and co-localizes with 6mA. In human cells, 4mC is anti-correlated with 5mC. Moreover, 4mC modifications are associated with increased gene expression. Transfection of human cells with a 4mC-modified luciferase reporter plasmid increases luciferase expression as compared to the unmethylated plasmid. These data suggest that 4mC promotes gene transcription, playing an opposing role to 5mC, which generally represses transcription. Thus 4mC modification of DNA is a previously unrecognized mechanism of gene regulation in eukaryotes, providing evidence for a complex epigenetic DNA code.

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N4-cytosine DNA methylation is involved in the maintenance of genomic stability in Deinococcus radiodurans

Project description:Purpose: DNA methylation has a global impact on gene expression Methods: Gene expression profiles of D. radiodurans R1 wild type and ΔM.DraR1 strains were generated by deep sequencing using Illumina HiSeqTM2500. Results: RNA-seq was used for differential expression gene analysis between wild-type and ΔM.DraR1 strains. A total of 1158 genes (766 upregulated genes and 392 downregulated genes) were differentially expressed in ΔM.DraR1 strain. GO enrichment analysis revealed that upregulated unigenes were significantly enriched in twelve subcategories. The majority of unigenes in the biological process category were associated with macromolecule metabolic processes. Interestingly, a number of unigenes were also associated with DNA recombination. Within the molecular function category, most unigenes were assigned to nucleic acid, DNA binding and hydrolase, and nucleoside triphosphatase activity. The KEGG enrichment analytical scatter diagram showed that the major pathways affected in the deletion strain belonged to ABC transport, two-component systems, DNA replication, homologous recombination, and protein export pathways. The majority of DNA damage response genes, such as ddrA, ddrB, ddrO, ddrG, ddrJ, ddrK, ddrD and pprA, were significantly upregulated. Several genes involved in DNA recombinational repair pathway including recA, recO, rexD, and ruvB were also significantly upregulated. Putative competence genes, including those encoding prepilin peptidase, CRP and CinA, were upregulated in the mutant strain. This gene expression pattern of the ΔM.DraR1 strain resembled that of D. radiodurans during recovery after exposure to acute radiation, indicating that the absence of N4-cytosine DNA methylation may result in intracellular stress. Conclusion: Absence of N4-cytosine DNA Methylation in D. radiodurans Leads to Expression Changes of Proteins Involved in DNA Damage Response

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Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-TAB-seq

Project description:N4-methylcytosine is a major DNA modification integral to restriction-modification (R-M) systems in bacterial genomes. Here we describe 4mC-Tet-Assisted Bisulfite-sequencing (4mC-TAB-seq), a method that accurately and rapidly reveals the genome-wide locations of N4-methylcytosines at single-base resolution. By coupling Tet-mediated oxidation with a modified sodium bisulfite conversion reaction, unmodified cytosines and 5-methylcytosines are read out as thymines, whereas N4-methylcytosines are read out as cytosines revealing their positions throughout the genome. 4mC-TAB-seq

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