N4-acetyldeoxycytosine DNA modification marks euchromatin regions in Arabidopsis thaliana.
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ABSTRACT:
PROVIDER: PRJNA708256 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13912623_1.fastq.gz | Fastqsanger.gz | |||
| SRR13912623_2.fastq.gz | Fastqsanger.gz | |||
| SRR13912624_1.fastq.gz | Fastqsanger.gz | |||
| SRR13912624_2.fastq.gz | Fastqsanger.gz | |||
| SRR13912625_1.fastq.gz | Fastqsanger.gz |
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Project description:We report the application of Next-generation sequencing (NGS) for high-throughput profiling of N4-acetylcytosine (4acC) DNA modification in Arabidopsis thaliana. We find that 4acC peaks mostly distribute in the euchromatin regions and are present in nearly half of the protein-coding genes in Arabidopsis. 4acC mainly locates around transcription start sites (TSSs) of protein-coding genes and positively correlates with gene expression level . Compared to non-4acC marked genes, 4acC marked genes display a higher methylation level of 5mC in the CG context within coding regions, but a lower methylation level of 5mC in the CHG and CHH contexts. In addition, 4acC peaks showed higher overlaps with active histone modification marks than by chance, but similar overlaps with repressive histone modification marks. We observed complex cooperative interactions among 4acC, 5mC, and histone modifications on gene transcription. 4acC containing genes with low level of mCG, or active histone modification marks displayed a higher expression. In sum, we have uncovered 4acC as a hitherto unknown epigenetic DNA mark that is associated with gene expression in Arabidopsis, and suggest potential cross-talks among epigenetic marks for gene expression.
2021-11-18 | GSE168538 | GEO
Project description:BackgroundDirect analogs of chemically modified bases that carry important epigenetic information, such as 5-methylcytosine (m5C)/5-methyldeoxycytosine (5mC), 5-hydroxymethylcytosine (hm5C)/5-hydroxymethyldeoxycytosine (5hmC), and N6-methyladenosine (m6A)/N6-methyldeoxyadenosine (6mA), are detected in both RNA and DNA, respectively. The modified base N4-acetylcytosine (ac4C) is well studied in RNAs, but its presence and epigenetic roles in cellular DNA have not been explored.ResultsHere, we demonstrate the existence of N4-acetyldeoxycytosine (4acC) in genomic DNA of Arabidopsis with multiple detection methods. Genome-wide profiling of 4acC modification reveals that 4acC peaks are mostly distributed in euchromatin regions and present in nearly half of the expressed protein-coding genes in Arabidopsis. 4acC is mainly located around transcription start sites and positively correlates with gene expression levels. Imbalance of 5mC does not directly affect 4acC modification. We also characterize the associations of 4acC with 5mC and histone modifications that cooperatively regulate gene expression. Moreover, 4acC is also detected in genomic DNA of rice, maize, mouse, and human by mass spectrometry.ConclusionsOur findings reveal 4acC as a hitherto unknown DNA modification in higher eukaryotes. We identify potential interactions of this mark with other epigenetic marks in gene expression regulation.
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Project description:Most genome-level analysis treats the two parental alleles equivalently, yet diploid genomes contain two parental genomes that are often epigenetically distinct. While single nucleotide polymorphisms (SNPs) can be used to distinguish these genomes, it would be useful to develop a generalized strategy for identifying candidate genes or regions showing allele-specific differences, independent of SNPs. We have explored this problem by looking for overlapping marks in the genome related to both euchromatin (histone H3 dimethyl lysine-4 [H3K4Me2]) and heterochromatin (DNA methylation [DNAm]). "Double hits" were defined by the intersection of H3K4Me2 and DNAm. For the top 5% of marks, defined by a sliding window, imprinted gene regions were enriched for double hits 5.4-fold. When the location information of CTCF binding sites were integrated, the "triple hits" were enriched 76-fold for known imprinted genes in the regions studied. The double hits in imprinted genes were found to occur usually at the site of alternative or antisense transcripts. In addition, four of four imprinted genes tested showing double hits also showed allele-specific methylation. We suggest that overlapping euchromatin/heterochromatin marks are common and are enriched for epigenetically distinct parental chromosome regions. Furthermore, we developed a novel approach to identifying allele-specific marks that is SNP independent, by fractionating using H3K4Me2 antibodies followed by DNA methylation analysis.
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Project description:Lamins are components of the peripheral nuclear lamina and interact with heterochromatic genomic regions, termed lamina-associated domains (LADs). In contrast to Lamin B11, lamin A/C also localizes throughout the nucleus, where it associates with the chromatin-binding protein lamina-associated polypeptide (LAP) 2alpha. Here we show lamin A/C also interacts with euchromatin, as determined by chromatin immunoprecipitation analyses of eu- and heterochromatin-enriched samples. By way of contrast, Lamin B11 was only found associated with heterochromatin. Euchromatic regions occupied by lamin A/C overlap with those bound by LAP2alpha, the depletion of which shifts binding of lamin A/C towards more heterochromatic regions. These alterations in lamin A/C chromatin interaction affect epigenetic histone marks in euchromatin without significantly affecting gene expression, while loss of lamin A/C in heterochromatic regions increased gene expression. Our data show a novel role of nucleoplasmic lamin A/C and LAP2alpha in regulating euchromatin. Examination of Lamin A/C, Lamin B1 and Lap2a DNA binding in Lap2alpha +/+ and Lap2a -/- cells and according changes in Histone modifications and gene expression
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Project description:Lamins are components of the peripheral nuclear lamina and interact with heterochromatic genomic regions, termed lamina-associated domains (LADs). In contrast to lamin B1, lamin A/C also localizes throughout the nucleus, where it associates with the chromatin-binding protein lamina-associated polypeptide (LAP) 2alpha. Here we show lamin A/C also interacts with euchromatin, as determined by chromatin immunoprecipitation analyses of eu- and heterochromatin-enriched samples. By way of contrast, lamin B1 was only found associated with heterochromatin. Euchromatic regions occupied by lamin A/C overlap with those bound by LAP2alpha, the depletion of which shifts binding of lamin A/C towards more heterochromatic regions. These alterations in lamin A/C chromatin interaction affect epigenetic histone marks in euchromatin without significantly affecting gene expression, while loss of lamin A/C in heterochromatic regions increased gene expression. Our data show a novel role of nucleoplasmic lamin A/C and LAP2alpha in regulating euchromatin. Examination of LaminA, LaminB and Lap2a DNA binding in Lap2alpha +/+ and Lap2a -/- cells and according changes in Histone modifications and gene expression
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