Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1103215 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Yggdrasil: An Eukaryotic Reference Genome Facility
| PRJNA955268 | ENA
Project description:Transcriptional regulation is a universal mechanism for a wide array of biological processes, and is driven in large part by genetic enhancer elements. These regulatory elements have been well-studied in animal species, yet their plant counterparts remain poorly characterized. While high-throughput profiling of animal genomes has yielded great success in identifying genetic enhancers through secondary characteristics – flanking histone posttranslational modifications (PTMs), chromatin accessibility, and the production of enhancer RNAs (eRNAs) – it is an active line of investigation as to whether these secondary characteristics can be used in a similar way to locate regulatory regions of plant genomes. Here, we compare the enrichment of the four histone PTMs most commonly associated with animal enhancers – H3K27ac, H3K27me3, H3K4me1, and H3K4me3 – between Drosophila melanogaster, Homo sapiens, and Arabidopsis thaliana genomes. Regions of accessible chromatin were identified through ATAC-seq or DNase-seq, and were analyzed as putative enhancer regions. Additionally, as it has been shown that enhancer activity varies widely from cell type to cell type, matched, single-cell type datasets were used for each species whenever available. Through the intersection of these data it becomes clear that there are distinct differences between the epigenetic makeup of plant and animal genomes. While these four histone PTMs are present at transcription start sites (TSSs) in all three of the species investigated, A. thaliana showed a marked depletion of these modifications upstream of the TSS, while the animal species showed bimodal enrichment. The plant histone PTM pattern is consistent with the pattern observed at unidirectional promoters, which was further supported by GRO-seq data. When intergenic regions of accessible chromatin were examined – putative enhancer regions – the plant epigenomes showed a one-sided, rather than bimodal, enrichment of all four of the histone PTMs. However, these sites retain the ability to produce eRNAs, suggesting that they are likely functionally active enhancer elements. While it is known that animal promoters and enhancers have bidirectional transcription, this analysis revealed that plant promoters and enhancers have a distinct pattern, and only exhibit histone PTM deposition and transcription in the sense direction. While further investigation is merited, this may speak to a fundamental difference between the transcriptional machinery of plant and animal kingdoms.
2020-06-11 | GSE152243 | GEO
Project description:To determine the optimal RNA-Seq approach for animal host-bacterial symbiont analysis, we compared transcriptome bias, depth and coverage achieved by two different mRNA capture and sequencing strategies applied to the marine demosponge Amphimedon queenslandica holobiont, for which genomes of the animal host and three most abundant bacterial symbionts are available.
2022-06-06 | GSE205425 | GEO
Project description:Several organisms belonging to diverse animal groups have retained Dnmt2 as their only bona fide DNA methyltransferase gene. However, recent studies have shown that Dnmt2 functions as a tRNA methyltransferase, which prompted us to analyze the methylomes of Dnmt2-only organisms at single-base resolution. Using whole-genome bisulfite sequencing we show here that the genomes of Schistosoma mansoni and Drosophila melanogaster lack detectable DNA methylation patterns. Residual unconverted cytosine residues shared many attributes with bisulfite deamination artifacts and were observed at comparable levels in a Dnmt2-deficient fly strain. Furthermore, genetically modified mouse embryonic stem cells that had retained Dnmt2 as their only bona fide DNA methyltransferase gene, did not show any detectable DNA methylation patterns. Our results thus uncover fundamental differences among animal methylomes and suggest that Dnmt2-only organisms lack biologically relevant DNA methylation patterns. Whole methylome analysis of Mus musculus. One sample was analyzed containing DNA from Dnmt1-/-, Dnmt3a-/- and Dnmt3b-/- mice.
2013-05-06 | E-GEOD-42170 | biostudies-arrayexpress