Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8208350_1.fastq.gz | Fastqsanger.gz | |||
| SRR8208350_2.fastq.gz | Fastqsanger.gz | |||
| SRR8208360_1.fastq.gz | Fastqsanger.gz | |||
| SRR8208360_2.fastq.gz | Fastqsanger.gz | |||
| SRR8208351_1.fastq.gz | Fastqsanger.gz |
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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:Genome editing tools with high precision are key to develop improved crops but current technologies to place new DNA into specific locations in plant genomes are low frequency and error-prone. Transposable elements (TEs) evolved to insert their DNA seamlessly into genomes, albeit in a quasi-random pattern. We developed a genome engineering tool that controls the TE insertion site and subsequently the delivery of any cargo attached to this TE. Using our tool, we demonstrated sequence-specific targeted delivery (guided by the CRISPR gRNA) of enhancers, an open reading frame and gene expression cassette into the genome of the model plant Arabidopsis, and we translated this technology to the crop soybean. We have engineered a ‘junk’ TE into a useful and accessible toolkit that enables the sequence-specific targeting of custom DNA into plant genomes.
2024-05-03 | GSE227104 | GEO
Project description:Genome editing tools with high precision are key to develop improved crops but current technologies to place new DNA into specific locations in plant genomes are low frequency and error-prone. Transposable elements (TEs) evolved to insert their DNA seamlessly into genomes, albeit in a quasi-random pattern. We developed a genome engineering tool that controls the TE insertion site and subsequently the delivery of any cargo attached to this TE. Using our tool, we demonstrated sequence-specific targeted delivery (guided by the CRISPR gRNA) of enhancers, an open reading frame and gene expression cassette into the genome of the model plant Arabidopsis, and we translated this technology to the crop soybean. We have engineered a ‘junk’ TE into a useful and accessible toolkit that enables the sequence-specific targeting of custom DNA into plant genomes.
2024-05-03 | GSE227103 | GEO
Project description:Long intergenic noncoding RNAs (lincRNAs) are widespread in cellular organisms, however, the origins and functions of many lincRNAs remain to be explored. Transposable elements (TEs) are widely distributed in many eukaryotic genomes, and often account for large fractions of plant and animal genomes. By using strand-specific RNA sequencing, we profiled the expression patterns of lincRNAs in Arabidopsis, rice and maize, and identified TE-associated lincRNAs (TE-lincRNAs). Stress regulation of some TE-lincRNAs was observed in Arabidopsis. Our findings indicate that TE-associated lincRNAs potentially play important roles in plant abiotic stress responses. Moreover, in the Arabidopsis chromatin remodelling mutant ddm1 that has an altered chromatin state, novel lincRNAs including TE-lincRNAs were generated. The novel lincRNAs were inherited in the subsequent generations in the wild type background, suggesting that lincRNAs could act as an adaptive reservoir in eukaryotes.
2017-01-21 | GSE76798 | GEO
Project description:Plant pathogenic Pseudomonas Genomes from Turkey Outbreaks
| PRJNA680595 | ENA
Project description:Histone modifications are of paramount importance during plant development. Investigating chromatin remodeling in developing oilseeds sheds light on the molecular mechanisms controlling fatty acid metabolism as well as facilitates the identification of new functional regions in oil crop genomes. The present study characterized the epigenetic modifications H3K4me3 in relationship with the expression of fatty acid related-genes and transcription factors in developing sunflower seeds.
2021-04-28 | GSE171309 | GEO
Project description:Eukaryotic cytosine methylation represses transposable elements, but also occurs in bodies of active genes. The extent to which these processes are conserved is unclear, and little is known about methylation outside of mammals, Arabidopsis thaliana, and Neurospora crassa. Utilizing deep bisulfite sequencing, we have quantified DNA methylation in five plant, seven animal, and five fungal genomes. We find that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons has evolved independently in the vertebrate lineage. We show that methylation of plant transposons in the CHG context extends to green algae, and present evidence for RNA-directed DNA methylation of fungal genes. We also show that antagonism between DNA methylation and histone H2A.Z is conserved between plants and animals. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes. Keywords: Epigenetics Examination of DNA methylation and transcription in plant, animal, and fungal genomes, and examination of how H2A.Z deposition relates to both methylation and transcription in puffer fish. Descriptions of the Samples' raw and processed data (provided as supplementary files) can be found in GSE19824_README.txt at the foot of this record.
2010-04-15 | E-GEOD-19824 | biostudies-arrayexpress
Project description:The POLYCOMB proteins are required for maintenance of silent chromatin states mediated by H3K27 trimethylation in animals, but POLYCOMB homologues are not found in plant genomes. Using DamID-chip, we found that the Arabidopsis chromodomain-containing protein LHP1 localizes to chromatin associated with H3K27me3 genome-wide. Furthermore, the LHP1 chromodomain binds H3K27me3 with high affinity. These results suggest that LHP1 shares similar functions with POLYCOMB. Keywords: DamID-Chip
2007-09-07 | GSE8169 | GEO