Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Conservation and divergence of methylation patterning in plants and animals

ABSTRACT: Conservation and divergence of methylation patterning in plants and animals

PROVIDER: PRJNA126633 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR039315.fastq.gz	Fastqsanger.gz
	SRR039316.fastq.gz	Fastqsanger.gz
	SRR039317.fastq.gz	Fastqsanger.gz
	SRR039318.fastq.gz	Fastqsanger.gz
	SRR039319.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 21

Similar Datasets

Conservation and divergence of methylation patterning in plants and animals

Project description:Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms. While DNA methylation likely has a conserved role in gene silencing, the levels and patterns of DNA methylation appear to vary drastically among different organisms. Here, we used shotgun genomic bisulfite sequencing (BS-Seq) to compare DNA methylation in eight diverse plant and animal genomes. We found that patterns of methylation are very similar in flowering plants with methylated cytosines detected in all sequence contexts, whereas CG methylation predominates in animals. Vertebrates have methylation throughout the genome except for CpG islands. Gene body methylation is conserved with clear preference for exons in most of the organisms. Furthermore, genes appear to be the major target of methylation in Ciona and honeybee. Among the eight organisms, the green alga Chlamydomonas has the most unusual pattern of methylation, having non-CG methylation enriched in exons of genes rather than in repeats and transposons. In addition, we demonstrate that the Dnmt1 cofactor Uhrf1 has a conserved function in maintaining CG methylation in both transposons and gene bodies in the mouse, Arabidopsis, and zebrafish genomes.

2010-04-09 | GSE21152 | GEO

Conservation and divergence of methylation patterning in plants and animals

2010-04-09 | E-GEOD-21152 | biostudies-arrayexpress

Conservation and divergence of methylation patterning in plants and animals.

Project description:Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms. Although DNA methylation likely has a conserved role in gene silencing, the levels and patterns of DNA methylation appear to vary drastically among different organisms. Here we used shotgun genomic bisulfite sequencing (BS-Seq) to compare DNA methylation in eight diverse plant and animal genomes. We found that patterns of methylation are very similar in flowering plants with methylated cytosines detected in all sequence contexts, whereas CG methylation predominates in animals. Vertebrates have methylation throughout the genome except for CpG islands. Gene body methylation is conserved with clear preference for exons in most organisms. Furthermore, genes appear to be the major target of methylation in Ciona and honey bee. Among the eight organisms, the green alga Chlamydomonas has the most unusual pattern of methylation, having non-CG methylation enriched in exons of genes rather than in repeats and transposons. In addition, the Dnmt1 cofactor Uhrf1 has a conserved function in maintaining CG methylation in both transposons and gene bodies in the mouse, Arabidopsis, and zebrafish genomes.

| S-EPMC2889301 | biostudies-literature

Functional conservation and divergence of the helix-turn-helix motif of E2 ubiquitin-conjugating enzymes

Project description:Supporting .raw data for "Functional conservation and divergence of the helix-turn-helix motif of E2 ubiquitin-conjugating enzymes", DOI: 10.15252/embj.2021108823 Related to Figure 1E and EV1A.

2021-11-17 | MSV000088403 | MassIVE

Zoo Conservation study

Project description:Microbiome of mammalian animals, implications for conservation

| PRJEB36809 | ENA

Conservation and divergence of small RNA pathways in vascular plants revealed by small RNA analyses in lycophytes and ferns

Project description:Conservation and divergence of small RNA pathways in vascular plants revealed by small RNA analyses in lycophytes and ferns

| PRJNA385013 | ENA

The conservation and divergence of epigenitic reprogramming during mammalian early development

Project description:The conservation and divergence of epigenitic reprogramming during mammalian early development

| PRJNA686960 | ENA

Conservation and divergence of DNA methylation patterns and functions in vertebrates

Project description:Conservation and divergence of DNA methylation patterns and functions in vertebrates

| PRJNA733071 | ENA

Conservation of the PBL-RBOH immune module in land plants

Project description:The rapid production of reactive oxygen species (ROS) is a key signaling output in plant immunity. In the angiosperm model species, Arabidopsis thaliana (hereafter Arabidopsis), recognition of non- or altered-self elicitor patterns by cell-surface immune receptors activates the receptor-like cytoplasmic kinases (RLCKs) of the AVRPPHB SUSCEPTIBLE 1 (PBS1)-like (PBL) family, particularly BOTRYTIS-INDUCED KINASE1 (BIK1)1–3. BIK1/PBLs in turn phosphorylate the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD) to induce apoplastic ROS production4,5. PBL and RBOH functions in plant immunity have been extensively characterized in flowering plants. Much less is known about the conservation of pattern-triggered ROS signaling pathways in non-flowering plants. In this study, we show that, in the liverwort Marchantia polymorpha (hereafter Marchantia), single members of RBOH and PBL families, namely MpRBOH1 and MpPBLa, are required for chitin-induced ROS production. MpPBLa directly interacts with and phosphorylates MpRBOH1 at specific, conserved sites within its cytosolic N-terminus and this phosphorylation is essential for chitin-induced MpRBOH1-mediated ROS production. Collectively, our work reveals the functional conservation of the PBL-RBOH module that controls pattern-triggered ROS production in land plants.

2023-02-06 | PXD038639 | Pride

Conservation and divergence of regulatory strategies and the origin of tetrapod digits

Project description:Conservation and divergence of regulatory strategies and the origin of tetrapod digits

| PRJNA207030 | ENA