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Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

ABSTRACT: Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

PROVIDER: PRJNA186672 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR648795.fastq.gz	Fastqsanger.gz
	SRR648796.fastq.gz	Fastqsanger.gz
	SRR648797.fastq.gz	Fastqsanger.gz
	SRR648798.fastq.gz	Fastqsanger.gz
	SRR648799.fastq.gz	Fastqsanger.gz

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Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

Project description:Two-thirds of gene promoters in mammals are associated with regions of non-methylated DNA, called CpG islands (CGIs), which counteract the repressive effects of DNA methylation. In lower vertebrates, computational CGI predictions often reside away from gene promoters, suggesting a major divergence in gene promoter architecture across vertebrates. By experimentally identifying non-methylated DNA in the genomes of seven diverse vertebrates, we instead reveal that non-methylated islands (NMIs) of DNA are a central feature of vertebrate gene promoters. Furthermore, NMIs are present at orthologous genes across vast evolutionary distances, revealing a surprising level of conservation in this epigenetic feature. By profiling NMIs in different tissues and developmental stages we uncover a unifying set of features that are central to the function of NMIs in vertebrates. Together these findings demonstrate an ancient logic for NMI usage at gene promoters and reveal an unprecedented level of epigenetic conservation across vertebrate evolution. Bio-CAP was used to identify non-methylated regions of the genome in seven diverse vertebrates (human, mouse, platypus, chicken, lizard, frog and zebrafish) across a number of tissues.

2013-01-22 | E-GEOD-43512 | biostudies-arrayexpress

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

2013-01-22 | GSE43512 | GEO

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates.

Project description:Two-thirds of gene promoters in mammals are associated with regions of non-methylated DNA, called CpG islands (CGIs), which counteract the repressive effects of DNA methylation on chromatin. In cold-blooded vertebrates, computational CGI predictions often reside away from gene promoters, suggesting a major divergence in gene promoter architecture across vertebrates. By experimentally identifying non-methylated DNA in the genomes of seven diverse vertebrates, we instead reveal that non-methylated islands (NMIs) of DNA are a central feature of vertebrate gene promoters. Furthermore, NMIs are present at orthologous genes across vast evolutionary distances, revealing a surprising level of conservation in this epigenetic feature. By profiling NMIs in different tissues and developmental stages we uncover a unifying set of features that are central to the function of NMIs in vertebrates. Together these findings demonstrate an ancient logic for NMI usage at gene promoters and reveal an unprecedented level of epigenetic conservation across vertebrate evolution. DOI:http://dx.doi.org/10.7554/eLife.00348.001.

| S-EPMC3583005 | biostudies-literature

Conservation and divergence of DNA methylation patterns and functions in vertebrates

Project description:Cytosine DNA methylation is a heritable epigenetic mark present in most eukaryotic groups. While the patterns and functions of DNA methylation have been extensively studied in mouse and human, their conservation in other vertebrates remain poorly explored. In this study, we interrogated the distribution and function of DNA methylation in primary cells of seven vertebrate species including bio-medical models and key livestock species.

2022-03-23 | GSE175615 | GEO

The methylome of a cartilaginous fish, Callorhinchus milii, reveals conservation of epigenetic regulation across jawed vertebrates

Project description:Background Methylation of CG dinucleotides constitutes a critical system of epigenetic memory in bony vertebrates, where it modulates gene expression and suppresses transposon activity. The genomes of studied vertebrates are pervasively hypermethylated, with the exception of regulatory elements such as transcription start sites (TSSs), where the presence of methylation is associated with gene silencing. This system is not found in the sparsely methylated genomes of invertebrates, and establishing how it arose during early vertebrate evolution is impeded by a paucity of epigenetic data from basal vertebrates. Methods We perform whole-genome bisulfite sequencing to generate the first genome-wide methylation profiles of a cartilaginous fish, the elephant shark Callorhinchus milii. Employing these to determine the elephant shark methylome structure and its relationship with expression, we compare this with higher vertebrates and an invertebrate chordate using published methylation and transcriptome data. Results Like higher vertebrates, the majority of elephant shark CG sites are highly methylated, and methylation is abundant across the genome rather than patterned in the mosaic configuration of invertebrates. This global hypermethylation includes transposable elements and the bodies of genes at all expression levels. Significantly, we document an inverse relationship between TSS methylation and expression in the elephant shark, supporting the presence of the repressive regulatory architecture shared by higher vertebrates. Conclusions Our demonstration that methylation patterns in a cartilaginous fish are characteristic of higher vertebrates imply the conservation of this epigenetic modification system across jawed vertebrates separated by 465 million years of evolution. In addition, these findings position the elephant shark as a valuable model to explore the evolutionary history and function of vertebrate methylation.

2017-03-24 | GSE96683 | GEO

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

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

Project description:Identification of the coding elements in the genome is a fundamental step to understanding the building blocks of living systems. Short peptides (< 100 aa) have emerged as important regulators of development and physiology, but their identification has been limited by their size. We have leveraged the periodicity of ribosome movement on the mRNA to define actively translated ORFs by ribosome footprinting. This approach identifies several hundred translated small ORFs in zebrafish and human. Computational prediction of small ORFs from codon conservation patterns corroborates and extends these findings and identifies conserved sequences in zebrafish and human, suggesting functional peptide products (micropeptides). These results identify micropeptideM-bM-^@M-^Pencoding genes in vertebrates, providing an entry point to define their function in vivo. Ribosome profiling experiments at five timepoints across zebrafish development in WT embryos

2014-04-04 | E-GEOD-53693 | biostudies-arrayexpress

Conservation of Regulatory Elements with Highly Diverged Sequences Across Large Evolutionary Distances [ChIP-seq]

Project description:Embryonic gene expression is remarkably conserved across vertebrates as observed, for instance, in the developing hearts of chicken and mouse which diverged >300 million years ago. However, most cis regulatory elements (CREs) are highly divergent, which makes orthology tracing based on sequence similarity difficult, especially at larger evolutionary distances. Some evidence suggests functional conservation of CREs despite sequence divergence. However, it remains unclear how widespread such functional conservation might be.

2025-03-06 | GSE263783 | GEO