Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole-genome DNA methylation map of japanese macaque sperm

ABSTRACT: It has been thought that epigenetic changes underlie the evolutionary divergence of phenotype between closely related species. However, the manner in which epigenetic changes are generated remains unknown. Although whole-genome DNA methylation profiles in some somatic tissues and sperm have been reported for humans and chimpanzees, a systematic analysis of these data has been lacking. In this manuscript, therefore, we analyzed these methylomes in detail, identified genomic regions with different DNA methylation levels, and examined the cell-type specificity and its association with changes in genomic sequence. Moreover, we generated a methylation map of Japanese macaque sperm and used it as an out-group to infer the evolutional history of methylation in these regions.

ORGANISM(S): Macaca fuscata

PROVIDER: GSE64829 | GEO | 2017/01/22

SECONDARY ACCESSION(S): PRJNA272129

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Gene expression analysis of Japanese macaque reveals potential markers of lip vermillion epithelium

Project description:Our histological findings showed that vermillion is present in the lip of Japanese macaque. In addition, the immunostaining pattern of K10 and SPRR3 of the lip of Japanese macaque is similar to that of a human. Thus, the transcriptome analysis of Japanese monkey can provide several unique genes specific to vermillion keratinocytes, which is required to develop a human lip/vermillion in vitro model.

2021-04-27 | GSE172126 | GEO

NRF2 loss recapitulates heritable impacts of paternal cigarette smoke exposure (RNA-seq)

Project description:There is growing evidence that paternal pre-conception cigarette smoke (CS) exposure is associated with increased risk of behavioral disorders and cancer in offspring. To characterize the effects of CS exposure on the sperm epigenome and offspring neurodevelopment, we investigated the impact of pre-conception paternal CS exposure on mouse sperm DNA methylation and gene expression in offspring. We further investigated the role of oxidative stress on sperm epigenetic changes using a mouse model (Nrf-/-) with impaired antioxidant capacity. Lastly, we evaluated the capacity for sperm DNA methylation to recover following removal of CS for 1-5 spermatogenic cycles (28-171 days). We found that smoking significantly impacts sperm DNA methylation as well as DNA methylation and gene expression in offspring. These changes were largely recapitulated in Nrf-/- mice independent of smoke exposure. Recovery experiments indicated that about half of differentially methylated regions returned to normal within 28 days of removal from smoke, however additional recovery following longer periods was not observed. Thus, we present strong evidence that cigarette smoke exposure induces paternally mediated, heritable epigenetic changes. Parallel studies performed in Nrf-/- mice provide evidence for oxidative stress as the predominant underlying mechanism for smoke-induced epigenetic changes to sperm as well as changes in the offspring of smoke-exposed sires. Lastly, recovery experiments indicate that while many epigenetic changes are corrected following removal from smoke exposure, aberrant methylation persists at a significant number of regions even after five spermatogenic cycles

2020-05-06 | GSE133740 | GEO

NRF2 loss recapitulates heritable impacts of paternal cigarette smoke exposure (RRBS)

2020-05-06 | GSE133739 | GEO

Age-Associated Epigenetic Change in Chimpanzees and Humans

Project description:Genome wide DNA methylation profiling of captive chimpanzees of ages spanning the chimpanzee lifespan (whole blood) Methylation levels have been shown to change with age at sites across the human genome. Change at some of these sites is so consistent across individuals that it can be used as an “epigenetic clock” to predict an individual’s chronological age within a few years. Studies of age-related epigenetic change in other mammals, including mice, whales, and canids, show that some but not all of the same loci as in humans undergo age-associated methylation changes. An in-depth comparison of chimpanzees with humans is of interest because the two species are genetically similar but differ in lifespan. To this end, we profiled genome-wide blood methylation levels for 113 samples from 83 chimpanzees aged 1-58 years (26 chimpanzees were sampled at multiple ages during their lifespan). We used this data to build a chimpanzee-specific epigenetic clock model as well as to compare genome-wide patterns of change with age between humans and chimpanzees more generally.

2020-08-23 | GSE136296 | GEO

Annual transcriptome dynamics of Japanese cedar (Cryptomeria japonica) in three regions

Project description:Investigation of annual transcriptome dynamics of Japanese cedar cuttings planted in three regions (Yamagata, Ibaraki and Kumamoto, Japan).

2024-01-22 | GSE77156 | GEO

Evolutionary and ontogenetic changes in RNA editing in human, chimpanzee and macaque brains

Project description:we used RNA-Seq to quantify the RNA editing level at more than 8,000 previously annotated exonic A-to-I RNA editing sites in two brain regions - prefrontal cortex and cerebellum - of humans, chimpanzees and rhesus macaques. We observed substantial conservation of RNA editing levels between the brain regions, as well as among the three primate species. Evolutionary changes in RNA editing were nonetheless evident among the species. Across lifespan, we observed an increase of the RNA editing level with advanced age in both brain regions of all three primate species.

2014-01-07 | GSE45244 | GEO

Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates

Project description:During germ cell and preimplantation development, mammalian cells undergo nearly complete reprogramming of DNA methylation patterns. We profiled the methylomes of human and chimp sperm as a basis for comparison to methylation patterns of ES cells. While the majority of promoters escape methylation in both ES cells and sperm, the corresponding hypomethylated regions show substantial structural differences. Repeat elements are heavily methylated in both germ and somatic cells; however, retrotransposons from several subfamilies evade methylation more effectively during male germ cell development, while other subfamilies show the opposite trend. Comparing methylomes of human and chimp sperm revealed a subset of differentially methylated promoters and strikingly divergent methylation in retrotransposon subfamilies, with an evolutionary impact that is apparent in the underlying genomic sequence. Thus, the features that determine DNA methylation patterns differ between male germ cells and somatic cells, and elements of these features have diverged between humans and chimpanzees.

2011-09-01 | GSE30340 | GEO

Discovery and capture of novel dynamic DNA methylation in human sperm with preferential links to altered folate metabolism

Project description:The sperm DNA methylation landscape is unique and critical for offspring health. If gamete-derived DNA methylation escapes reprogramming in early embryos, epigenetic defects in sperm may be transmitted to the next generation. Current techniques to assess sperm DNA methylation show bias towards CpG dense regions and do not target areas of dynamic methylation, those predicted to be environmentally sensitive and tunable regulatory elements. Thus, this study aim to assess variation in human sperm DNA methylation and design a targeted capture panel to interrogate the human sperm methylome.

| EGAS00001003617 | EGA

Epigenetic profiling at mouse imprinted gene clusters

Project description:Epigenetic profiling of DNA methylation, histone H3 lysine 4 trimethylation and histone H3 lysine 9 trimethylation at imprinted gene clusters in the mouse. Imprinted control regions were identified by comparing DNA and histone methylation patterns between sperm, heart and cerebellum.

2010-05-18 | E-GEOD-16588 | biostudies-arrayexpress

Epigenetic Alterations in Dense Human Spermatozoa for Assisted Reproduction

Project description:Selected human sperms with ART technique demonstrate many changes in the genetic and epigenetic aspects. There are many evidances shown that DNA damange and histone retention ratio have significant improved after selection with different methods. These changes may relate with DNA epigenetic changes, however no evidance demonstate these relevance. In this study, MeDIP-ChIP method has been employed to detect DNA methylation loci in human sperm genome processed with density selection. Results demonstrated that DNA methylation changed in specific gene location. comparison the DNA methylation site between 3 pair human sperm DNA samples before or after density selection

2016-08-01 | E-GEOD-71339 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data