Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative sperm methylome analysis provide insights into complex phenotypes and epigenome evolution

ABSTRACT: Using whole-genome bisulfite sequencing (WGBS), we profiled 18 DNA methylomes of cattle sperms that were collected from 18 representative age-matched Holstein bulls with high reliable phenotypes on many complex traits, including sire-conception rate (SCR), gestation length (GL), sire calving ease (SCE), cow conception rate (CCR) and body depth (BDE). Through comparison with human sperm methylome, we observed that genomic regions with differetial DNA methylation levels were enriched for GWAS signals and had important evolutionary impact. By comparing animals with extreme SCR, we showed that differentially methylated regions (DMR) associated with SCR and aging were significantly and selectively enriched for GWAS signals of male fertility traits in cattle. In addition, we detected ans compared DMRs assocaited with GL, CCR, SCE and BDE. We integrated GWAS signals of 37 complex traits with DMRs associated with GL to provide insights into genetic basis of GL.

ORGANISM(S): Bos taurus

PROVIDER: GSE119263 | GEO | 2019/03/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genetic effects on liver chromatin accessibility identify disease regulatory variants [genotypes]

Project description:Identifying the molecular mechanisms by which genome-wide association study (GWAS) loci influence traits remains challenging. Chromatin accessibility quantitative trait loci (caQTL) help identify GWAS loci that may alter GWAS traits by modulating chromatin structure, but caQTL have been identified in a limited set of human tissues. Here we mapped caQTL in human liver tissue in 20 liver samples and identified 3,123 caQTL. The caQTL variants are enriched in liver tissue promoter and enhancer states and frequently disrupt binding motifs of transcription factors expressed in liver. We predicted target genes for 861 caQTL peaks using proximity, chromatin interactions, correlation with promoter accessibility or gene expression, and colocalization with expression QTL. Using GWAS signals for 19 liver function and/or cardiometabolic traits, we identified 110 colocalized caQTL and GWAS signals, 56 of which contained a predicted caPeak target gene. At the LITAF LDL-cholesterol GWAS locus, we validated that a caQTL variant showed allelic differences in protein binding and transcriptional activity. These caQTL contribute to the epigenomic characterization of human liver and help identify molecular mechanisms and genes at GWAS loci.

2021-05-01 | GSE164938 | GEO

Genetic effects on liver chromatin accessibility identify disease regulatory variants [RNA-seq]

2021-05-01 | GSE164876 | GEO

Genetic effects on liver chromatin accessibility identify disease regulatory variants [ATAC-seq]

2021-05-01 | GSE164870 | GEO

Readthrough Events in Plants Reveal Unprecedented Plasticity of Stop Codons

Project description:Stop codon readthrough (SCR) has important biological implications but remains largely uncharacterized. Here, we identify 1,009 SCR events in plants using a proteogenomic strategy. Plant SCR candidates tend to have shorter transcript lengths and fewer exons and splice variants than non-SCR transcripts. Mass spectrometry evidence shows that stop codons involved in SCR events can be recoded as 20 standard amino acids, some of which are also supported by suppressor transfer RNA analysis. We also observe multiple functional signals in 34 maize extended proteins and characterize the structural and subcellular localization changes in the extended protein of BASIC TRANSCRIPTION FACTOR 3. Furthermore, the SCR events exhibit non-conserved signature and the extensions likely undergo protein-coding selection. Overall, our study not only characterizes that SCR events are commonly present in plants but also identifies the unprecedented recoding plasticity of stop codons, which provides important insights into the flexibility of genetic decoding.

2024-02-02 | PXD035958 | Pride

Readthrough Events in Plants Reveal Unprecedented Plasticity of Stop Codons

2024-02-02 | PXD038762 | Pride

Maintenance of cell fate by the Polycomb Group gene Sex combs extra enables a partial epithelial mesenchymal transition in Drosophila (Pol2 dataset)

Project description:Epigenetic silencing by Polycomb group (PcG) complexes can promote epithelial-mesenchymal transition (EMT) and stemness and is associated with malignancy of solid cancers. Here we report a role for Drosophila PcG repression in a partial EMT event that occurs during wing disc eversion, an early event during metamorphosis. In a screen for EMT genes required for eversion we identified the PcG genes Sex combs extra (Sce) and Sex combs midleg (Scm). Depletion of Sce or Scm resulted in internalised wings and thoracic clefts, and loss of Sce inhibited the EMT of the peripodial epithelium and basement membrane breakdown, ex vivo. Targeted DamID (TaDa) using Dam-Pol II showed that Sce knockdown caused a genomic transcriptional response consistent with maintenance of an epithelial fate. Surprisingly only 17 genes were significantly upregulated in Sce-depleted cells, including Abd-B, abd-A, caudal, and nubbin. Each of these loci were enriched for Dam-Pc binding. Of the four genes, only Abd-B was robustly upregulated in cells lacking Sce expression. RNAi knockdown of all four genes could partly suppress the Sce RNAi eversion phenotype, though Abd-B had the strongest effect. Our results suggest that in the absence of continued PcG repression peripodial cells express genes such as Abd-B which regulate epithelial state and thereby disrupt eversion. Our results emphasise the important role that PcG suppression can play in maintaining cell states required for morphogenetic events throughout development and suggest that PcG repression of Hox genes may affect epithelial traits that could contribute to metastasis.

2020-12-31 | GSE153903 | GEO

Maintenance of cell fate by the Polycomb Group gene Sex combs extra enables a partial epithelial mesenchymal transition in Drosophila (Pc dataset)

2020-12-31 | GSE153904 | GEO

An integrated approach to identify environmental modulators of genetic risk factors for complex traits

Project description:Complex traits and diseases can be influenced by both genetics and environment. However, given the large number of environmental stimuli and power challenges for gene-by-environment testing, it remains a critical challenge to identify and prioritize specific disease-relevant environmental exposures. We propose a novel framework for leveraging signals from transcriptional responses to environmental perturbations to identify disease-relevant perturbations that can modulate genetic risk for complex traits and inform the functions of genetic variants associated with complex traits. We perturbed human skeletal muscle, fat, and liver relevant cell lines with 21 perturbations affecting insulin resistance, glucose homeostasis, and metabolic regulation in humans and identified thousands of environmentally responsive genes. By combining these data with GWAS from 31 distinct polygenic traits, we show that the heritability of multiple traits is enriched in regions surrounding genes responsive to specific perturbations and, further, that environmentally responsive genes are enriched for associations with specific diseases and phenotypes from the GWAS catalog. Overall, we demonstrate the advantages of large-scale characterization of transcriptional changes in diversely stimulated and pathologically relevant cells to identify disease-relevant perturbations.

2021-07-09 | GSE179347 | GEO

A Comparative Liver Label-Free Liquid Chromatography-Mass Spectrometry Proteomic Profile Highlights Putative Metabolic Differences Between two Pig Breeds

Project description:Pig breeds have different attitude to traits like growth rate, carcass composition and reproduction parameters as well as other traits. These traits considered as external traits or end phenotypes are the outcome of complex biological processes and interactions. The main goal of pig breeding programs and the basis for crossbreeding is finding a balance between these traits. In pig production, Large White and Duroc breeds are commonly used to optimise respectively fertility and growth ability and differ on several production traits, indeed the first breed as a high fertility characters whereas Duroc is used as terminal sire for her growth performance and good carcass quality traits. In this study, we have used a quantitative label-free LC-MS proteomics approach to characterise and compare the liver proteome of two heavy Italian pig breeds, Italian Duroc and Italian Large White to identify difference due to their different genetic background. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 703094.

2018-09-13 | PXD009771 | Pride

Dynamic complexity of genetic regulatory effects in response to a high cholesterol, high fat diet in baboons

Project description:Steady-state expression quantitative trait loci (eQTLs) explain only a fraction of disease-associated loci identified through genome-wide association studies (GWAS), while eQTLs involved in gene-by-environment (GxE) interactions have rarely been characterized in humans due to experimental challenges. Using a baboon model, we found hundreds of eQTLs that emerge in adipose, liver, and muscle after prolonged exposure to high dietary fat and cholesterol. Diet-responsive eQTLs exhibit genomic localization and genic features that are distinct from steady-state eQTLs. Furthermore, the human orthologs associated with diet-responsive eQTLs are enriched for GWAS genes associated with human metabolic traits, suggesting that context-responsive eQTLs with more complex regulatory effects are likely to explain GWAS hits that do not seem to overlap with standard eQTLs. Our results highlight the complexity of genetic regulatory effects and the potential of eQTLs with disease-relevant GxE interactions in enhancing the understanding of GWAS signals for human complex disease using nonhuman primate models.

2023-12-27 | GSE227346 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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