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Omics score: 1002

MCGILL

ABSTRACT: Organisation EGAO00000000332

PROVIDER: EGAO00000000332 | EGA |

REPOSITORIES: EGA

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Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation.

Busche Stephan S Shao Xiaojian X Caron Maxime M Kwan Tony T Allum Fiona F Cheung Warren A WA Ge Bing B Westfall Susan S Simon Marie-Michelle MM Barrett Amy A Bell Jordana T JT McCarthy Mark I MI Deloukas Panos P Blanchette Mathieu M Bourque Guillaume G Spector Timothy D TD Lathrop Mark M Pastinen Tomi T Grundberg Elin E

Genome biology 20151223

<h4>Background</h4>CpG methylation variation is involved in human trait formation and disease susceptibility. Analyses within populations have been biased towards CpG-dense regions through the application of targeted arrays. We generate whole-genome bisulfite sequencing data for approximately 30 adipose and blood samples from monozygotic and dizygotic twins for the characterization of non-genetic and genetic effects at single-site resolution.<h4>Results</h4>Purely invariable CpGs display a bimod ...[more]

PMID: 26699896

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Chromatin Reprogramming of In Vitro Fertilized and Somatic Cell Nuclear Transfer Bovine Embryos During Embryonic Genome Activation [single cell ATAC-seq]

Project description:Reprogramming of the gamete into a developmentally competent embryo identity is a fundamental aspect of preimplantation development. One of the most important processes of this reprogramming is the transcriptional awakening during embryonic genome activation (EGA), which robustly occurs in fertilized embryos but is defective in most somatic cell nuclear transfer (SCNT) embryos. However, little is known about the genome-wide underlying chromatin landscape during EGA in SCNT embryos and how it differs from a fertilized embryo. By profiling open chromatin genome-wide in both types of bovine embryos, we find that SCNT embryos fail to reprogram a subset of the EGA gene targets that are normally activated in fertilized embryos. Importantly, a small number of transcription factor (TF) motifs explain most chromatin regions that fail to open in SCNT embryos suggesting that over-expression of a limited number of TFs may provide more robust reprogramming. One such TF, the zygotically-expressed bovine gene DUXC which is a homologue of EGA factors DUX/DUX4 in mouse/human, is alone capable of activating ~84% of all EGA transcripts that fail to activate normally in SCNT embryos. Additionally, single-cell chromatin profiling revealed low intra-embryo heterogeneity but high inter-embryo heterogeneity in SCNT embryos and an uncoupling of cell division and open chromatin reprogramming during EGA. Surprisingly, our data also indicate that transcriptional defects may arise downstream of promoter chromatin opening in SCNT embryos, suggesting additional mechanistic insights into how and why transcription at EGA is dysregulated. We anticipate that our work will lead to altered SCNT protocols to increase the developmental competency of bovine SCNT embryos.

2025-06-01 | GSE236607 | GEO

Chromatin Reprogramming of In Vitro Fertilized and Somatic Cell Nuclear Transfer Bovine Embryos During Embryonic Genome Activation [ATAC-Seq]

2025-06-01 | GSE236604 | GEO

Chromatin Reprogramming of In Vitro Fertilized and Somatic Cell Nuclear Transfer Bovine Embryos During Embryonic Genome Activation [20230618-SMART-seq]

2025-06-01 | GSE236605 | GEO

Chromatin Reprogramming of In Vitro Fertilized and Somatic Cell Nuclear Transfer Bovine Embryos During Embryonic Genome Activation [WGS-bovine-EJG]

2025-06-01 | GSE236608 | GEO

RNA-Seq of polyA mRNA from rare types of cultured or uncultured primary cells of different haemopoetic lineages from healthy individuals in the BLUEPRINT epigenome project (Expression Atlas tissue view)

Project description:This experiment contains a subset of data from the BLUEPRINT Epigenome project ( http://www.blueprint-epigenome.eu ), which aims at producing a reference haemopoetic epigenomes for the research community. 29 samples of primary cells or cultured primary cells of different haemopoeitc lineages from cord blood are included in this experiment. This ArrayExpress record contains only meta-data. Raw data files have been archived at the European Genome-Phenome Archive (EGA, www.ebi.ac.uk/ega) by the consortium, with restricted access to protect sample donors' identity. The relevant accessions of EGA data sets is EGAD00001001165. Details on how to apply for data access via the BLUEPRINT data access committee are on the EGA data set pages. The mapping of samples to these EGA accessions can be found in the 'Sample Data Relationship Format' file of this ArrayExpress record. Information on individual samples and sequencing libraries can also be found on the BLUEPRINT data coordination centre (DCC) website: http://dcc.blueprint-epigenome.eu

2015-09-30 | E-MTAB-3819 | biostudies-arrayexpress

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