Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

An alternative pluripotent state confers interspecies chimaeric competency [WGBS]

ABSTRACT: In this study, we show that by simple modulation of extrinsic signaling pathways, a new class of pluripotent stem cells, referred to as region selective epiblast stem cells (rsEpiSCs), could be efficiently derived from different stages of the early embryo. rsEpiSCs share features of primed pluripotency yet are distinct from EpiSCs in their molecular characteristics and ability to colonize post-implantation embryos. We performed whole-genome bisulfite sequencing (WGBS) experiments to compare the DNA methylation landscapes of conventional EpiSCs and rsEpiSCs. Compare the DNA methylation profiles in 2 pluripotent stem cell types (LP-EpiSCs and conventional EpiSCs) in mouse. Two replicates are examined for each cell type.

ORGANISM(S): Mus musculus

SUBMITTER: Christopher Benner

PROVIDER: E-GEOD-63568 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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An alternative pluripotent state confers interspecies chimaeric competency.

Wu Jun J Okamura Daiji D Li Mo M Suzuki Keiichiro K Luo Chongyuan C Ma Li L He Yupeng Y Li Zhongwei Z Benner Chris C Tamura Isao I Krause Marie N MN Nery Joseph R JR Du Tingting T Zhang Zhuzhu Z Hishida Tomoaki T Takahashi Yuta Y Aizawa Emi E Kim Na Young NY Lajara Jeronimo J Guillen Pedro P Campistol Josep M JM Esteban Concepcion Rodriguez CR Ross Pablo J PJ Saghatelian Alan A Ren Bing B Ecker Joseph R JR Izpisua Belmonte Juan Carlos JC

Nature 20150506 7552

Pluripotency, the ability to generate any cell type of the body, is an evanescent attribute of embryonic cells. Transitory pluripotent cells can be captured at different time points during embryogenesis and maintained as embryonic stem cells or epiblast stem cells in culture. Since ontogenesis is a dynamic process in both space and time, it seems counterintuitive that these two temporal states represent the full spectrum of organismal pluripotency. Here we show that by modulating culture paramet ...[more]

PMID: 25945737

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Project description:The parasitoid wasp Nasonia vitripennis is an emerging genetic model for functional analysis of DNA methylation. Here, we characterize genome-wide methylation at a base-pair resolution, and compare these results to gene expression across five developmental stages and to methylation patterns reported in other insects. An accurate assessment of DNA methylation across the genome is accomplished using bisulfite sequencing of adult females from a highly inbred line. One-third of genes show extensive methylation over the gene body, yet methylated DNA is not found in non-coding regions and rarely in transposons. Methylated genes occur in small clusters across the genome. Methylation demarcates exon-intron boundaries, with elevated levels over exons, primarily in the 5’ regions of genes. It is also elevated near the sites of translational initiation and termination, with reduced levels in 5’ and 3’ UTRs. Methylated genes have higher median expression levels and lower expression variation across development stages than non-methylated genes. There is no difference in frequency of differential splicing between methylated and non-methylated genes, and as yet no established role for methylation in regulating alternative splicing in Nasonia. Phylogenetic comparisons indicate that many genes maintain methylation status across long evolutionary time scales. Nasonia methylated genes are more likely to be conserved in insects, but even those that are not conserved show broader expression across development than comparable non-methylated genes. Finally, examination of duplicated genes shows that those paralogs that have lost methylation in the Nasonia lineage following gene duplication evolve more rapidly, show decreased median expression levels, and increased specialization in expression across development. Methylation of Nasonia genes signals constitutive transcription across developmental stages, whereas non-methylated genes show more dynamic developmental expression patterns. We speculate that loss of methylation may result in increased developmental specialization in evolution and acquisition of methylation may lead to broader constitutive expression. Whole-genome bisulfite sequencing of 24-hour adult female Nasonia vitripennis whole body samples using Iilumina GAIIx and HiSeq2000.

Dataset Information

An alternative pluripotent state confers interspecies chimaeric competency [WGBS]

Publications

An alternative pluripotent state confers interspecies chimaeric competency.

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