Genomics

Dataset Information

157

Naked mole rat cells show resistance to iPSC reprogramming and signs of more stable epigenome


ABSTRACT: Naked mole rat (NMR) is a valuable model for aging and cancer research due to its exceptional longevity and resistance to tumorigenesis. In an effort to generate NMR induced pluripotent stem cells (iPSCs) we observed that reprogramming efficiency of NMR fibroblasts in repsonse to OSKM overexpression was drasticaly lower than that of mouse fibroblasts. To understand the cause of NMR resistance to reprogramming we screened for factors that improve reprogramming effciency. We identified that expression of SV40 Large T (LT) dramatically improved reprogramming of NMR fibroblasts. Inactivation of Rb alone, but not p53, was suffcient to improve reprogramming effciency suggesting that NMR chromatin structure is refractory to reprogramming. Analysis of global histone landscape using quantitative mass spectrometry revealed that NMR fibroblasts had higer levels of repressive H3K27 methylation marks, and lower levels of activating H3K27 acetylation mark than the mouse fibroblasts. Furthermore, the NMR cells had lower levels of permissive H2A.Z acetylation marks. ChIP showed that of E-cadherin had repressive H3K9me3 histone mark in the NMR, but was poised with a bivalent H3K4me3/H3K27me3 in the mouse. Expression of LT reduced the levels of H3K9me3 mark on E-cadherin promoter. ATAC-seq revealed that NMR had more open chromatin globally, however, NMR promoters were more closed than mouse promoters. Expression of LT antigen led to massive opening of the NMR promoters including gene promoters required for reprogramming. Cumulatively, these data suggest that NMR has more stable epigenome than mouse, which resists reprogramming and may contribute to NMR longevity and cancer resistance. Overall design: ATAC-seq in mouse and naked mole rate fibroblast cell lines.

INSTRUMENT(S): Illumina HiSeq 2500 (Mus musculus)

SUBMITTER: Shi Yang  

PROVIDER: GSE83585 | GEO | 2017-06-21

SECONDARY ACCESSION(S): PRJNA326430

REPOSITORIES: GEO

Similar Datasets

2011-11-07 | E-GEOD-30764 | ArrayExpress
| GSE75606 | GEO
2011-10-12 | E-GEOD-30337 | ArrayExpress
| GSE104215 | GEO
2011-10-12 | GSE30337 | GEO
2018-06-21 | PXD008720 | Pride
2018-01-30 | GSE107194 | GEO
| GSE98667 | GEO
| GSE98744 | GEO
| GSE98663 | GEO