Biomedical Research Foundation, Academy of Athens, Athens, Greece.
Biomedical Research Foundation, Academy of Athens, Athens, Greece
Mol Cell Biol. 2018 Apr 30;38(10). doi: 10.1128/MCB.00669-17. Print 2018 May 15.
Transcription factor-induced reprogramming of somatic cells to pluripotency is mediated via profound alterations in the epigenetic landscape. The histone variant macroH2A1 (mH2A1) is a barrier to the cellular reprogramming process. We demonstrate here that mH2A1 blocks reprogramming and contributes to the preservation of cell identity by trapping cells at the very early stages of the process, namely, at the mesenchymal-to-epithelial transition (MET). We provide a comprehensive analysis of the genomic sites occupied by the mH2A1 nucleosomes in human fibroblasts and embryonic stem (ES) cells and how they affect the reprogramming of fibroblasts to pluripotency. We have integrated chromatin immunoprecipitation sequencing (ChIP-seq) data with transcriptome sequencing (RNA-seq) data using cells containing reduced levels of mH2A1 and have inferred mH2A1-centered gene-regulatory networks that support the fibroblast and ES cell fates. We found that the exact positions of mH2A1 nucleosomes in regulatory regions of specific network genes with key regulatory roles guarantee the functional robustness of the regulatory networks. Using the reconstructed networks, we can predict and validate several components and their interactions in the establishment of stable cell types by limiting progression to alternative cell fates.
转录因子诱导体细胞重编程为多能性是通过表观遗传景观的深刻改变介导的。组蛋白变体巨组蛋白 A1（mH2A1）是细胞重编程过程的障碍。我们在这里证明，mH2A1 通过在细胞重编程过程的早期阶段（即间质到上皮转化（MET））将细胞困住，从而阻止重编程并有助于保持细胞身份。我们对人成纤维细胞和胚胎干细胞（ES 细胞）中 mH2A1 核小体占据的基因组位点进行了全面分析，并研究了它们如何影响成纤维细胞向多能性的重编程。我们使用含有 mH2A1 水平降低的细胞，将染色质免疫沉淀测序（ChIP-seq）数据与转录组测序（RNA-seq）数据进行了整合，并推断了支持成纤维细胞和 ES 细胞命运的以 mH2A1 为中心的基因调控网络。我们发现，在具有关键调控作用的特定网络基因的调控区域中，mH2A1 核小体的确切位置保证了调控网络的功能稳健性。使用重建的网络，我们可以通过限制向替代细胞命运的进展来预测和验证稳定细胞类型建立过程中的几个组件及其相互作用。
