Integrative CUT&Tag-RNA-Seq analysis of histone variant macroH2A1-dependent orchestration of human induced pluripotent stem cell reprogramming.
Niccolò LiorniAlessandro NapoliStefano CastellanaSebastiano GiallongoDaniela ŘehákováOriana Lo ReIrena KoutnáTommaso MazzaManlio VinciguerraPublished in: Epigenomics (2023)
Aim: Human induced pluripotent stem cells (iPSCs) are inefficiently derived from somatic cells by overexpression of defined transcription factors. Overexpression of H2A histone variant macroH2A1.1, but not macroH2A1.2, leads to increased iPSC reprogramming by unclear mechanisms. Materials & methods: Cleavage under targets and tagmentation (CUT&Tag) allows robust epigenomic profiling of a low cell number. We performed an integrative CUT&Tag-RNA-Seq analysis of macroH2A1-dependent orchestration of iPSCs reprogramming using human endothelial cells. Results: We demonstrate wider genome occupancy, predicted transcription factors binding, and gene expression regulated by macroH2A1.1 during reprogramming, compared to macroH2A1.2. MacroH2A1.1, previously associated with neurodegenerative pathologies, specifically activated ectoderm/neural processes. Conclusion: CUT&Tag and RNA-Seq data integration is a powerful tool to investigate the epigenetic mechanisms occurring during cell reprogramming.
Keyphrases
- rna seq
- single cell
- induced pluripotent stem cells
- endothelial cells
- transcription factor
- gene expression
- dna methylation
- high glucose
- stem cells
- induced apoptosis
- pluripotent stem cells
- electronic health record
- bone marrow
- oxidative stress
- mesenchymal stem cells
- vascular endothelial growth factor
- big data
- endoplasmic reticulum stress
- network analysis
- pi k akt