GSE137692
Transcriptional dynamics of transposable elements when converting fibroblast cells of Macaca mulatta to neuroepithelial stem cells [mmu-14-samples]
Transposable elements (TE) account for more than 50% of human genome. It has been reported that some types of TEs are dynamically regulated in the reprogramming of human cell lines. However, it is largely unknown whether some TEs in Macaca mulatta are also regulated during the reprogramming of cell lines of monkey. Here, we systematically examined the transcriptional activities of TEs during the conversion of Macaca mulatta fibroblast cells to neuroepithelial stem cells (NESCs). Hundreds of TEs were dynamically regulated during the reprogramming of Macaca mulatta fibroblast cells. Furthermore, 60 Long Terminal Repeats (LTRs), as well as some integrase elements, of MacERV3 were transiently activated during the early stages of the conversion process. These LTRs were potentially bound by critical transcription factors for reprogramming, such as KLF4 and ETV5. These results suggest that the transcription of TEs are delicately regulated during the reprogramming of Macaca mulatta fibroblast cells. Although the family of ERVs activated during the reprogramming of fibroblast cells in Macaca mulatta are different from those in the reprogramming of human fibroblast cells, our results suggest that the activation of some ERVs is a conserved mechanism in primates for converting fibroblast cells to stem cells. Overall design: The fibroblast cells of Macaca mulatta were induced to neuroepithelial stem cells to identify critical transposable elements (TEs) that may contribute to the reprogramming procedure. During the conversion procedure, cells were collected at 7 different stages and were sequenced with RNA-seq to obtain the expression levels of genes and TEs. The enriched cis-regulatory motifs in LTRs of MacERV3 were analyzed to find putative transcription factors of the LTRs. Then, the correlation coefficient values of TFs and LTRs were analyzed to further support the regulatory relations between the identified TFs and LTRs.