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Series GSE137692 Query DataSets for GSE137692
Status Public on Dec 31, 2020
Title Transcriptional dynamics of transposable elements when converting fibroblast cells of Macaca mulatta to neuroepithelial stem cells [mmu-14-samples]
Organism Macaca mulatta
Experiment type Expression profiling by high throughput sequencing
Summary 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.
 
Contributor(s) Zheng Y
Citation(s)
  • Liu D, Liu L, Duan K, Guo J et al. Transcriptional dynamics of transposable elements when converting fibroblast cells of Macaca mulatta to neuroepithelial stem cells. BMC Genomics 2021 Jun 4;22(Suppl 3):405. PMID: 34082708
Submission date Sep 19, 2019
Last update date Jun 09, 2021
Contact name Yun Zheng
E-mail(s) zhengyun5488@gmail.com
Organization name Yunnan Agricultural University
Street address 452 Fengyuan Road
City Kunming
State/province Yunnan
ZIP/Postal code 650201
Country China
 
Platforms (1)
GPL14954 Illumina HiSeq 2000 (Macaca mulatta)
Samples (14)
GSM4085044 RF-P3-S1
GSM4085045 RF-P3-S2
GSM4085046 RF-iN-d5-S1
Relations
BioProject PRJNA566329
SRA SRP222479

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE137692_mmul-RNA-seq-FPKM.xlsx 4.1 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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