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| Status |
Public on Jun 30, 2021 |
| Title |
ZBTB12-HERVH-LncRNA axis is a molecular barrier for dedifferentiation of human stem cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Development is generally viewed as one-way traffic of cell state transition from primitive to developmentally advanced states. However, molecular mechanisms that ensure the unidirectional transition remain largely unknown. NanoCAGE sequencing identified an evolutionarily conserved zinc finger repressor, ZBTB12, as a molecular barrier for dedifferentiation of human pluripotent stem cells (hPSCs). Single cell RNA sequencing revealed that ZBTB12 is essential for three germ layer differentiation by blocking hPSC dedifferentiation. Mechanistically, ZBTB12 serves as a master repressor of human endogenous retrovirus H (HERVH). Active HERVH loci drive the expression of overlapping long non-coding RNAs (lncRNAs) whose downregulation by ZBTB12 is necessary for pluripotency exit and lineage derivation. Overall, we have identified a ZBTB12-HERVH-lncRNA axis as molecular machinery that safeguards the unidirectional transition of stem cell fates.
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| Overall design |
To identify TFs that regulate hESC differentiation, we established an hESC-derived neural differentiation model and performed nanoCAGE sequencing from cells collected at Day 0, Day 5, Day 15 and Day 23 with two replicates at each time point. Novel candidate TF-ZBTB12 was identified for further functional study. Then ChIP-seq data of ZBTB12 was done to show its binding sites. Moreover, transcriptome was profiling for the KD of ZBTB12 and NANOG in hESC cells.
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| Contributor(s) |
Liu G, Kosik KS, Jang J |
| Citation missing |
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| |
| Submission date |
Aug 22, 2018 |
| Last update date |
Jun 30, 2021 |
| Contact name |
Guojing Liu |
| E-mail(s) |
guojing_liu@ucsb.edu
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| Phone |
1-805-893-4586
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| Organization name |
University of California, santa barbara
|
| Street address |
552 University Rd
|
| City |
santa barbara |
| State/province |
CA |
| ZIP/Postal code |
93106 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (23)
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| Relations |
| BioProject |
PRJNA487458 |
| SRA |
SRP158631 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE118946_H9D0_chr.tss.anno.txt.gz |
2.2 Mb |
(ftp)(http) |
TXT |
| GSE118946_H9D15_chr.tss.anno.txt.gz |
4.2 Mb |
(ftp)(http) |
TXT |
| GSE118946_H9D23_chr.tss.anno.txt.gz |
4.6 Mb |
(ftp)(http) |
TXT |
| GSE118946_H9D5_chr.tss.anno.txt.gz |
3.9 Mb |
(ftp)(http) |
TXT |
| GSE118946_Input.bw |
610.0 Mb |
(ftp)(http) |
BW |
| GSE118946_PolII.bw |
559.4 Mb |
(ftp)(http) |
BW |
| GSE118946_README_Supplementary_Files.txt |
835 b |
(ftp)(http) |
TXT |
| GSE118946_ZB12-flag_peaks.txt.gz |
92.1 Kb |
(ftp)(http) |
TXT |
| GSE118946_ZBTB12_flag.bw |
583.0 Mb |
(ftp)(http) |
BW |
| GSE118946_polII_peaks.txt.gz |
778.2 Kb |
(ftp)(http) |
TXT |
| GSE118946_sc_zb_nc_nanog_tophat_merge.repeats.cpm.ge1.txt.gz |
9.4 Mb |
(ftp)(http) |
TXT |
| GSE118946_siNC_nanog_scramble_ZB.cpm.fil.txt.gz |
653.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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