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Series GSE213418 Query DataSets for GSE213418
Status Public on Sep 20, 2022
Title KLF4 inhibits early neural differentiation of ESCs by coordinating specific 3D chromatin structure, a new mechanism of early neural differentiation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Circular RNA has been reported to be dynamically expressed during embryonic development and regulates human embryonic stem cells (hESCs), but the identification and regulation of functional circular RNA in mouse embryonic stem cells (mESC) remains unclear.
Neural differentiation of embryonic stem cells (ESCs) requires precisely orchestrated gene regulation, a process governed in part by changes in 3D chromatin structure. How these changes regulate gene expression in this context remains unclear. In this study, we observed enrichment of the transcription factor KLF4 at some poised or closed enhancers at TSS-linked regions of genes associated with neural differentiation. Combination analysis of ChIP, HiChIP and RNA-seq data indicated that KLF4 loss in ESCs induced changes in 3D chromatin structure, including increased chromatin interaction loops between neural differentiation-associated genes and active enhancers, leading to upregulated expression of neural differentiation-associated genes and therefore early neural differentiation. This study suggests KLF4 inhibits early neural differentiation by regulation of 3D chromatin structure, which is a new mechanism of early neural differentiation.
Conclusions: Our study suggests KLF4 inhibits early neural differentiation by regulation of 3D chromatin structure, which is a new mechanism of early neural differentiation.
 
Overall design Two biological replicates were analyzed for each experimental condition. WT and KO cells were RNA-seq/HiChIP in ESCs or neuro induction at day 12.
 
Contributor(s) Lu W, Bi J, Wang W
Citation(s) 36477888
Submission date Sep 15, 2022
Last update date Jan 11, 2023
Contact name Niannian Li
Organization name Nankai University
Department college of Life Sciences
Street address No. 94 Weijin Road, Nankai District, Tianjin
City Tianjin
State/province Tianjin
ZIP/Postal code 300071
Country China
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (26)
GSM6585932 RNA-Seq of Mus musculus: NPC-WT-Rep1
GSM6585933 RNA-Seq of Mus musculus: NPC-WT-Rep2
GSM6585934 RNA-Seq of Mus musculus: NPC-KLF4-KO-Rep1
Relations
BioProject PRJNA880652

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Supplementary file Size Download File type/resource
GSE213418_E14_NPC.interactions.all.mango.BEDPE.gz 1.7 Mb (ftp)(http) BEDPE
GSE213418_RAW.tar 5.8 Gb (http)(custom) TAR (of BW, TXT)
GSE213418_ko_npc.interactions.all.mango.BEDPE.gz 5.8 Mb (ftp)(http) BEDPE
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
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