Unknown

Dataset Information

0

KLF4 inhibits early neural differentiation of ESCs by coordinating specific 3D chromatin structure.

ABSTRACT: 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.

SUBMITTER: Bi J 

PROVIDER: S-EPMC9757050 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

Json Xml
altmetric image

Publications

KLF4 inhibits early neural differentiation of ESCs by coordinating specific 3D chromatin structure.

Bi Jinfang J   Wang Wenbin W   Zhang Meng M   Zhang Baoying B   Liu Man M   Su Guangsong G   Chen Fuquan F   Chen Bohan B   Shi Tengfei T   Zheng Yaoqiang Y   Zhao Xueyuan X   Zhao Zhongfang Z   Shi Jiandang J   Li Peng P   Zhang Lei L   Lu Wange W  

Nucleic acids research 20221101 21

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  ...[more]

Similar Datasets

Transcriptomics KLF4 inhibits early neural differentiation of ESCs by coordinating specific 3D chromatin structure
2022-06-01 | GSE194068 | GEO
Transcriptomics KLF4 inhibits early neural differentiation of ESCs by coordinating specific 3D chromatin structure, a new mechanism of early neural differentiation
2022-09-20 | GSE213418 | GEO
Genomics KLF4 inhibits early neural differentiation of ESCs by coordinating specific 3D chromatin structure
| PRJNA798967 | ENA
Genomics KLF4 inhibits early neural differentiation of ESCs by coordinating specific 3D chromatin structure, a new mechanism of early neural differentiation
| PRJNA880652 | ENA
Transcriptomics Two enhancers synergistically regulate HoxB genes expressions and retinoic acid-induced early ESCs differentiation through 3D chromatin structure
2021-03-01 | GSE165725 | GEO
Genomics Dynamic alterations of 3D chromatin structure during differentiation
2019-08-27 | E-MTAB-2063 | biostudies-arrayexpress
Transcriptomics Dynamic alterations of 3D chromatin structure during differentiation RNA-seq
2019-08-27 | E-MTAB-2125 | biostudies-arrayexpress
Unknown MYOD1 inhibits avian adipocyte differentiation via miRNA-206/KLF4 axis.
| S-EPMC8101123 | biostudies-literature
Unknown Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons.
| S-EPMC7322528 | biostudies-literature
Unknown HMGA1 orchestrates chromatin compartmentalization and sequesters genes into 3D networks coordinating senescence heterogeneity.
| S-EPMC11319441 | biostudies-literature