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Series GSE247796

Query DataSets for GSE247796

Status

Public on Dec 31, 2023

Title

Structural basis of the DEK-nucleosome complex and its functional implications

Organism

Experiment type

Expression profiling by high throughput sequencing
Other

Summary

The nuclear factor Dek is notably enriched within chromatin; nevertheless, the precise binding mechanism of Dek to the nucleosome remains elusive. In this study, we employ cryo-electron microscopy (cryo-EM) to elucidate the high-resolution structure of the Dek-Nucleosome Core Particle (NCP) complex. We identify specific domains responsible for DEK interaction with the histone octamer and DNA within the nucleosome. The veracity of these binding domains is confirmed through a series of meticulous biochemical experiments. Subsequently, cellular experiments reveal that Dek lacking nucleosome-binding capacity exhibits a deficiency in chromatin interaction. Remarkably, this impairment induces a shift towards the primitive endoderm fate in mouse embryonic stem cells, underscoring the pivotal role of Dek in determining cell fate through its nucleosomal interactions.

Overall design

HA-labeled wild-type DEK and various key domain mutations were overexpressed in DEK-knockout cells. CUT&Tag for HA was employed to assess the impact of mutations on the distribution of Dek on chromatin, while RNA-seq was used to identify transcriptomic changes induced by these mutations in the cells.

Contributor(s)

Yunfan S, Yanhong L, Hongda H, Kai Y

Citation missing

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Submission date

Nov 15, 2023

Last update date

Jan 01, 2024

Contact name

shen yunfan

E-mail(s)

shenyunfan.csu@outlook.com

Organization name

central south university

Street address

xiangya road

City

changsha

State/province

hunan

ZIP/Postal code

410000

Country

China

Platforms (1)

Illumina HiSeq 2000 (Mus musculus)

Samples (26)

More...

GSM7900895	RNA-seq of parental E14TG2a cells repeat 1
GSM7900896	RNA-seq of parental E14TG2a cells repeat 2
GSM7900897	RNA-seq of Dek-KO E14TG2a cells repeat 1

GSM7900898	RNA-seq of Dek_KO E14TG2a cells repeat 2
GSM7900899	RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-WT repeat 1
GSM7900900	RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-WT repeat 2
GSM7900901	RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-R58/V63/R653A repeat 1
GSM7900902	RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-R58/V63/R653A repeat 2
GSM7900903	RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-LRM_deletion repeat 1
GSM7900904	RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-LRM_deletion repeat 2
GSM7900905	RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-R58/V63/R653A+LRM_deletion repeat 1
GSM7900906	RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-R58/V63/R653A+LRM_deletion repeat 2
GSM7900907	RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-CTD_deletion repeat 1
GSM7900908	RNA-seq of Dek-KO E14TG2a cells complemented with HA-Dek-CTD_deletion repeat 2
GSM7900909	HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-WT repeat 1
GSM7900910	HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-WT repeat 2
GSM7900911	HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-R58/V63/R653A repeat 1
GSM7900912	HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-R58/V63/R653A repeat 2
GSM7900913	HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-LRM_deletion repeat 1
GSM7900914	HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-LRM_deletion repeat 2
GSM7900915	HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-R58/V63/R653A+LRM_deletion repeat 1
GSM7900916	HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-R58/V63/R653A+LRM_deletion repeat 2
GSM7900917	HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-CTD_deletion repeat 1
GSM7900918	HA-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-CTD_deletion repeat 2
GSM7900919	IgG-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-WT repeat 1
GSM7900920	IgG-CUT&Tag of Dek-KO E14TG2a cells complemented with HA-Dek-WT repeat 2

Relations

BioProject

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE247796_RAW.tar	1.2 Gb	(http)(custom)	TAR (of BW, NARROWPEAK, TXT)
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Raw data are available in SRA

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