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Series GSE260914 Query DataSets for GSE260914
Status Public on Mar 08, 2024
Title ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary Gene expression is orchestrated by transcription factors (TFs), which bind to DNA in a sequence-specific manner, and by spatial genome structure, which constrains and shapes TF activity. Zinc finger protein 143 (ZNF143/ZFP143) is a TF that has been implicated in both gene activation and 3D genome organisation. We have generated an acute ZNF143/ZFP143 depletion system to study its direct consequences on chromatin looping and gene transcription. The effects of ZNF143/ZFP143 depletion are inconsistent with it being a looping factor, which we further confirmed by systematic analysis of previous studies. However, degradation of ZNF143/ZFP143 led to the down-regulation of hundreds of its targets, which were found to be enriched in nuclear-encoded mitochondrial genes. By studying the consequences of ZNF143/ZFP143 loss in monoculture and in an in vitro embryonic development model, we establish ZNF143/ZFP143 as a conserved transcriptional regulator of cell proliferation and differentiation by modulating mitochondrial functions.
 
Overall design Analysis of chromatin occupancy (ZFP143 and CTCF), nascent RNA, 3D genome structure in ZFP143 transcription factor depletion using the dTAG degron system in mESCs. Analysis of open chromatin and stable RNA in ZFP143 depletion in stem cell-derived differentiation models.
 
Contributor(s) Magnitov MD, Maresca M, Teunissen H, de Wit E
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Submission date Mar 05, 2024
Last update date Mar 08, 2024
Contact name Mikhail Magnitov
Organization name The Netherlands Cancer Institute
Street address Plesmanlaan 121
City Amsterdam
ZIP/Postal code 1066CX
Country Netherlands
 
Platforms (2)
GPL16417 Illumina MiSeq (Mus musculus)
GPL21626 NextSeq 550 (Mus musculus)
Samples (57)
GSM8127949 ChIPseq_Input_CTCF
GSM8127950 ChIPseq_Input_ZFP143
GSM8127951 ChIPseq_CTCF_DMSO
Relations
BioProject PRJNA1083999

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
GSE260914_4c_normalised_counts_per_fragment.tsv.gz 48.5 Mb (ftp)(http) TSV
GSE260914_4c_viewpoints.txt.gz 194 b (ftp)(http) TXT
GSE260914_CTCF_peaks.bed.gz 181.4 Kb (ftp)(http) BED
GSE260914_RAW.tar 1.7 Gb (http)(custom) TAR (of BW, HIC, MCOOL)
GSE260914_TTseq_DMSO_forward.bw 26.5 Mb (ftp)(http) BW
GSE260914_TTseq_DMSO_reverse.bw 25.6 Mb (ftp)(http) BW
GSE260914_TTseq_dTAG_24H_forward.bw 29.1 Mb (ftp)(http) BW
GSE260914_TTseq_dTAG_24H_reverse.bw 28.1 Mb (ftp)(http) BW
GSE260914_TTseq_dTAG_2H_forward.bw 28.2 Mb (ftp)(http) BW
GSE260914_TTseq_dTAG_2H_reverse.bw 27.3 Mb (ftp)(http) BW
GSE260914_TTseq_dTAG_6H_forward.bw 28.9 Mb (ftp)(http) BW
GSE260914_TTseq_dTAG_6H_reverse.bw 27.9 Mb (ftp)(http) BW
GSE260914_ZFP143_peaks.bed.gz 77.3 Kb (ftp)(http) BED
GSE260914_rnaseq_RA_differentiation.gene_counts.txt.gz 569.9 Kb (ftp)(http) TXT
GSE260914_ttseq_ZFP143_depletion_time_course.gene_counts.txt.gz 594.1 Kb (ftp)(http) TXT
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