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| Status |
Public on Mar 07, 2024 |
| Title |
Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function [PRO-seq] |
| Organism |
Mus musculus |
| Experiment type |
Other
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| Summary |
Interactions between distal loci in mammalian genomes, including those involving enhancers and promoters, are thought to be a central mechanism of gene regulation in mammals, yet the protein regulators of these interactions remain largely undetermined. The zinc finger transcription factor ZNF143/ZFP143 has been strongly implicated as a factor that regulates chromatin interactions, functioning either with or without CTCF. However, ZNF143/ZFP143’s role in this process and its function with or without CTCF are not well understood. Here, we tagged both CTCF and ZNF143/ZFP143 with dual-purpose degron/imaging tags to combinatorically assess their loop function and effect on each other. We find that ZNF143/ZFP143 possesses no general looping function, and that it largely functions independently to CTCF. Instead, ZNF143/ZFP143 is an essential and highly conserved transcription factor possessing an extremely stable chromatin residence time (>20 min) that regulates an important subset of mitochondrial and ribosomal genes.
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| Overall design |
We generated two replicates of Micro-C, ZFP143 ChIP-seq, CTCF ChIP-seq, and PRO-seq per cell line and condition in two mouse embryonic stem cell (mESC) cell lines with the following conditions: untreated, three-hour ZFP143 depletion by 5-Ph-IAA/HaloPROTAC3 treatment, three-hour CTCF depletion by dTag-13 treatment, or three-hour depletion of both ZFP143 and CTCF. We also generated two replicates of Micro-C, ZFP143 ChIP-seq, CTCF ChIP-seq, and PRO-seq per condition in an additional mESC cell line with untreated and three-hour ZFP143 depletion by dTag-13 conditions. Additionally, we performed two replicates of Micro-C per condition in a HEK293T cell line with untreated and three-hour ZNF143 depletion by IAA conditions.
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| Contributor(s) |
Narducci DN, Hansen AS |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Feb 21, 2024 |
| Last update date |
Mar 08, 2024 |
| Contact name |
Domenic Narducci |
| E-mail(s) |
domenicn@mit.edu
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| Organization name |
Massachusetts Institute of Technology
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| Department |
Biological Engineering
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| Lab |
Anders Hansen
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| Street address |
Building 56 Room 787B, 32 Vassar Street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (20)
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| GSM8091547 |
JM8.N4 mESC, clone A untreated, PRO-seq, rep. 1 |
| GSM8091548 |
JM8.N4 mESC, clone A ∆ZFP143 3h, PRO-seq, rep. 1 |
| GSM8091549 |
JM8.N4 mESC, clone A ∆CTCF 3h, PRO-seq, rep. 1 |
| GSM8091550 |
JM8.N4 mESC, clone A ∆ZFP143/∆CTCF 3h, PRO-seq, rep. 1 |
| GSM8091551 |
JM8.N4 mESC, clone B untreated, PRO-seq, rep. 1 |
| GSM8091552 |
JM8.N4 mESC, clone B ∆ZFP143 3h, PRO-seq, rep. 1 |
| GSM8091553 |
JM8.N4 mESC, clone B ∆CTCF 3h, PRO-seq, rep. 1 |
| GSM8091554 |
JM8.N4 mESC, clone B ∆ZFP143/∆CTCF 3h, PRO-seq, rep. 1 |
| GSM8091555 |
JM8.N4 mESC, clone A untreated, PRO-seq, rep. 2 |
| GSM8091556 |
JM8.N4 mESC, clone A ∆ZFP143 3h, PRO-seq, rep. 2 |
| GSM8091557 |
JM8.N4 mESC, clone A ∆CTCF 3h, PRO-seq, rep. 2 |
| GSM8091558 |
JM8.N4 mESC, clone A ∆ZFP143/∆CTCF 3h, PRO-seq, rep. 2 |
| GSM8091559 |
JM8.N4 mESC, clone B untreated, PRO-seq, rep. 2 |
| GSM8091560 |
JM8.N4 mESC, clone B ∆ZFP143 3h, PRO-seq, rep. 2 |
| GSM8091561 |
JM8.N4 mESC, clone B ∆CTCF 3h, PRO-seq, rep. 2 |
| GSM8091562 |
JM8.N4 mESC, clone B ∆ZFP143/∆CTCF 3h, PRO-seq, rep. 2 |
| GSM8091563 |
JM8.N4 mESC, clone D untreated, PRO-seq, rep. 1 |
| GSM8091564 |
JM8.N4 mESC, clone D ∆ZFP143 3h, PRO-seq, rep. 1 |
| GSM8091565 |
JM8.N4 mESC, clone D untreated, PRO-seq, rep. 2 |
| GSM8091566 |
JM8.N4 mESC, clone D ∆ZFP143 3h, PRO-seq, rep. 2 |
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| This SubSeries is part of SuperSeries: |
| GSE256246 |
Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function. |
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| Relations |
| BioProject |
PRJNA1078740 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE256227_RAW.tar |
2.2 Gb |
(http)(custom) |
TAR (of BEDGRAPH) |
SRA Run Selector |
| Raw data are available in SRA |
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