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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 [ChIP-seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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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 (60)
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| GSM8091487 |
JM8.N4 mESC, clone A untreated, CTCF ChIP-seq, rep. 1 |
| GSM8091488 |
JM8.N4 mESC, clone A ∆ZFP143 3h, CTCF ChIP-seq, rep. 1 |
| GSM8091489 |
JM8.N4 mESC, clone A ∆CTCF 3h, CTCF ChIP-seq, rep. 1 |
| GSM8091490 |
JM8.N4 mESC, clone A ∆ZFP143/∆CTCF 3h, CTCF ChIP-seq, rep. 1 |
| GSM8091491 |
JM8.N4 mESC, clone B untreated, CTCF ChIP-seq, rep. 1 |
| GSM8091492 |
JM8.N4 mESC, clone B ∆ZFP143 3h, CTCF ChIP-seq, rep. 1 |
| GSM8091493 |
JM8.N4 mESC, clone B ∆CTCF 3h, CTCF ChIP-seq, rep. 1 |
| GSM8091494 |
JM8.N4 mESC, clone B ∆ZFP143/∆CTCF 3h, CTCF ChIP-seq, rep. 1 |
| GSM8091495 |
JM8.N4 mESC, clone A untreated, CTCF ChIP-seq, rep. 2 |
| GSM8091496 |
JM8.N4 mESC, clone A ∆ZFP143 3h, CTCF ChIP-seq, rep. 2 |
| GSM8091497 |
JM8.N4 mESC, clone A ∆CTCF 3h, CTCF ChIP-seq, rep. 2 |
| GSM8091498 |
JM8.N4 mESC, clone A ∆ZFP143/∆CTCF 3h, CTCF ChIP-seq, rep. 2 |
| GSM8091499 |
JM8.N4 mESC, clone B untreated, CTCF ChIP-seq, rep. 2 |
| GSM8091500 |
JM8.N4 mESC, clone B ∆ZFP143 3h, CTCF ChIP-seq, rep. 2 |
| GSM8091501 |
JM8.N4 mESC, clone B ∆CTCF 3h, CTCF ChIP-seq, rep. 2 |
| GSM8091502 |
JM8.N4 mESC, clone B ∆ZFP143/∆CTCF 3h, CTCF ChIP-seq, rep. 2 |
| GSM8091503 |
JM8.N4 mESC, clone D untreated, CTCF ChIP-seq, rep. 1 |
| GSM8091504 |
JM8.N4 mESC, clone D ∆ZFP143 3h, CTCF ChIP-seq, rep. 1 |
| GSM8091505 |
JM8.N4 mESC, clone D untreated, CTCF ChIP-seq, rep. 2 |
| GSM8091506 |
JM8.N4 mESC, clone D ∆ZFP143 3h, CTCF ChIP-seq, rep. 2 |
| GSM8091507 |
JM8.N4 mESC, clone A untreated, ZNF143 ChIP-seq, rep. 1 |
| GSM8091508 |
JM8.N4 mESC, clone A ∆ZFP143 3h, ZNF143 ChIP-seq, rep. 1 |
| GSM8091509 |
JM8.N4 mESC, clone A ∆CTCF 3h, ZNF143 ChIP-seq, rep. 1 |
| GSM8091510 |
JM8.N4 mESC, clone A ∆ZFP143/∆CTCF 3h, ZNF143 ChIP-seq, rep. 1 |
| GSM8091511 |
JM8.N4 mESC, clone B untreated, ZNF143 ChIP-seq, rep. 1 |
| GSM8091512 |
JM8.N4 mESC, clone B ∆ZFP143 3h, ZNF143 ChIP-seq, rep. 1 |
| GSM8091513 |
JM8.N4 mESC, clone B ∆CTCF 3h, ZNF143 ChIP-seq, rep. 1 |
| GSM8091514 |
JM8.N4 mESC, clone B ∆ZFP143/∆CTCF 3h, ZNF143 ChIP-seq, rep. 1 |
| GSM8091515 |
JM8.N4 mESC, clone A untreated, ZNF143 ChIP-seq, rep. 2 |
| GSM8091516 |
JM8.N4 mESC, clone A ∆ZFP143 3h, ZNF143 ChIP-seq, rep. 2 |
| GSM8091517 |
JM8.N4 mESC, clone A ∆CTCF 3h, ZNF143 ChIP-seq, rep. 2 |
| GSM8091518 |
JM8.N4 mESC, clone A ∆ZFP143/∆CTCF 3h, ZNF143 ChIP-seq, rep. 2 |
| GSM8091519 |
JM8.N4 mESC, clone B untreated, ZNF143 ChIP-seq, rep. 2 |
| GSM8091520 |
JM8.N4 mESC, clone B ∆ZFP143 3h, ZNF143 ChIP-seq, rep. 2 |
| GSM8091521 |
JM8.N4 mESC, clone B ∆CTCF 3h, ZNF143 ChIP-seq, rep. 2 |
| GSM8091522 |
JM8.N4 mESC, clone B ∆ZFP143/∆CTCF 3h, ZNF143 ChIP-seq, rep. 2 |
| GSM8091523 |
JM8.N4 mESC, clone D untreated, ZNF143 ChIP-seq, rep. 1 |
| GSM8091524 |
JM8.N4 mESC, clone D ∆ZFP143 3h, ZNF143 ChIP-seq, rep. 1 |
| GSM8091525 |
JM8.N4 mESC, clone D untreated, ZNF143 ChIP-seq, rep. 2 |
| GSM8091526 |
JM8.N4 mESC, clone D ∆ZFP143 3h, ZNF143 ChIP-seq, rep. 2 |
| GSM8091527 |
JM8.N4 mESC, clone A untreated, Input, rep. 1 |
| GSM8091528 |
JM8.N4 mESC, clone A ∆ZFP143 3h, Input, rep. 1 |
| GSM8091529 |
JM8.N4 mESC, clone A ∆CTCF 3h, Input, rep. 1 |
| GSM8091530 |
JM8.N4 mESC, clone A ∆ZFP143/∆CTCF 3h, Input, rep. 1 |
| GSM8091531 |
JM8.N4 mESC, clone B untreated, Input, rep. 1 |
| GSM8091532 |
JM8.N4 mESC, clone B ∆ZFP143 3h, Input, rep. 1 |
| GSM8091533 |
JM8.N4 mESC, clone B ∆CTCF 3h, Input, rep. 1 |
| GSM8091534 |
JM8.N4 mESC, clone B ∆ZFP143/∆CTCF 3h, Input, rep. 1 |
| GSM8091535 |
JM8.N4 mESC, clone A untreated, Input, rep. 2 |
| GSM8091536 |
JM8.N4 mESC, clone A ∆ZFP143 3h, Input, rep. 2 |
| GSM8091537 |
JM8.N4 mESC, clone A ∆CTCF 3h, Input, rep. 2 |
| GSM8091538 |
JM8.N4 mESC, clone A ∆ZFP143/∆CTCF 3h, Input, rep. 2 |
| GSM8091539 |
JM8.N4 mESC, clone B untreated, Input, rep. 2 |
| GSM8091540 |
JM8.N4 mESC, clone B ∆ZFP143 3h, Input, rep. 2 |
| GSM8091541 |
JM8.N4 mESC, clone B ∆CTCF 3h, Input, rep. 2 |
| GSM8091542 |
JM8.N4 mESC, clone B ∆ZFP143/∆CTCF 3h, Input, rep. 2 |
| GSM8091543 |
JM8.N4 mESC, clone D untreated, Input, rep. 1 |
| GSM8091544 |
JM8.N4 mESC, clone D ∆ZFP143 3h, Input, rep. 1 |
| GSM8091545 |
JM8.N4 mESC, clone D untreated, Input, rep. 2 |
| GSM8091546 |
JM8.N4 mESC, clone D ∆ZFP143 3h, Input, 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 |
PRJNA1078735 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE256226_RAW.tar |
8.3 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
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