| 2021 |
ZC3H4 depletion causes upregulation and extension of hundreds of unstable non-coding transcripts (particularly antisense RNAs and enhancer RNAs from super-enhancers), and ZC3H4 occupies these loci, indicating a direct role in restricting non-coding transcription. Engineered tethering of ZC3H4 to reporter RNA promotes its degradation by the nuclear exosome. ZC3H4 loss also causes a substantial reduction in cell proliferation. |
siRNA knockdown with nascent RNA sequencing, ChIP/occupancy analysis, reporter tethering assay, cell proliferation assay |
eLife |
High |
33913806
|
| 2023 |
ZC3H4 forms a 'Restrictor' complex with WDR82 and ARS2, and additionally associates with the nuclear exosome targeting (NEXT) complex. The domains of ZC3H4 that contact ARS2 and WDR82 are required for ncRNA restriction. Restrictor co-transcriptionally controls an overlapping population of ncRNAs, and its function is enabled by PNUTS. U1 snRNA shields protein-coding transcripts from Restrictor and PNUTS at hundreds of genes. |
Co-immunoprecipitation, domain mutagenesis, nascent RNA sequencing, genetic depletion experiments |
Molecular cell |
High |
37329883
|
| 2023 |
A conserved basic domain of ARS2 binds a conserved acidic-rich short linear motif (SLiM) in ZC3H4. This interaction recruits ZC3H4 to chromatin to elicit RNAPII termination, independent of CPA and Integrator pathways. ZC3H4 in turn forms a direct connection to the NEXT complex to facilitate rapid degradation of the nascent RNA, coupling transcription termination to RNA decay. |
Biochemical binding assays, domain mapping, chromatin immunoprecipitation, nascent RNA sequencing upon depletion |
Molecular cell |
High |
37329882
|
| 2024 |
ZC3H4/WDR82 (Restrictor) co-purifies with PP1 phosphatase and its nuclear targeting subunit PNUTS, which binds directly to WDR82. AlphaFold predicts a quaternary PPWZ complex. A dominant-negative PP1 H66K-PNUTS substrate trap inhibits antisense transcription termination and CTD Ser5 dephosphorylation, and these activities require the PNUTS-WDR82 binding domain. CTD Ser5 hyperphosphorylation is associated with higher RNAPII processivity, suggesting PP1-mediated Ser5 dephosphorylation by PPWZ is coupled to termination. |
Co-purification/mass spectrometry, AlphaFold structural prediction, dominant-negative PP1 substrate trap, nascent RNA sequencing, CTD phosphorylation analysis |
bioRxivpreprint |
Medium |
bio_10.1101_2024.07.12.603302
|
| 2025 |
ZC3H4 deficiency leads to increased replication stress, R-loop formation, and transcription-replication conflicts (TRCs) at ncRNA loci, causing DNA damage, abnormal mitosis, and cellular senescence. ZC3H4 preferentially binds genomic regions prone to TRCs and R loops, where it suppresses ncRNA bursts, thereby safeguarding genome integrity. |
ZC3H4 knockout/depletion, super-resolution microscopy, biochemical analysis, bioinformatic analysis of binding sites, DNA damage and senescence assays |
Science advances |
High |
40531993
|
| 2025 |
The Restrictor complex (ZC3H4/WDR82) promiscuously suppresses early RNAPII elongation genome-wide, but this activity is blocked at most mRNAs by the presence of a 5′ splice site. Restrictor reduces the rate of transcription elongation rather than directly terminating RNAPII, rendering it susceptible to termination by other machineries. Restrictor is a critical determinant of transcription directionality at divergent promoters and prevents transcriptional interference. |
Unbiased sequence screens, rapid protein degradation (degron), nascent RNA sequencing (TT-seq/PRO-seq), splicing mutant analysis |
bioRxivpreprint |
Medium |
bio_10.1101_2025.01.08.631787
|
| 2021 |
ZC3H4 is essential for early mouse embryogenesis: homozygous mutant embryos are lost by E7.5, fail to hatch or form inner cell mass colonies, display severe DNA breaks, reduced cell proliferation, and compromised epiblast and primitive endoderm specification. |
In vivo mouse knockout, blastocyst outgrowth assay, immunofluorescence for lineage markers, DNA damage assay (γH2AX), ROS measurement |
Biology of reproduction |
High |
33246328
|
| 2025 |
ZC3H4 ablation in prostate stromal cells phenocopies mitochondrial Complex I inhibition, causing elevated mitochondrial superoxide (mtROS), altered mitochondrial membrane potential, abnormal mitochondrial morphology, altered NAD+/NADH ratio, and reduced Complex I function, in addition to altered cell-matrix adhesion, fibronectin upregulation, anoikis resistance, and stress-induced premature senescence. |
CRISPR/Cas9 ablation, mitochondrial function assays (mtROS, membrane potential, NAD+/NADH, CI activity), cell adhesion/anoikis assays |
Cell death & disease |
Medium |
41120279
|
| 2025 |
HPV16 E2 protein recruits ZC3H4 in a BRD4-dependent manner to specifically activate the HPV16 late promoter P670. ZC3H4 and E2 co-localize in cells with high P670 activity, and ZC3H4 knockdown in differentiated HPV16- or HPV31-positive cells reduces late viral transcripts in an E2-BRD4-dependent manner. Knockdown of ZC3H4 does not increase viral antisense (uaRNA) transcripts, indicating ZC3H4 enhances late transcription independently of antisense suppression. |
Biotin proximity ligation screen, reporter assay, co-localization (immunofluorescence), siRNA knockdown, RT-qPCR |
Journal of virology |
Medium |
40801544
|
| 2020 |
The transcription factor ELK-1 acts at the ZC3H4 promoter to transcriptionally upregulate ZC3H4 expression in response to SiO2-induced oxidative stress, placing ELK-1 upstream of ZC3H4 in the silica-EMT signaling axis. |
Promoter reporter assay, ChIP, siRNA knockdown, Western blotting |
Laboratory investigation |
Medium |
32218530
|
| 2022 |
ZC3H4 activates fibroblasts via the sigmar1/ER stress pathway; specific knockdown of ZC3H4 attenuates SiO2-induced fibroblast activation (COL1A1, COL3A1, ACTA1 expression) and migration. ER stress blockade also inhibits ZC3H4 expression, demonstrating a positive feedback loop between ER stress and ZC3H4. |
CRISPR/Cas9 knockdown, ER stress inhibitor treatment, Western blotting, scratch/3D migration assay |
Toxicology and applied pharmacology |
Low |
34979141
|
| 2022 |
ZC3H4 knockdown in SiO2-exposed monocytes reduces ZC3H4-induced autophagy, which in turn reverses ZC3H4-mediated downregulation of IL-10 secretion. IL-10 from infiltrating monocytes inhibits fibroblast activation and migration, attenuating pulmonary fibrosis. |
CRISPR/Cas9 knockdown, ELISA, Western blotting, cell functional assays |
Respiratory research |
Low |
35962397
|
| 2023 |
ZC3H4 governs SiO2-induced epithelial cell migration through the ROCK/p-PYK2/p-MLC2 signaling pathway, as demonstrated by CRISPR/Cas9 knockdown of ZC3H4 and pathway inhibitor experiments. |
CRISPR/Cas9 knockdown, pathway inhibitors (ROCK, PYK2, MLC2), 2D migration assay, Western blotting |
Environmental toxicology and pharmacology |
Low |
37866415
|