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Showing TUT4 — ZCCHC11 is a alias.

TUT4

Terminal uridylyltransferase 4 · UniProt Q5TAX3

Length
1644 aa
Mass
185.2 kDa
Annotated
2026-06-10
25 papers in source corpus 19 papers cited in narrative 20 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

TUT4 (Zcchc11/ZCCHC11/TENT3A) is a cytoplasmic non-canonical terminal uridylyl transferase that adds 3' uridine tails to a broad range of RNA substrates to control their fate and silencing activity (PMID:19703396, PMID:19701194, PMID:35797480). Its best-characterized role is in let-7 microRNA biogenesis: TUT4 is recruited by Lin28 to a GGAG motif in the terminal loop of pre-let-7 and oligo-uridylates the precursor, blocking Dicer processing and marking the transcript for decay by the exonuclease DIS3L2 (PMID:19703396, PMID:19713958, PMID:26114892). Beyond pre-let-7, TUT4 uridylates a defined subset of mature miRNAs through a bipartite sequence motif, an event that does not change miRNA abundance but relieves miRNA-mediated silencing of targets such as IL-6 and IGF-1 mRNAs, linking TUT4 to cytokine output and postnatal growth (PMID:19701194, PMID:23209448, PMID:25223788); it is the predominant TUTase for bulk mature-miRNA uridylation, with loss of uridylation replaced by adenylated isomiRs (PMID:36071058). TUT4 also uridylates replication-dependent histone mRNAs to target them for degradation after DNA replication (PMID:21051505), and restricts LINE-1 retrotransposition and viral RNAs by uridylating their 3' ends to promote decay (PMID:30122351, PMID:37085578). Mechanistically, TUT4 operates through two modules — a catalytic module (CM) and a Lin28-interacting module (LIM) — that switch the enzyme from mono-U to processive oligo-U addition; structural work defined how Lin28 drives ternary complex formation, how the CM finger clamps the duplex stem of pre-let-7 during elongation, and how the enzyme follows an ordered kinetic mechanism with UTP binding before RNA and strong selectivity for UTP (PMID:28671666, PMID:35797480, PMID:41521656). Distinct from its enzymatic functions, TUT4 acts through an N-terminal C2H2 zinc-finger region as a negative regulator of TLR/NF-κB signaling via TIFA and as a uridyltransferase-independent promoter of G1/S cell cycle progression (PMID:22006926, PMID:16643855).

Mechanistic history

Synthesis pass · year-by-year structured walk · 13 steps
  1. 2009 High

    Established TUT4 as the enzyme that executes Lin28-directed pre-let-7 uridylation, answering how Lin28 blocks let-7 maturation at the molecular level.

    Evidence Biochemical identification, knockdown, catalytically inactive mutant, and in vitro uridylation assays in mouse ES cells, replicated by two labs

    PMID:19703396 PMID:19713958

    Open questions at the time
    • Did not resolve the fate of uridylated pre-let-7 (decay enzyme unknown at this stage)
    • Did not define domain requirements for Lin28 interaction
  2. 2009 High

    Extended TUT4 activity to mature miRNAs, showing uridylation of miR-26a as a mechanism to control cytokine output.

    Evidence Knockdown, small RNA sequencing, and in vitro nucleotidyltransferase assay with IL-6 readout

    PMID:19701194

    Open questions at the time
    • Did not define the sequence determinants distinguishing uridylated mature miRNAs
    • Mechanism by which uridylation alters silencing not resolved
  3. 2010 High

    Identified histone mRNAs as a non-miRNA substrate class, showing uridylation couples to mRNA decay after DNA replication.

    Evidence siRNA knockdown with direct detection of uridylated histone transcripts and degradation assays

    PMID:21051505

    Open questions at the time
    • Downstream decay machinery for uridylated histone mRNAs not identified
    • Trigger linking replication status to uridylation not defined
  4. 2011 Medium

    Revealed a catalysis-independent function: an N-terminal region of TUT4 promotes G1/S progression independent of uridyltransferase activity.

    Evidence Knockdown, overexpression, catalytic point and truncation mutants, cell cycle analysis

    PMID:22006926

    Open questions at the time
    • Direct molecular partners of the N-terminal region in cell cycle control not identified
    • Single-lab finding without orthogonal mechanistic validation
  5. 2012 High

    Mapped the Lin28 interaction to a single C2H2 zinc finger and showed TUT7 acts redundantly, clarifying the determinants of let-7 control.

    Evidence Domain truncation, reconstitution assays, and ES cell knockdown

    PMID:22898984

    Open questions at the time
    • Did not provide atomic structure of the zinc finger-Lin28 interface
    • Relative contributions of TUT4 vs TUT7 in other tissues unresolved
  6. 2012 High

    Demonstrated in vivo physiological relevance: mature-miRNA uridylation relieves silencing of IGF-1 to support postnatal growth.

    Evidence Zcchc11-knockout mice with deep small RNA sequencing, reporter assays, and IGF-1 measurements

    PMID:23209448

    Open questions at the time
    • Molecular mechanism by which uridylation reduces silencing capacity not fully resolved
    • Full set of physiologically relevant miRNA targets undefined
  7. 2014 High

    Defined substrate specificity for mature-miRNA uridylation through a bipartite RNA motif and identified TRIM25 as an RNA-specific cofactor enhancing pre-let-7 uridylation.

    Evidence In vitro uridylation with motif mapping, zebrafish developmental readout; RNA pulldown/MS and co-IP for TRIM25

    PMID:25223788 PMID:25457611

    Open questions at the time
    • Structural basis of TRIM25 activation of TUT4 not resolved
    • Generality of TRIM25 cofactor role across substrates unknown
  8. 2017 High

    Provided the structural and mechanistic basis for the mono-U to oligo-U switch, defining the catalytic and Lin28-interacting modules.

    Evidence Crystal structure of TUT7 catalytic module in monoU state, domain mutants, and in vitro reconstitution

    PMID:28671666

    Open questions at the time
    • Full ternary complex during processive elongation not captured at this stage
    • Conformational dynamics of the switch inferred rather than directly observed
  9. 2018 High

    Established TUT4 as a host restriction factor for LINE-1 retrotransposition, with divergent cytoplasmic roles for TUT4 vs TUT7 and cooperation with MOV10.

    Evidence Knockdown, retrotransposition reporter assays, subcellular localization, and co-IP with MOV10 in human cells and mouse testes

    PMID:30122351

    Open questions at the time
    • Precise determinants directing TUT4 to LINE-1 mRNA not defined
    • Mechanistic interplay between uridylation and MOV10 RNPase activity incomplete
  10. 2022 High

    Refined the enzymatic and selectivity logic: kinetic ordered mechanism and zinc-finger surfaces underlying substrate diversity, plus establishment of TUT4 as the dominant bulk-miRNA uridylase.

    Evidence In vitro kinetics and nucleotide specificity assays; NMR of ZnF2 RNA-binding surfaces; CRISPR knockouts of TENT2/TUT4/TUT7 with deep sequencing

    PMID:34719327 PMID:35797480 PMID:36071058

    Open questions at the time
    • How distinct ZnF2 surfaces are deployed on specific targets in cells not directly observed
    • Cellular consequences of let-7a/AKT axis modulation only partially characterized
  11. 2023 Medium

    Extended TUT4 antiviral surveillance to coronavirus subgenomic RNAs with short poly(A) tails, marking them for decay.

    Evidence Splint-ligation poly(A) length assay, siRNA knockdown, and viral replication measurement for MHV

    PMID:37085578

    Open questions at the time
    • Single virus model; generality across coronaviruses untested
    • Decay enzyme acting on uridylated viral RNA not directly identified in this study
  12. 2024 Medium

    Distinguished TUT4 from TUT7 in a synthetic-lethal cancer context, establishing TUT4/7 uridylation as a pharmacologically targetable RNA salvage pathway.

    Evidence CRISPR knockout, FOCAD re-expression rescue, and selective TUT4/7 inhibitors in vitro and in vivo

    PMID:39235218

    Open questions at the time
    • Why TUT7 but not TUT4 is required in FOCAD-deleted cells mechanistically unclear
    • Single-lab pathway placement partially inferred
  13. 2026 High

    Captured the elongation-stage ternary complex, resolving how Lin28 anchoring and CM-LIM cooperation enable processive oligo-uridylation of pre-let-7.

    Evidence Cryo-EM of human TUT4-Lin28A-pre-let-7 with biochemical validation

    PMID:41521656

    Open questions at the time
    • Structural basis for substrate selection beyond pre-let-7 not addressed
    • Dynamics of repeated UTP incorporation cycles inferred from static states

Open questions

Synthesis pass · forward-looking unresolved questions
  • How TUT4's catalysis-independent N-terminal functions (cell cycle, NF-κB regulation) integrate mechanistically with its RNA uridylation activity remains unresolved.
  • No structural or interaction map linking the N-terminal zinc-finger region to cell cycle effectors
  • Whether enzymatic and non-enzymatic activities operate in the same cellular contexts is unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140098 catalytic activity, acting on RNA 5 GO:0016740 transferase activity 4 GO:0003723 RNA binding 3
Localization
GO:0005829 cytosol 2 GO:0005634 nucleus 1
Pathway
R-HSA-8953854 Metabolism of RNA 5 R-HSA-168256 Immune System 4 R-HSA-1640170 Cell Cycle 1
Partners
DIS3L2LIN28AMOV10TIFATRIM25TUT7

Evidence

Reading pass · 20 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2009 TUT4 (TUTase4) was identified as the uridylyl transferase responsible for adding oligouridine tails to pre-let-7, thereby blocking Dicer processing. Lin28 recruits TUT4 to pre-let-7 by recognizing a tetra-nucleotide sequence motif (GGAG) in the terminal loop of the precursor. Biochemical identification, knockdown experiments, in vitro uridylation assays Cell High 19703396
2009 Zcchc11 (TUT4) is the 3' terminal uridylyl transferase responsible for Lin28-mediated pre-let-7 uridylation in mouse embryonic stem cells. The activity is UTP-dependent and selective for let-7 precursors. Knockdown of Zcchc11 or overexpression of a catalytically inactive TUTase relieves inhibition of let-7 processing, leading to accumulation of mature let-7 and repression of let-7 target reporter genes. Knockdown, overexpression of catalytically inactive mutant, in vitro uridylation assay, reporter gene assay Nature structural & molecular biology High 19713958
2009 Zcchc11 (TUT4) is a ribonucleotidyltransferase with preference for uridine that uridylates mature miR-26a at its 3' end, abrogating IL-6 repression by miR-26a and thereby promoting IL-6 mRNA stability and expression. Knockdown, small RNA sequencing, poly(A) tail length assay, in vitro nucleotidyltransferase assay Nature cell biology High 19701194
2010 ZCCHC11 (TUT4) is the cytoplasmic terminal U-transferase responsible for 3' uridylation of replication-dependent histone mRNAs, targeting them for degradation following inhibition or completion of DNA replication. Knockdown of ZCCHC11 selectively blocked histone mRNA degradation and reduced the proportion of uridylated histone transcripts. siRNA knockdown, detection of uridylated histone mRNAs, degradation assays RNA (New York, N.Y.) High 21051505
2011 Zcchc11 (TUT4) promotes G1-to-S phase cell cycle progression by increasing expression of cyclins D1 and A and CDK4, through both Rb-dependent and Rb-independent mechanisms. Importantly, this proliferative activity is independent of its uridyltransferase activity, as a catalytically inactive point mutant retains full effect, and is driven by the N-terminal region of the protein lacking RNA-binding and uridyltransferase domains. Loss-of-function (knockdown), gain-of-function (overexpression), catalytic domain point mutants, truncation mutants, cell cycle analysis The Journal of biological chemistry Medium 22006926
2012 A single C2H2-type zinc finger domain of Zcchc11 (TUT4) is responsible for the functional interaction with Lin28, enabling Lin28-enhanced pre-let-7 uridylation. Zcchc6 (TUT7) functions redundantly with Zcchc11 in Lin28-mediated let-7 biogenesis control in embryonic stem cells. Biochemical dissection, domain truncation, reconstitution assays, embryonic stem cell knockdown RNA (New York, N.Y.) High 22898984
2012 Zcchc11 (TUT4) mediates terminal uridylation of diverse mature miRNAs in neonatal mouse liver. This uridylation does not alter miRNA abundance but relieves miRNA-mediated silencing of IGF-1 mRNA, leading to enhanced IGF-1 expression that is required for postnatal growth and survival. Zcchc11-knockout mice, deep small RNA sequencing, reporter assays, measurement of IGF-1 mRNA and protein PLoS genetics High 23209448
2014 TUT4 (Zcchc11) and TUT7 (Zcchc6) selectively 3' mono-uridylate a specific subset of mature miRNAs involved in cell differentiation and Hox gene control. A bipartite sequence motif in the miRNA is necessary and sufficient to confer Zcchc6/11-catalyzed uridylation. Loss of uridylation leads to concomitant gain of 3' mono-adenylation on the same miRNAs. In vitro uridylation assay, cell knockdown, small RNA sequencing, zebrafish TUTase inhibition with developmental phenotype readout Nucleic acids research High 25223788
2014 Trim25, an E3 ubiquitin ligase, acts as an RNA-specific cofactor for Lin28a/TUT4-mediated uridylation. Trim25 binds the conserved terminal loop (CTL) of pre-let-7 and activates TUT4, allowing more efficient Lin28a-mediated uridylation; this provides additional substrate specificity beyond Lin28a alone. RNA pulldown coupled with quantitative mass spectrometry, co-immunoprecipitation, in vitro uridylation assay Cell reports Medium 25457611
2015 Small molecule inhibitors of Zcchc11 (TUT4) TUTase activity were identified via a high-throughput biochemical screen. The study established that Zcchc11 TUTase activity is pharmacologically targetable and that uridylated pre-let-7 is targeted for decay by the downstream exonuclease Dis3l2. High-throughput enzymatic screen (~15,000 compounds), biochemical TUTase activity assay RNA biology Medium 26114892
2006 ZCCHC11 (TUT4) interacts with TIFA (TRAF-interacting protein with FHA domain) and functions as a negative regulator of TLR-mediated NF-κB activation. ZCCHC11 is mostly nuclear but translocates to the cytoplasm in response to LPS and binds TIFA. The N-terminal region containing the C2H2-type zinc finger motif is sufficient for NF-κB suppression. GST-TIFA affinity purification, mass spectrometry, siRNA knockdown, overexpression, subcellular localization by fractionation Biochemical and biophysical research communications Medium 16643855
2017 TUT4 and TUT7 utilize two multidomain functional modules during the switch from monoU to oligoU addition: a catalytic module (CM) essential for both activities, and a Lin28-interacting module (LIM) indispensable for oligoU. A crystal structure of TUT7 CM trapped in the monoU state revealed a duplex-RNA-binding pocket that orients group II pre-let-7 hairpins for monoU addition. The switch to oligoU requires the ZK domain of Lin28 to drive stable ternary complex formation, and ZK2 of TUT4(7) aids oligoU addition by engaging the growing oligoU tail through uracil-specific interactions. Crystal structure of TUT7 catalytic module, domain mutants, biochemical reconstitution, in vitro uridylation assays Nature structural & molecular biology High 28671666
2018 TUT4 and TUT7 uridylate LINE-1 mRNA 3' ends to restrict retrotransposition. TUT4 is enriched in cytoplasmic foci and destabilizes LINE-1 mRNAs, while TUT7 adds uridines in the cytoplasm to inhibit initiation of reverse transcription after mRNA reimport to the nucleus. TUT4/7 cooperate with the helicase/RNPase MOV10 to counteract the RNA chaperone activity of L1-ORF1p. TUT4/TUT7 knockdown, retrotransposition reporter assays, subcellular fractionation/localization, co-immunoprecipitation with MOV10 Cell High 30122351
2021 TUT4(7) ZnF2 contains two distinct RNA-binding surfaces used for interactions with different RNA nucleobases in different target miRNAs, encoding diversity in TUT4(7) selectivity. Unlike other CCHC zinc fingers, ZnF2 acts independently of ZnF3. ZnF1 has lost intrinsic RNA-binding capability. NMR with functional validation, RNA-binding assays, mutagenesis of ZnF domains RNA biology Medium 34719327
2022 Kinetic characterization of TUT4 (Zcchc11) revealed a steady-state ordered mechanism where UTP adds before RNA. The enzyme uridylates substrates as small as dinucleotides, preferentially uridylates RNA lacking base-pairing near the 3' terminus, and shows nucleotide selectivity (UTP > CTP > ATP >> GTP) manifested in Km,XTP rather than kcat. In vitro kinetic assays, substrate titrations, nucleoside triphosphate specificity assays Biochemistry High 35797480
2022 TUT4 is the predominant TUTase for uridylating most mature miRNAs, while TUT7 is largely dispensable for bulk miRNA uridylation. Loss of uridylation leads to replacement by adenylated isomiRs. TUT4/7-mediated uridylation also indirectly controls oncogenic signaling via the let-7a/AKT phosphorylation axis. CRISPR knockout of TENT2, TUT4, TUT7 individually and in combination, deep sequencing, Northern blot, in vitro assays Nature communications High 36071058
2023 TUT4 and TUT7 uridylate subgenomic RNAs of the mouse hepatitis virus (MHV coronavirus), particularly transcripts with poly(A) tails shorter than ~22 nucleotides. Depletion of TUT4/7 increases MHV replication capacity, indicating that TUT4/7-mediated uridylation marks viral subgenomic RNAs for decay and delays viral replication. Splint-ligation poly(A) tail length assay, TUT4/7 siRNA knockdown, viral replication measurement Communications biology Medium 37085578
2024 In FOCAD-deleted cancer cells, TUT7 (and the downstream exonuclease DIS3L2) function as a salvage mechanism to degrade aberrant RNA. TUT4 knockout does not impair proliferation in FOCAD-deleted cells, whereas TUT7 or DIS3L2 knockout does. FOCAD deficiency post-transcriptionally disrupts SKI complex stability, creating TUT7 dependency. Selective TUT4/7 small molecule inhibitors substantially reduce uridylation and show antiproliferative activity in vitro and in vivo specifically in FOCAD-deleted cancer. CRISPR knockout, FOCAD re-expression rescue, pharmacological TUT4/7 inhibitors, in vitro and in vivo proliferation assays Molecular cancer therapeutics Medium 39235218
2026 Cryo-EM structure of human TUT4 complexed with Lin28A and oligo-uridylated pre-let-7 at the elongation stage revealed that: (1) the Lin28-interacting module (LIM) anchors pre-let-7 via Lin28A interactions with the terminal stem-loop; (2) the catalytic module (CM) associates with LIM through protein-protein interactions; (3) the duplex stem region of pre-let-7 is surrounded by CM and LIM, with the upper portion unwinding to position the 3' end in the CM catalytic site; (4) during processive oligo-uridylation, the CM finger domain clamps the double-stranded region, further stabilizing the complex. Cryo-EM structure determination, biochemical analysis of TUT4–Lin28A–pre-let-7 ternary complex Nucleic acids research High 41521656
2025 In the ZAP-mediated RNA decay pathway, the 5' cleavage fragment generated by KHNYN endonuclease undergoes TUT4/TUT7-mediated 3' uridylation followed by degradation by DIS3L2. ZAP and TRIM25 interact with TUT7, DIS3L2, and XRN1 in an RNase-resistant manner, and viral infection promotes these interactions to drive viral RNA decay. Co-immunoprecipitation, RNase-resistant interaction assays, viral RNA decay measurement bioRxivpreprint Low

Source papers

Stage 0 corpus · 25 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2009 TUT4 in concert with Lin28 suppresses microRNA biogenesis through pre-microRNA uridylation. Cell 669 19703396
2009 Lin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in mouse embryonic stem cells. Nature structural & molecular biology 423 19713958
2009 Zcchc11-dependent uridylation of microRNA directs cytokine expression. Nature cell biology 248 19701194
2012 Lin28-mediated control of let-7 microRNA expression by alternative TUTases Zcchc11 (TUT4) and Zcchc6 (TUT7). RNA (New York, N.Y.) 176 22898984
2013 miR-26a enhances miRNA biogenesis by targeting Lin28B and Zcchc11 to suppress tumor growth and metastasis. Oncogene 100 24056962
2010 The human cytoplasmic RNA terminal U-transferase ZCCHC11 targets histone mRNAs for degradation. RNA (New York, N.Y.) 86 21051505
2014 Selective microRNA uridylation by Zcchc6 (TUT7) and Zcchc11 (TUT4). Nucleic acids research 85 25223788
2018 Uridylation by TUT4/7 Restricts Retrotransposition of Human LINE-1s. Cell 74 30122351
2014 Trim25 Is an RNA-Specific Activator of Lin28a/TuT4-Mediated Uridylation. Cell reports 71 25457611
2012 Zcchc11 uridylates mature miRNAs to enhance neonatal IGF-1 expression, growth, and survival. PLoS genetics 46 23209448
2017 Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis. Nature structural & molecular biology 45 28671666
2022 TENT2, TUT4, and TUT7 selectively regulate miRNA sequence and abundance. Nature communications 44 36071058
2015 Identification of small molecule inhibitors of Zcchc11 TUTase activity. RNA biology 43 26114892
2006 A novel Zinc finger protein, ZCCHC11, interacts with TIFA and modulates TLR signaling. Biochemical and biophysical research communications 41 16643855
2011 Terminal uridyltransferase enzyme Zcchc11 promotes cell proliferation independent of its uridyltransferase activity. The Journal of biological chemistry 16 22006926
2011 E2F1 and KIAA0191 expression predicts breast cancer patient survival. BMC research notes 14 21453498
2023 TUT4/7-mediated uridylation of a coronavirus subgenomic RNAs delays viral replication. Communications biology 13 37085578
2021 RNA uridyl transferases TUT4/7 differentially regulate miRNA variants depending on the cancer cell type. RNA (New York, N.Y.) 12 34949722
2022 Terminal Uridylyltransferases TUT4/7 Regulate microRNA and mRNA Homeostasis. Cells 8 36497000
2024 Targeting the Synthetic Lethal Relationship between FOCAD and TUT7 Represents a Potential Therapeutic Opportunity for TUT4/7 Small-Molecule Inhibitors in Cancer. Molecular cancer therapeutics 5 39235218
2022 Differentially Expressed mRNAs and Potential Mechanisms of Radiation-Induced TUT4-/- Esophageal Cell Injury. Dose-response : a publication of International Hormesis Society 3 36324561
2022 Kinetic and Mechanistic Studies of the Terminal Uridylyltransferase, Zcchc11 (TUT4). Biochemistry 2 35797480
2021 The distinct RNA-interaction modes of a small ZnF domain underlay TUT4(7) diverse action in miRNA regulation. RNA biology 1 34719327
2026 Mechanistic insights into Lin28-dependent oligo-uridylylation of pre-let-7 by TUT4. Nucleic acids research 0 41521656
2025 Potential protective regulatory effects on radiation-induced esophageal injury in TUT4-/- mice. Frontiers in oncology 0 40933885

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