| 2010 |
TDRD3 Tudor domain functions as a 'reader' of asymmetric dimethylarginine (aDMA) marks on histones (H3R17me2a deposited by CARM1 and H4R3me2a deposited by PRMT1), identified by protein domain microarray. TDRD3 itself acts as a transcriptional coactivator, and this coactivator activity requires an intact Tudor domain. TDRD3 is recruited to an estrogen-responsive element in a CARM1-dependent manner, and ChIP-seq shows it localizes predominantly to transcriptional start sites. |
Protein domain microarray, co-immunoprecipitation, ChIP-seq, Tudor domain mutagenesis, estrogen-responsive element reporter assay |
Molecular cell |
High |
21172665
|
| 2008 |
TDRD3 co-sediments with FMRP on actively translating polyribosomes and accumulates in cytoplasmic stress granules (SGs) in response to cellular stress. The Tudor domain is both required and sufficient for SG recruitment, and the methyl-binding surface of the Tudor domain is important for this process. Pull-down experiments identified five novel TDRD3-interacting partners, including SERPINE1 mRNA-binding protein 1 and DDX3 (DEAD/H box-3), which are also novel SG constituents. |
Polyribosome sedimentation, immunofluorescence, stress induction assays, Tudor domain deletion/mutation analysis, GST pull-down |
Human molecular genetics |
High |
18632687
|
| 2008 |
TDRD3 harbors an OB-fold domain and a ubiquitin-associated (UBA) domain capable of binding tetra-ubiquitin. TDRD3 directly interacts with FMRP and its autosomal homologs FXR1 and FXR2 via biochemical experiments. Overexpression of TDRD3 in cells induces SG formation and co-localization with endogenous FMRP. The disease-associated FMRP missense mutation I304N severely impairs interaction with TDRD3. |
Biochemical pull-down/co-immunoprecipitation, domain characterization, overexpression/immunofluorescence, UBA-tetra-ubiquitin binding assay |
Human molecular genetics |
Medium |
18664458
|
| 2012 |
Crystal structures of the TDRD3 Tudor domain in complex with small molecules reveal that TDRD3 preferentially recognizes asymmetric dimethylarginine (aDMA) marks, in contrast to SMN which preferentially binds symmetric dimethylarginine. Quantitative binding characterization established distinct specificity profiles: TDRD3 selectively binds aDMA; SMN is promiscuous and prefers sDMA; SPF30 is the weakest binder, recognizing only GAR motif sequences. |
Crystal structure determination, quantitative binding assays (fluorescence polarization, ITC), peptide library screening |
PloS one |
High |
22363433
|
| 2012 |
NMR solution structure of the TDRD3 Tudor domain bound to asymmetrically dimethylated RNA Polymerase II CTD reveals that a unique aromatic cavity with tyrosine at position 566 acts as a selectivity filter for aDMA recognition, distinguishing it from other Tudor domain-containing proteins that bind symmetric dimethylarginine. Mutational analysis confirmed key residues required for aDMA selectivity. |
NMR structure determination, mutagenesis, binding assays |
Nucleic acids research |
High |
23066109
|
| 2017 |
USP9X is identified as a TDRD3-interacting protein; the interaction is mediated through the Tudor domain of TDRD3 and arginine methylation of USP9X. USP9X stabilizes TDRD3 protein by preventing its ubiquitination (knockdown of USP9X increases TDRD3 ubiquitination). TDRD3 is essential for USP9X localization to stress granules. TDRD3 also regulates MCL1 (a USP9X deubiquitination target), suggesting TDRD3 modulates USP9X deubiquitinase activity. |
GST pull-down, co-immunoprecipitation, USP9X knockdown with ubiquitination assay, immunofluorescence in Tdrd3-null MEFs |
Cell discovery |
Medium |
28101374
|
| 2017 |
Crystal structures of TOP3B catalytic domain, TDRD3 DUF1767-OB-fold domains, and their complex reveal that the OB-fold domain of TDRD3 binds the toroidal-shaped catalytic domain of TOP3B. The TDRD3 OB-fold insertion loop and core region both contribute to the interaction; hydrophobic core surface and insertion loop termini are essential. Key structural elements Arg96, Val109, Phe139, and the short insertion loop of TDRD3 confer specificity for TOP3β over the non-cognate TOP3α. |
Crystal structure determination (3.44 Å complex, 1.62 Å TDRD3 domain, 3.6 Å complex), pull-down binding assays with mutagenesis |
Scientific reports |
High |
28176834
|
| 2021 |
TDRD3 directly interacts with the DExH-box helicase DHX9 via its Tudor domain, recruiting DHX9 to target gene promoters. DHX9 resolves R-loops at promoters in a helicase-activity-dependent manner. Additionally, TDRD3 stimulates DHX9 helicase activity via its OB-fold domain, which likely binds single-stranded DNA in R-loop structures. Together DHX9 and TOP3B suppress promoter-associated R-loops downstream of TDRD3 recruitment. |
Co-immunoprecipitation, ChIP, R-loop detection assays (DRIP), helicase activity assays, domain deletion analysis, DHX9 helicase-dead mutant |
Nucleic acids research |
High |
34329467
|
| 2022 |
TDRD3 localizes to stress granules partly based on the methylation status of G3BP1. TDRD3 overexpression forms granules containing translation components independently of G3BP. TDRD3 is cleaved by enteroviral 2A proteinase. TDRD3 knockdown alters transcriptional regulation of numerous IFN effectors (including recruitment of IRF3, IRF7, TBK1, STING to SGs), establishing TDRD3 as an antiviral restriction factor. |
Immunofluorescence, knockdown/knockout experiments, viral infection assays, transcriptional analysis, co-localization studies |
PLoS pathogens |
Medium |
35085371
|
| 2023 |
TDRD3 stabilizes TOP3B by recruiting the deubiquitinase USP9X to form a TDRD3-USP9X complex; inactivation of USP9X destabilizes TOP3B. MIB1 E3 ligase independently mediates TOP3B ubiquitylation and proteasomal degradation by directly interacting with TOP3B independently of TDRD3. The TDRD3-USP9X complex works downstream of MIB1. Loss of TDRD3 increases TOP3B cleavage complexes (TOP3Bccs) in DNA and RNA, induces R-loops, γH2AX, and growth defects. TDRD3 biochemically increases the turnover rate of TOP3B. |
Co-immunoprecipitation, ubiquitylation assays, TOP3Bcc measurement, γH2AX assays, knockdown/double-knockdown epistasis, DRIP-seq for R-loops, growth assays |
Nature communications |
High |
37980342
|
| 2024 |
In Tdrd3-null mice, the TOP3B-TDRD3 complex is essential for normal brain function; loss of TDRD3 causes defects in cognitive behaviors, synaptic plasticity, adult neurogenesis, and neuronal activity-dependent transcription. Multiple neurodevelopmentally critical genes show reduced levels in mature but not nascent transcripts in Tdrd3-null mice, indicating a post-transcriptional (not transcriptional) regulatory role of the complex. |
Tdrd3-null mouse generation, behavioral assays, electrophysiology (synaptic plasticity), neurogenesis assays, RNA-seq comparing nascent vs. mature transcripts |
Progress in neurobiology |
Medium |
38216113
|
| 2024 |
PRMT1 methylates stress granule constituent RNA-binding proteins on their RGG motifs, and TDRD3 as an aDMA reader enhances RNA binding to recruit additional RNAs and RBPs, thereby lowering the percolation threshold and promoting stress granule assembly. |
Methylation assays, stress granule formation assays, RNA-binding assays, deletion/mutation analysis |
International journal of biological macromolecules |
Medium |
39097054
|
| 2024 |
TDRD3 contains UBA and LC3-interacting region (LIR) motifs similar to selective autophagy receptor p62/SQSTM1. KO of TDRD3 reduces starvation-induced autophagy; reintroduction restores it dose-dependently. TDRD3 levels decrease during autophagy (consistent with receptor turnover). The LIR3 motif of TDRD3 mediates interaction with LC3B (shown by Co-IP and colocalization). TDRD3 LIR motifs also regulate SG condensation, SG decay rate upon stress release, and SG formation kinetics. |
TDRD3 KO/rescue experiments, autophagy flux assays, co-immunoprecipitation (LIR3-LC3B), immunofluorescence/super-resolution microscopy, deletion mutant analysis |
bioRxivpreprint |
Low |
39345463
|
| 2018 |
NMR fragment screening identified 14 small molecule hits against the TDRD3 Tudor domain aromatic cage. Crystal structure of the TDRD3 Tudor domain with hit 1 reveals it protrudes into the aromatic cage, inducing a distinct binding mode with aromatic residues tilting to accommodate π-π stacking and N596 side chain rotating 3.1 Å to form a hydrogen bond. This structural plasticity distinguishes TDRD3 from SMN, 53BP1, and SND1 Tudor domains. |
NMR fragment-based screening, competitive fluorescence polarization, ITC, crystal structure determination (PDB: 5YJ8) |
The FEBS journal |
High |
29645362
|
| 2026 |
In Treg-specific Tdrd3-knockout mice, TDRD3 is required for iTreg (but not thymic Treg) differentiation. Mechanistically, TDRD3 is recruited by transcription factor FOXO1 (presumably in a methylation-dependent manner) to activate Klf2 expression, which is essential for Treg differentiation. Enforced Klf2 expression in Tdrd3-deficient CD4+ T cells rescues both iTreg development and suppressive function. |
Treg-specific conditional Tdrd3 knockout mouse, adoptive transfer colitis model, Klf2 rescue by enforced expression, ChIP/transcriptional analysis |
Science advances |
Medium |
41576154
|