TDRD3 (Q9H7E2) - the reader the new H4R3me2a entry could not name, and it brings TOP3B to the MYC promoter and keeps R loops off it

No three-dimensional model is available for this protein, so the map above is the whole picture. That is itself informative: AlphaFold does not model chains this long, and the parts that have been crystallised are held under the entries for the individual domains.

• Nothing here supports an intervention. TDRD3 has never been studied in a KMT2A-rearranged cell, every functional claim comes from non-haematopoietic systems, and the entry's own reading is that the direction of benefit is unclear.
• The specific hazard worth stating: TDRD3 loss INCREASES R loops. In a disease whose own break-machinery beat asks how the KMT2A locus comes to rearrange, deliberately raising transcription-replication conflict in a child is a mutagenic proposition, not a clean vulnerability.
• The PRMT1 consequence should be quoted with both signs or not at all. If H4R3me2a recruits TOP3B to the MYC promoter, PRMT1 inhibition would be predicted to lower MYC and raise R loops there simultaneously. This graph treats PRMT1 as attractive; that attractiveness was established without this consideration.
• Do not call TDRD3 'the' reader of H4R3me2a. A tandem PHD inside KMT2D reads the same residue, so there are at least two.

1. TOP3B has no entry and zero mentions in a graph with 237 R-loop mentions. It is the enzyme that does the work in this mechanism and the obvious next entry.
2. Is TDRD3 or TOP3B a dependency in KMT2A-rearranged lines? Neither has been checked against DepMap here, and that is a cheap query against data this project already uses.
3. Does PRMT1 inhibition lower MYC and raise R loops at the same promoter? The two predictions come from the same mark and have opposite clinical signs, and no published experiment tests them together. This graph already treats PRMT1 as an attractive target.
4. H4R3me2a now has at least two structurally unrelated readers - TDRD3's Tudor domain and the tandem PHD(4-6) inside KMT2D. Which dominates at a given locus, and does the fusion change the balance? KMT2A's own PHD1-3 cassette is lost from every 5' fusion and has never been tested for H4R3 binding.
5. Is the nuclear TDRD3 pool separable from the cytoplasmic majority? A reader whose bulk is cytoplasmic needs a compartment-resolved measurement before any dependency claim, and none exists.
6. CARM1 is named 13 times here and has no entry, while it is the writer of the second mark TDRD3 reads.

1. E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database

   TDRD3 is UniProt Q9H7E2, TDRD3_HUMAN, Tudor domain-containing protein 3, 651 aa. Subcellular location is annotated as Cytoplasm and Nucleus. It has exactly two annotated domains: a UBA domain at 193-233 and a Tudor domain at 555-615.

   UniProtKB entry Q9H7E2 (TDRD3_HUMAN), fields accession, protein_name, gene_names, length, cc_subcellular_location, ft_domain, fetched 2026-09-22
   ▸What this evidence cannot show

   Accession, entry name, length and both domain coordinate pairs were read from the JSON response, not from recall. The fetch requested only those fields, so absence of any other domain or motif here is an absence in the QUERY. UniProt lists Cytoplasm and Nucleus without ranking them, and PMID 28101374 states the majority of cellular TDRD3 is cytoplasmic - so the nuclear pool that does the chromatin reading is a minority fraction, which the record does not convey.

   ▸Evidence that argues against this (1)

   • A two-domain protein of 651 aa is mostly unannotated: the record assigns function to 101 residues out of 651. Nothing here says what the other 550 do, and the coactivator literature attributes the activity to the Tudor domain by mutation rather than by mapping the whole protein.
2. E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

   TDRD3 is a reader of asymmetric dimethyl-arginine histone marks. CARM1 and PRMT1 are transcriptional coactivators that deposit H3R17me2a and H4R3me2a respectively, and a protein-domain microarray approach identified the Tudor domain-containing protein TDRD3 as a reader of these marks. TDRD3 is itself a transcriptional coactivator, and that coactivator activity requires an intact Tudor domain. It is recruited to an estrogen-responsive element.

   TDRD3 is an effector molecule for arginine-methylated histone marks. · Yang Y, Lu Y, Espejo A, Wu J, Xu W, Liang S, Bedford MT · Molecular Cell 2011
   PMID 21172665DOI
   ▸What this evidence cannot show

   Abstract-level; the full text was not read, so the binding affinities, the specificity against other methyl-arginine states, and whether H4R3me2s or H4R3me0 compete were not established here. A protein-domain microarray is an in-vitro binding screen: it establishes that the Tudor domain can read the mark, not that this is the dominant reader in any cell. The estrogen-responsive-element system is not haematopoietic. Title, journal, year, DOI and first author verified live by efetch 2026-09-22.

   ▸Evidence that argues against this (2)

   • Being A reader is not being THE reader. This project has repeatedly found that the first-described binder of a mark is one of several, and nothing in this abstract excludes other Tudor- or PHD-domain proteins reading H4R3me2a - indeed mark-h4r3me2a's own companion finding is that a tandem PHD inside KMT2D reads the same residue's unmethylated and me2a states (PMID 23249737). So H4R3me2a has at least two structurally unrelated readers, and calling TDRD3 'the' reader would be wrong.
   • The majority of cellular TDRD3 is cytoplasmic (PMID 28101374, Narayanan et al., Cell Discovery), where it interacts with USP9X and has anti-apoptotic activity in breast-cancer cells. A reader whose bulk sits outside the nucleus is a weaker candidate for a rate-setting chromatin function than the 2011 paper alone implies.
3. E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

   TDRD3 delivers topoisomerase III beta to methylated chromatin and thereby suppresses R loops at a gene this project cares about. TOP3B was identified as a component of the TDRD3 complex; TDRD3 serves as a molecular bridge between TOP3B and arginine-methylated histones; the TDRD3-TOP3B complex is recruited to the c-MYC gene promoter PRIMARILY BY THE H4R3me2a MARK and promotes c-MYC gene expression; TOP3B relaxes negative supercoiled DNA and reduces transcription-generated R loops in vitro; and TDRD3 knockdown in cells increases R-loop formation.

   Arginine methylation facilitates the recruitment of TOP3B to chromatin to prevent R loop accumulation. · Yang Y, McBride KM, Hensley S, Lu Y, Chedin F, Bedford MT · Molecular Cell 2014
   PMID 24507716DOI
   ▸What this evidence cannot show

   Abstract-level; the full text, the cell systems and the magnitude of the R-loop change were not read. 'Primarily by the H4R3me2a mark' is the authors' phrasing and the abstract does not give the residual contribution of H3R17me2a or of mark-independent recruitment. The R-loop reduction by TOP3B is shown IN VITRO in the abstract, with the cellular claim resting on a knockdown. None of this is in a haematopoietic cell or a KMT2A-rearranged context, and MYC regulation in one system does not transfer to a fusion-driven leukaemia.

   ▸Evidence that argues against this (2)

   • This makes TDRD3 look like a coherent therapeutic thought and it should not be read that way yet. The direction is awkward: TDRD3 loss INCREASES R loops, so removing this reader adds replication-transcription conflict rather than relieving it - which in a fusion-driven leukaemia could be either a vulnerability or a mutagenic hazard, and this graph's own break-machinery beat is about how KMT2A comes to rearrange in the first place. An intervention that raises R loops at MYC in a paediatric leukaemia is not obviously a good idea.
   • The MYC link cuts against a simple arginine-axis story too. If H4R3me2a is the mark that brings TOP3B to the MYC promoter and PRMT1 writes it, then PRMT1 inhibition - which this graph treats as an attractive option because PRMT1 is a near-pan MLL-fusion cofactor - would be predicted to LOWER MYC and simultaneously RAISE R loops there. Those two consequences have opposite signs for a patient, and no published experiment tests them together.
4. E4moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database

   TDRD3 has never been studied in a KMT2A-rearranged context. TDRD3[tiab] AND (MLL[tiab] OR KMT2A[tiab]) returns 0 with a parsed querytranslation and warninglist ['No items found.']; TDRD3[tiab] AND leukemia[tiab] returns 2, neither concerning KMT2A-rearranged disease; TDRD3[tiab] alone returns 51. Before this entry TDRD3 was named in exactly one file in this corpus - mark-h4r3me2a, written hours earlier in the same cycle - and TOP3B is named zero times across 2,016 entries.

   NCBI esearch against PubMed, 2026-09-22, with querytranslation and warninglist recorded for each zero; corpus counts by direct grep over data/graph/nodes.
   ▸What this evidence cannot show

   A parsed zero bounds INDEXED TITLES AND ABSTRACTS ONLY, and this project has been burned by exactly this shape: a genuinely reported fact living in a supplementary table returns a clean zero. TDRD3 could well appear in a proteomic or screen table in a KMT2A paper. The zero was not re-run a second time, which this project's own rule requires for a load-bearing zero, so it is reported at moderate rather than strong confidence.

   ▸Evidence that argues against this (1)

   • The query itself nearly produced a false absence in the other direction, which is the more instructive failure. TDRD3[tiab] AND H4R3[tiab] returns 0, while the compact spellings return the three papers that establish the entire reader relationship. Had the residue form been trusted, this entry would have concluded TDRD3 has no H4R3 literature at all.

• binds →H4R3me2a - the activating arginine mark that a KMT2-family enzyme's OWN tandem PHD module reads, where the Kabuki-syndrome mutations sit, and which no KMT2A-fusion study has ever measured

  reads H4R3me2a through its Tudor domain; identified by protein-domain microarray, coactivator activity requires an intact Tudor domain (PMID 21172665)

• depends on →PRMT1 — an MLL-fusion cofactor whose first-in-human inhibitor was terminated for lack of efficacy and toxicity

  PRMT1 writes the mark TDRD3 reads, so the reader depends on the writer this graph already treats as a near-pan MLL-fusion cofactor

• regulates →MYC - named in a hundred entries of this graph and, until now, written in none

  the TDRD3-TOP3B complex is recruited to the c-MYC promoter PRIMARILY by H4R3me2a and promotes MYC expression (PMID 24507716)

• related to →Measure replication stress directly in KMT2A-rearranged cells instead of inferring it from a dependency ranking

  TDRD3 knockdown increases R-loop formation, and that experiment records the transcription-replication-conflict hypothesis as never tested in this disease

• related to →H3R2me2a - the asymmetric arginine mark two residues from H3K4 that LOCKS the WRAD module off the histone tail, and the first arginine mark node in this graph

  sibling arginine mark written by PRMT6; TDRD3 reads the H4R3 and H3R17 asymmetric marks rather than H3R2, so the reader layers of the two residues are distinct

• ← refutesFive new arginine-axis entries in one day, and not one of their genes is a selective dependency - in an instrument that recovers MEN1 at p=5e-05 and TDRD3 is not a dependency at all

  TDRD3 is not a dependency in any line (+0.0671 over 1,258 screens) -- answers that entry own open question against it

• ← part ofTOP3B (O95985) - the only human topoisomerase that works on RNA as well as DNA, delivered to the MYC promoter by an arginine mark, and it has poisons

  TOP3B is a component of the TDRD3 complex; TDRD3 bridges it to arginine-methylated histones (PMID 24507716)

• ← analogous toCARM1 / PRMT4 (Q86X55) - the H3R17me2a writer, and the enzyme whose product is read by the KMT2A C-terminus that every fusion deletes

  two halves of the arginine layer that this graph had only half-written: TDRD3 is a methylarginine READER delivering effectors, and CARM1 is a WRITER whose product has a reader in KMT2A's own deleted C-terminus

• recruits →DHX9 / RNA helicase A (Q08211) - the other TDRD3 effector, and it is itself the 3' partner of a leukaemia fusion

  TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution (PMID 34329467) - the SECOND effector, alongside TOP3B; gene-tdrd3 presents TOP3B as the mechanism and does not mention this one