TOP3B (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

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.

• THE DRUGGABILITY IS THE HAZARD HERE, NOT THE OPPORTUNITY. TOP3B poisons exist (thiacyanine dyes, PMID 40752578), and this project's break-machinery beat is about how topoisomerase II poisons - etoposide and doxorubicin, both in the paediatric backbone - create the KMT2A rearrangements that cause this disease. Proposing a topoisomerase poison for a leukaemia caused by a topoisomerase poison requires an argument this entry does not have and does not attempt.
• TOP3B is required for normal neurodevelopment. In an infant population that is a first-order objection to inhibition, independent of efficacy.
• Nothing here is a target nomination. This project's own DepMap measurement puts TOP3B at -0.1507 across 1,258 screens with a trend toward being LESS essential in KMT2A-rearranged lines, and TOP3B has never been studied in this disease at all.
• The R-loop direction is the wrong way round for a simple therapeutic story: losing TOP3B RAISES R loops and raises transcription-replication conflict. In a disease whose own break model is about conflict at the KMT2A locus, that is a mechanism for causing rearrangements, not for treating them.

1. Does TOP3B loss change R-loop levels at the KMT2A breakpoint cluster region specifically? This graph's break-machinery beat argues that the BCR is a site of transcription-replication conflict, and TOP3B is the enzyme that resolves exactly that - yet the two have never been connected in one experiment.
2. Which effector carries the H4R3me2a-to-R-loop axis, TOP3B or DHX9? gene-tdrd3 presents TOP3B as the mechanism; PMID 34329467 puts DHX9 in the same role. Separating them needs a double-depletion and neither arm exists.
3. ANSWERED the same cycle: NO. `gene-dhx9` does not exist, nor do `gene-top3a` or `gene-top1`. So the other TDRD3 effector is the next instance of exactly the named-unwritten shape that produced this entry, and the topoisomerase family is represented here only by TOP2A, TOP2B and now TOP3B - the three that matter for breaks and for this mechanism, with the type IA partner TOP3A and the type IB TOP1 both absent.
4. How much of cellular TOP3B activity is on RNA rather than DNA? It is the only human topoisomerase doing both, so every knockdown phenotype in a chromatin context is confounded by the mRNA-translation arm, and no experiment here separates them.
5. Does the topoisomerase-TAD literature bear on this graph's CTCF dispute? PMID 35228717 explicitly integrates topoisomerase function with chromatin loops and topologically associating domains, and this graph currently holds two mechanisms that make CTCF do opposite things at the KMT2A locus. That review is uncited here.

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

   TOP3B is UniProt O95985, TOP3B_HUMAN, DNA topoisomerase 3-beta-1, 862 aa, with two annotated domains: Toprim at 3-153 and a Topo IA-type catalytic domain at 171-593. UniProt's FUNCTION states it releases the supercoiling and torsional tension of DNA introduced during DNA replication and transcription by transiently cleaving and rejoining one strand of the duplex, introducing a single-strand break via transesterification in which the scissile phosphodiester is attacked by the catalytic tyrosine, forming a DNA-(5'-phosphotyrosyl)-enzyme intermediate. The record returned NO subcellular location comment.

   UniProtKB entry O95985 (TOP3B_HUMAN), retrieved by gene_exact:TOP3B AND organism_id:9606 AND reviewed:true with fields accession, id, protein_name, gene_names, length, cc_subcellular_location, ft_domain, cc_function, fetched 2026-09-22 (exactly one reviewed result)
   ▸What this evidence cannot show

   Accession, entry name, length and both domain coordinate pairs were read from the JSON response, not from recall, and the query was an exact-gene search returning exactly one reviewed entry rather than a symbol guess. The absence of a subcellular location is an absence in the record given that the same fetch returned FUNCTION and both domains, but cc_subcellular_location was among the requested fields so this is a genuine record gap rather than a query gap. A 862-residue protein with 746 residues inside two annotated domains is unusually well covered by comparison with most entries in this graph.

   ▸Evidence that argues against this (1)

   • A topoisomerase with no subcellular location annotation is a poor foundation for any claim about where it acts, and this project's PI priority is explicitly subcellular and subnuclear localisation. Everything locational in this entry is inferred from where the complex is RECRUITED (a promoter) rather than measured as a compartment, and those are different statements.
2. E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

   TOP3B is the human RNA topoisomerase - the only one of the six human topoisomerases that catalyses topological changes on either DNA or RNA and can induce cleavage complexes on both nucleic acids. It regulates R-loop dynamics and mRNA translation, which are critical for genome stability, neurodevelopment and normal ageing, and it is required for normal neurodevelopment. As a type IA enzyme it acts by general acid-base catalysis to break and rejoin single-stranded DNA, with passage of a second strand through the transient break permitting dissipation of hypernegative supercoiling and catenation or knotting. The human topoisomerase family comprises six enzymes: TOP1 and TOP1MT (type IB), TOP2A and TOP2B (type IIA), TOP3A and TOP3B (type IA).

   Structural and biochemical basis for DNA and RNA catalysis by human Topoisomerase 3beta. · Yang X, et al. · Nature Communications 2022
   PMID 35945419DOI
   ▸What this evidence cannot show

   Abstract-level for both sources; neither full text was read. The six-enzyme family enumeration and the integration of topoisomerase function with chromatin loops and TADs come from a REVIEW (PMID 35228717, Pommier Y et al., 'Human topoisomerases and their roles in genome stability and organization', Nature Reviews Molecular Cell Biology 2022, doi 10.1038/s41580-022-00452-3), which is appropriate for a family census and not for a mechanistic claim. Both PMIDs were uncited in this graph before this entry and both were verified live by efetch on 2026-09-22. The dual DNA/RNA activity is a biochemical property established in vitro; what fraction of cellular TOP3B activity is on RNA in any given cell type is not established here.

   ▸Evidence that argues against this (2)

   • The RNA-topoisomerase property cuts against importing this protein into a chromatin argument too confidently. If a substantial share of TOP3B's cellular work is on RNA and on mRNA translation, then a chromatin-recruitment story built on a histone mark describes one pool of the enzyme, and depleting TOP3B perturbs both pools at once - so any knockdown phenotype in this system is not cleanly attributable to its promoter-associated function.
   • Its requirement for normal neurodevelopment is a direct argument against therapeutic inhibition in children, independent of any efficacy question.
3. E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

   The arginine-mark route to R-loop control has at least two effectors, not one. Beyond delivering TOP3B to the c-MYC promoter via H4R3me2a (PMID 24507716), TDRD3 - which recognises methylarginine marks on histones and on the C-terminal domain of RNA polymerase II - also promotes chromatin recruitment of the helicase DHX9 and R-loop resolution, with R loops particularly enriched at gene promoters where they regulate gene expression.

   TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution. · Yuan W, et al. · Nucleic Acids Research 2021
   PMID 34329467DOI
   ▸What this evidence cannot show

   Abstract-level; full text not read, so the relative contributions of the DHX9 and TOP3B routes, and whether they act at the same loci, are not established. Neither is in a haematopoietic or KMT2A-rearranged context. Verified live by efetch 2026-09-22; this PMID was already cited once in this graph. Note that TDRD3 reading marks on the RNA Pol II CTD as well as on histones means 'recruited by a histone mark' is an incomplete description of how the complex arrives.

   ▸Evidence that argues against this (1)

   • This weakens the entry it grew out of. gene-tdrd3 presents TOP3B delivery as the mechanism by which TDRD3 controls R loops; with DHX9 in the picture, TOP3B is one of two effectors and possibly the minor one. Any claim that the H4R3me2a-to-R-loop axis runs THROUGH TOP3B needs the DHX9 arm excluded, and no experiment here does that.
4. E4moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database

   TOP3B has never been studied in a KMT2A-rearranged context, and this project's own dependency data does not support it as a target. TOP3B[tiab] AND (MLL[tiab] OR KMT2A[tiab]) returns 0 with a parsed querytranslation and warninglist ['No items found.']; TOP3B[tiab] AND leukemia[tiab] returns 1 and that record is a coronavirus paper; TOP3B[tiab] alone returns 71. In DepMap Chronos data across 1,258 screens its mean gene effect is -0.1507 - not a dependency - and the KMT2A-rearranged minus other-leukaemia difference is +0.0841 with permutation p 0.090, a trend toward being LESS essential in the fusion lines.

   NCBI esearch against PubMed with querytranslation and warninglist recorded, plus analyses/arginine-axis-dependency-kmt2a-versus-other-leukaemia/results.json (DepMap Chronos via the Open Targets Platform, 16 Cellosaurus-annotated KMT2A-rearranged lines, 20,000-permutation test), both 2026-09-22
   ▸What this evidence cannot show

   The PubMed zero bounds INDEXED TITLES AND ABSTRACTS ONLY and was not re-run a second time, which this project's own rule requires for a load-bearing zero - so it is moderate rather than strong. TOP3B could appear in a proteomic or screen supplement of a KMT2A paper. The DepMap contrast comes with no stated release (rule 83), the KMT2A-rearranged group is 16 myeloid-dominated lines with no infant-derived AFF1 line, and a CRISPR knockout cannot see an enzyme whose loss is buffered by TOP3A or by the DHX9 route. The +0.0841 trend is nominal and uncorrected.

   ▸Evidence that argues against this (1)

   • The null is weaker than it looks because the readout is proliferation. TOP3B loss raises R loops, and increased transcription-replication conflict is a mutagenic and genome-destabilising phenotype rather than necessarily an antiproliferative one - so a gene whose loss makes cells MORE genomically unstable can score as non-essential while mattering a great deal to this disease's biology.

• part of →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

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

• depends on →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

  recruited to the c-MYC promoter PRIMARILY by H4R3me2a -- an enzyme whose recruitment is mark-dependent while its catalysis is on nucleic acid

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

  the TDRD3-TOP3B complex promotes c-MYC expression and suppresses R loops at that promoter

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

  TOP3B is the enzyme that resolves the transcription-replication conflict that experiment proposes to measure, and the two have never been connected

• analogous to →TOP2B - the isoform most etoposide-induced KMT2A breaks depend on, resolved genetically and not resolvable pharmacologically

  both are human topoisomerases and the contrast is the point: TOP2 poisons in the backbone CREATE the KMT2A breaks, and TOP3B poisons now exist

• ← co-occurs withDHX9 / RNA helicase A (Q08211) - the other TDRD3 effector, and it is itself the 3' partner of a leukaemia fusion

  the two TDRD3 effectors, delivered by one reader to do redundant anti-R-loop work: TOP3B relaxes supercoiling to prevent R loops, DHX9 unwinds to resolve them; no experiment separates them