NHLH1 / HEN1 / NSCL1 - a TAL1-family bHLH factor found by cross-hybridising with the T-ALL oncogene, whose knockout mouse is normal and whose only imaging call puts it in the GOLGI

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.

• NHLH1's knockout mouse is normal. A target whose complete loss produces no phenotype in its own tissue is the definition of a target that cannot be drugged to effect, and nothing in this entry should be read as proposing otherwise.
• If the Golgi call is right, then a BioID row placing NHLH1 near a chromatin protein is an artefact of over-expression - and the same objection applies to every one of the eleven TF baits in this deposition, most of which have better localisation evidence than NHLH1 but none of which was measured in a leukaemic cell.

1. Where is NHLH1 actually? A sequence rule says nucleus and one weak antibody says Golgi. For a protein whose only claim on this project is a nuclear proximity row, that is the question that decides whether the row can mean anything, and it is one immunofluorescence away from an answer.
2. Is NHLH1 expressed in haematopoietic cells at all? It is a neuronal factor by every functional account, HPA records cell-line RNA only as cancer-enhanced in lung cancer, and the knockout is neurologically silent. If NHLH1 is not expressed in blood, this entry describes an over-expression artefact and should be reclassified as a declined interface.
3. Does the SCL/TAL-1 family connection run any deeper than sequence? Three of five family members are T-ALL genes and NHLH1 is not one of them. Whether NHLH1 can heterodimerise with the E-proteins that TAL1 and LYL1 use, and whether it competes with them, is a biochemistry question from the 1990s that appears never to have been asked.
4. HEN1 is a contaminated search token shared with an Arabidopsis methyltransferase and is absent from this project's symbol-collision registry. How many other previous symbols in the interactome tail are contaminated and unregistered? A sweep of previous symbols against the registry would answer it in one pass.

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

   Göös et al. identified 6,703 BioID and 1,536 AP-MS protein-protein interactions for 109 human transcription factors in HEK293 Flp-In cells; in the resulting IntAct deposition IM-28767, NHLH1 is one of eleven transcription-factor baits whose BioID neighbourhood contained KMT2A.

   Human transcription factor protein interaction networks. · Göös H, Kinnunen M, Salokas K, Tan Z, Liu X, Yadav L, Zhang Q, Wei GH, Varjosalo M · Nat Commun 2022
   PMID 35140242DOI
   ▸What this evidence cannot show

   Abstract read; full text and supplementary tables not read. All baits are over-expressed tagged constructs in embryonic kidney cells, and NHLH1 is a neuronal factor, so this construct is markedly ectopic.

   ▸Evidence that argues against this (1)

   • Eleven of 102 transcription factors recovering the same protein, in an ordering that is nearly monotonic in how much each bait labelled, is the signature of a non-specific prey rather than of eleven relationships. source 2026
2. E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database

   IntAct serves the NHLH1-KMT2A record as PSI-MI MI:1314 proximity-dependent biotin identification, MI:1060 spoke expansion, NHLH1 experimental role MI:0496 bait and KMT2A MI:0498 prey, MI-score 0.27, host taxid:9606 Homo sapiens HEK293flp-in embryonic kidney cell, IMEx IM-28767, publication PMID 35140242.

   IntAct molecular interaction database (EMBL-EBI), PSICQUIC MITAB 2.7, pubid:35140242, retrieved 2026-09-23 2026
   ▸What this evidence cannot show

   Retrieved live 2026-09-23; 8,331 rows fetched against an endpoint-declared count of 8,331. Rule 93: PSICQUIC is a floor relative to IntAct REST. Spoke expansion means the binary pair was never measured.

   ▸Evidence that argues against this (1)

   • MI-score 0.27 is the deposition-wide value on every row in this arm and carries no pair-specific information. source 2026
3. E3moderate confidence 3 of 5: One strong study, or several smaller consistent ones.dataset

   In IM-28767's BioID arm NHLH1 recovered 71 of 946 human preys, ranking 45th of 102 baits by reach against a panel median of 58.5; under a null holding both margins NHLH1 recovering KMT2A has p = 0.128, the third lowest of the eleven KMT2A-TF pairs, which is NOT RESOLVED under the pre-registered thresholds.

   analyses/interactome-tail-size-and-abundance-adjudication/ - orientation.py, pair_null.py, adjudication.json (this repository), pre-registered in PREREGISTRATION.md 2026
   ▸What this evidence cannot show

   20,000 draws, seed 20260923. Bonferroni over the 62 pairs tested is 0.0008 and nothing survives it. The ordering of the eleven KMT2A-TF pairs is nearly monotonic in bait width, so NHLH1's third place is largely a fact about how much the NHLH1 construct labelled.

   ▸Evidence that argues against this (1)

   • A small protein expressed ectopically in a kidney cell will have a labelling behaviour set by its construct and its stability, not by its biology. NHLH1 is 133 residues, the smallest of the eleven baits, and small-protein BioID constructs are dominated by the BirA moiety. source 2026
4. E4moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database

   UniProt Q02575 is 133 aa with a bHLH domain at residues 75-127 and a disordered region at 1-79, and assigns subcellular location Nucleus with evidence code ECO:0000255 from PROSITE rule PRU00981 - a sequence-based inference from the bHLH domain, not an experimental observation.

   UniProtKB Q02575 (HEN1_HUMAN / NHLH1) 2026
   ▸What this evidence cannot show

   Fetched live 2026-09-23. ECO:0000255 is 'match to sequence model evidence' - the nucleus call is generated by a rule that fires on the bHLH domain, so it cannot be independent evidence that a bHLH protein is nuclear. This graph distinguishes ECO:0000269 (experimental) from ECO:0000305 (curator inference); ECO:0000255 is weaker than either.

   ▸Evidence that argues against this (1)

   • The Human Protein Atlas's only immunofluorescence call for NHLH1 is GOLGI APPARATUS, main and only. A sequence rule and an imaging experiment disagree, and the imaging experiment is the only measurement of the two. source 2026
5. E5established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper

   The HEN1 gene was identified on the basis of cross-hybridisation with TAL1, a known bHLH gene implicated in T-cell acute lymphoblastic leukaemia; in-situ fluorescence hybridisation localised human HEN1 to chromosome band 1q22; HEN1 and HEN2 are co-expressed in the IMR-32 human neuroblastoma cell line and encode highly related proteins of 133 and 135 residues sharing 98% amino acid identity in their bHLH domains.

   HEN1 and HEN2: a subgroup of basic helix-loop-helix genes that are coexpressed in a human neuroblastoma. · Brown L, Espinosa R, Le Beau MM, Siciliano MJ, Baer R · Proc Natl Acad Sci U S A 1992
   PMID 1528853DOI
   ▸What this evidence cannot show

   Abstract read; full text not read. The cytogenetic band reported here is 1q22 by in-situ hybridisation; HGNC currently places NHLH1 at 1q23.2, and that discrepancy is a resolution difference between 1992 FISH and current assembly coordinates, not a conflict about identity. Being FOUND by cross-hybridisation with an oncogene is a statement about sequence similarity and nothing more.

   ▸Evidence that argues against this (1)

   • The paper's own conclusion is developmental and neural: the HEN1/HEN2 subgroup 'may serve important regulatory functions in the developing nervous system'. Nothing in it proposes a haematopoietic or oncogenic role for HEN1 itself. source 1992
6. E6established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper

   SCL/TAL-1 encodes a bHLH transcription factor essential for the development of all haemopoietic lineages and acting as a T-cell oncogene; four related mammalian genes have been described - LYL-1, TAL-2, NSCL1 and NSCL2 - all with a high degree of bHLH sequence similarity to SCL/TAL-1, and two of them, LYL-1 and TAL-2, have also been implicated in the pathogenesis of T-cell acute lymphoblastic leukaemia.

   The pufferfish SLP-1 gene, a new member of the SCL/TAL-1 family of transcription factors. · Göttgens B, Gilbert JG, Barton LM, Aparicio S, Hawker K, Mistry S, Vaudin M, King A, Bentley D, Elgar G, Green AR · Genomics 1998
   PMID 9503016DOI
   ▸What this evidence cannot show

   Abstract read; full text not read. This is a 1998 comparative-genomics paper whose subject is a pufferfish gene; the family statement is background in its introduction. It is cited for the family membership and for the explicit fact that NSCL1 is one of the members NOT implicated in T-ALL.

   ▸Evidence that argues against this (1)

   • The sentence that matters cuts against NHLH1: of the five family members, the two named as T-ALL genes are LYL-1 and TAL-2, and NSCL1 is not among them. Family membership is the reason to notice NHLH1 and also the reason not to over-read it. source 1998
7. E7strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

   NSCL-1 was disrupted by homologous recombination with the coding region replaced by a beta-galactosidase reporter; NSCL-1 mutant mice are viable and fertile on various genetic backgrounds and show no obvious signs of neurological malfunction, with no differences in mutant or heterozygous neuronal cell distribution in diencephalon, hippocampus, neocortex or cerebellum at any developmental stage, normal cortical lamination, unaltered NeuroD and SCG-10 expression in developing cranial ganglia, and - unlike Math1 or NeuroD2 nulls - no cerebellar developmental defect; NSCL-1/NSCL-2 double mutants show no additional malformation of the central nervous system despite largely overlapping expression, which the authors state argues against simple functional redundancy within the NSCL gene family.

   The neuronal basic helix-loop-helix transcription factor NSCL-1 is dispensable for normal neuronal development. · Krüger M, Braun T · Mol Cell Biol 2002
   PMID 11784856DOI
   ▸What this evidence cannot show

   Abstract read; full text not read. The analysis is neural; the abstract does not report a haematopoietic examination, so 'dispensable' is established for neuronal development and NOT tested in blood. A silent knockout can still mask a conditional or stress-dependent requirement, which the authors themselves gesture at by testing the double mutant.

   ▸Evidence that argues against this (1)

   • A knockout with no phenotype in its own expression domain does not exclude a role elsewhere, and this graph's own ELF1 entry records a factor whose requirement appears only under acute stimulation. Absence of a baseline phenotype is weak evidence of dispensability, but it is the only functional evidence NHLH1 has. source 2002
8. E8weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.database

   The Human Protein Atlas assigns NHLH1 a main subcellular location of Golgi apparatus with no additional location, reliability 'Approved', classes it as a transcription factor with molecular function developmental protein and DNA-binding, and records its cell-line RNA as cancer enhanced with 3.8 nTPM in lung cancer lines.

   Human Protein Atlas v25.1, proteinatlas.json.gz record for NHLH1 (ENSG00000171786), retrieved 2026-09-23 2026
   ▸What this evidence cannot show

   'Approved' is HPA's lowest reliability tier above unreliable - a single antibody with partial supporting evidence. A Golgi call for a bHLH transcription factor is biologically surprising and is at least as likely to be antibody cross-reactivity as a real pool. It is recorded because it is the ONLY experimental localisation NHLH1 has, and because the alternative on offer is a sequence rule.

   ▸Evidence that argues against this (1)

   • A surprising localisation at the weakest reliability tier is exactly the kind of database row this project has been burned by, and the correct response is neither to believe it nor to discard it but to record that NHLH1 has no trustworthy localisation at all. source 2026
9. E9established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database

   PubMed returns zero records for (NHLH1 OR NSCL1 OR HEN1) AND KMT2A in titles and abstracts and zero for the same three names against MLL; (NHLH1 OR NSCL1) AND (leukemia OR leukaemia) returns 3 records, all of which are family or paralogue papers rather than results about NHLH1 in a leukaemia; the whole NHLH1 literature is 42 records.

   NCBI PubMed esearch via scripts/pubmed_safe.py, run 2026-09-23; querytranslation recorded: ("NHLH1"[Title/Abstract] OR "NSCL1"[Title/Abstract] OR "HEN1"[Title/Abstract]) AND "MLL"[Title/Abstract] 2026
   ▸What this evidence cannot show

   Both zeros carry a non-empty querytranslation and a warninglist reading 'No items found.'. NAME LIST TRIED: NHLH1, NSCL1, HEN1. NOT TRIED: NSCL, bHLHa35, NSCL-1 (hyphenated - a different string from NSCL1, and the form the knockout paper uses in its own title). HEN1 IS A CONTAMINATED TOKEN - it is also the Arabidopsis small-RNA methyltransferase HUA ENHANCER 1 - which makes the query broader and the zero stronger, not weaker. Bounded by titles and abstracts only.

   ▸Evidence that argues against this (1)

   • The hyphenated form NSCL-1 was not queried and is the spelling used in the title of the knockout paper this entry cites. Rule 72: singular, plural and punctuation variants are different strings, and a name list that misses the form the primary literature actually uses is the classic way a false zero is produced. The zero should be read as bounded by three of at least five spellings. source 2026

• related to →KMT2A / MLL1 — the gene that breaks

  NHLH1 bait / KMT2A prey, one MI:1314 BioID spoke row, IM-28767; p = 0.128, NOT RESOLVED, and NHLH1 has no trustworthy localisation

• related to →LMO2 (rhombotin-2) - a bridging LIM-only protein, higher in pro-B and MLL-rearranged B-ALL, anti-selective in KMT2A-rearranged lines, and a physical partner of the KDM5A module that NUP98::KDM5A retains

  NHLH1 is a member of the SCL/TAL-1 bHLH family whose leukaemogenic members work through the TAL1-LMO2 complex; NHLH1 itself is NOT implicated in T-ALL

• part of →A 109-transcription-factor BioID network puts KMT2A next to MYC, YY1 and the ETS and KLF families - and AF10 next to ERG and KLF5

  one of the eleven TF baits recovering KMT2A in IM-28767

• supports →Prey recovery in the two BioID depositions tracks SIZE and not abundance - and the interactome tail was being scored on the wrong side of the pair, because every one of the 22 partners is the BAIT and every core protein is the PREY

  third of the eleven by p and third by bait narrowness - the ordering is the ordering of labelling breadth

• co-occurs with →NFYC / NF-YC - a histone-fold transcription factor whose partner subunit carries an H2B-like ubiquitination, and the most selective of the eleven TF baits that reached KMT2A

  two of the eleven TF baits recovering KMT2A in IM-28767, ranked 3rd and 1st by the both-margins null