mitfa (nacre) encodes microphthalmia-associated transcription factor a, a basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factor of the MiT/TFE family and one of two zebrafish co-orthologs of human MITF that arose in the teleost genome duplication (the other is mitfb). The 412-residue protein carries the MiT/TFE N-terminal region, the bHLH-LZ DNA-binding and dimerization domain and the MiT/TFE C-terminal region, and resembles the melanocyte-specific M isoform of mammalian MITF. mitfa is expressed in all embryonic melanogenic cells, including neural crest melanoblasts and the retinal pigment epithelium (RPE), and is the master transcriptional regulator of neural crest-derived melanophore (melanocyte) development: nacre null mutants lack melanophores throughout life, have supernumerary iridophores, and misexpression of mitfa induces ectopic melanized cells. Temperature-sensitive alleles show that mitfa is needed at several steps of melanophore differentiation (dct onset, progression to pigmentation and maintenance of dendritic form) but not to establish melanocyte stem cells. mitfa acts in parallel with TFAP2 factors and represses tfec in melanoblasts, biasing multipotent pigment progenitors away from the iridophore fate. mitfa is not required for RPE development, where it is redundant with mitfb and tfec; with tfec it is required in cranial neural crest cells for choroid (optic) fissure closure, and with mitfb and tfec it contributes to xanthophore development.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of sequence-specific cis-regulatory DNA binding from the MiT/TFE node (PTN005248237), grounded in mammalian MITF/TFE3/TFEB. mitfa retains the full bHLH-LZ domain, and mitfa missense substitutions in the DNA-binding domain abolish or impair its activity in vivo. Reason: mitfa is inside the MiT/TFE clade, carries an intact basic region, and there is no evidence of loss of DNA binding; a DNA-binding-domain missense allele identical to mouse alleles is dominant negative, consistent with DNA binding being central to its function. Supporting Evidence: PMID:40123122 Harboring a missense substitution in the DNA-binding domain identical to previously isolated alleles of mouse PMID:21146516 asparagine to tyrosine amino acid substitution in the DNA-binding domain |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | IBA GO_REF:0000033 | ACCEPT | Summary: Core molecular function of mitfa, inferred from the MiT/TFE family node. mitfa itself (ZFIN:ZDB-GENE-990910-11) is among the descendant evidences, reflecting its own IDA annotation from PMID:11543618; this is expected, not circular. Reason: Transcription factor activity is the ancestral and retained function of the MiT/TFE family and is directly supported for mitfa. Supporting Evidence: PMID:10433906 nac(w2) is a mutation in a zebrafish gene encoding a basic helix-loop-helix/leucine zipper transcription factor related to microphthalmia (Mitf) |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | IDA PMID:11543618 Duplicate mitf genes in zebrafish: complementary expression ... | ACCEPT | Summary: Direct assay from Lister et al. 2001 (abstract-only in cache), which characterized both zebrafish mitf proteins. The abstract supports the conserved melanogenic activity of the paralogs; the transcriptional assay details are in the full text that the curator read. Reason: Consistent with the family function, the IBA, and in vivo evidence that mitfa drives melanogenic gene expression (e.g. dct) and ectopic melanization. Deferring to the curator for the assay details. Supporting Evidence: PMID:11543618 These data suggest that mitfa and mitfb together may recapitulate the expression and functions of a single ancestral Mitf gene PMID:21146516 mitfa is required at several stages of melanocyte differentiation, including for expression of the early melanoblast marker dct |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Nuclear site of action inferred for the MiT/TFE family; appropriate for a sequence-specific transcription factor. Reason: A DNA-binding transcription factor acts in the nucleus; no evidence of divergence. Supporting Evidence: file:DANRE/mitfa/mitfa-deep-research-falcon.md Mitfa performs its primary function in the **nucleus**, where it regulates transcription at E-box-like elements. |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: Automated nuclear localization, consistent with the IBA and TF function. Reason: Consistent with the IBA nucleus annotation and the transcription factor activity. |
| GO:0005654 nucleoplasm | IC PMID:11543618 Duplicate mitf genes in zebrafish: complementary expression ... | ACCEPT | Summary: Curator inference of nucleoplasmic location from the directly assayed transcription factor activity. Reason: A reasonable IC from GO:0000981; consistent with the nuclear annotations. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Family-level (ARBA) subcellular-location mapping. MiT/TFE proteins can be retained in the cytoplasm under some conditions, but no zebrafish mitfa-specific localization data were found. Reason: Plausible for a MiT/TFE factor whose activity is regulated by nuclear entry, but the active pool is nuclear and there is no mitfa-specific evidence; retained as non-core. |
| GO:0006351 DNA-templated transcription | IDA PMID:11543618 Duplicate mitf genes in zebrafish: complementary expression ... | MODIFY | Summary: Companion BP annotation to the IDA for transcription factor activity. A sequence-specific transcription factor regulates RNA polymerase II transcription rather than executing DNA-templated transcription itself. Reason: The essence (mitfa controls transcription) is sound, but the regulatory term matches the molecular function better; the same change is made for mitfb so the pair stays consistent. Proposed replacements: regulation of transcription by RNA polymerase II Supporting Evidence: PMID:10433906 nac(w2) is a mutation in a zebrafish gene encoding a basic helix-loop-helix/leucine zipper transcription factor related to microphthalmia (Mitf) |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the MiT/TFE C-terminal domain; broad but correct. Reason: Correct general parent of the RNA polymerase II-specific regulation term. |
| GO:0006357 regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | ACCEPT | Summary: Family-level process for a RNA polymerase II transcription factor. Reason: Correct and at an appropriate level of generality for the MF. |
| GO:0007623 circadian rhythm | IDA PMID:26278158 Identification and expression of lypc, a novel dark-inducibl... | UNDECIDED | Summary: Annotation from a paper describing lypc, a dark-inducible Ly6 gene in pigment cells. The cached abstract does not mention mitfa; the IDA probably reflects diurnal variation of mitfa expression measured in the full text, which is not available here. Reason: Cannot verify the evidence (abstract only, mitfa not mentioned). Rhythmic expression alone would not show that mitfa acts in the circadian rhythm process, but without the full text this is left undecided rather than removed. Supporting Evidence: PMID:26278158 the expression of lypc displays a clear rhythmic pattern, and dark exposure apparently stimulated its expression |
| GO:0030318 melanocyte differentiation | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference placed at the MITF node (PTN000000863), seeded by the zebrafish mitfa and mitfb experimental annotations. mitfa's own experimental annotation is a legitimate descendant evidence. Reason: The core biological process of mitfa, strongly supported by mutant evidence. Supporting Evidence: PMID:10433906 Homozygous nacre (nac(w2)) mutants lack melanophores throughout development but have increased numbers of iridophores. |
| GO:0030318 melanocyte differentiation | IGI PMID:20862309 Differentiation of zebrafish melanophores depends on transcr... | ACCEPT | Summary: Genetic interaction with tfap2a/tfap2e knockdown: forced mitfa expression partially restores melanophore differentiation in Tfap2-deficient embryos. Reason: Consistent with mitfa acting in melanocyte differentiation in parallel with TFAP2. Supporting Evidence: PMID:20862309 forcing expression of mitfa in tfap2a/e doubly-deficient embryos partially restores melanophore differentiation |
| GO:0030318 melanocyte differentiation | IGI PMID:28249010 TFAP2 paralogs regulate melanocyte differentiation in parall... | ACCEPT | Summary: Genetic interaction between mitfa and tfap2a in melanocyte development. Reason: Full text shows a synergistic mitfa;tfap2a interaction affecting melanocytes. Supporting Evidence: PMID:28249010 we observed a genetic interaction between mitfa and tfap2a affecting melanocyte development in zebrafish |
| GO:0030318 melanocyte differentiation | IGI PMID:28249010 TFAP2 paralogs regulate melanocyte differentiation in parall... | ACCEPT | Summary: Same genetic interaction as above, recorded with a positive-effect qualifier. Reason: Supported by the mitfa;tfap2a double-mutant analysis. Supporting Evidence: PMID:28249010 tfap2a+/- embryos in both mitfa mutant backgrounds had significantly fewer melanocytes in the ventral stripe |
| GO:0030318 melanocyte differentiation | IMP PMID:10433906 nacre encodes a zebrafish microphthalmia-related protein tha... | ACCEPT | Summary: The founding nacre paper: mitfa null mutants lack neural crest melanophores; the defect is cell autonomous and rescued by wild-type mitfa. Reason: Definitive loss-of-function and rescue evidence for the core process. Supporting Evidence: PMID:10433906 Transient expression of the wild-type nacre gene restored melanophore development in nacre(-/-) embryos. |
| GO:0030318 melanocyte differentiation | IMP PMID:11543618 Duplicate mitf genes in zebrafish: complementary expression ... | ACCEPT | Summary: nacre/mitfa mutants perturb neural crest melanocytes (Lister et al. 2001). Reason: Consistent with the nacre phenotype. Supporting Evidence: PMID:11543618 Mutations in the zebrafish nacre/mitfa gene, expressed in all embryonic melanogenic cells, perturb only neural crest melanocytes |
| GO:0030318 melanocyte differentiation | IMP PMID:15300437 A requirement for kit in embryonic zebrafish melanocyte diff... | ACCEPT | Summary: mitfa morpholino knockdown delays melanoblast development; used as a tool to reveal a kit requirement. Reason: The morphant delay of melanoblast development is consistent with mitfa's role. Supporting Evidence: PMID:15300437 When melanoblast development in zebrafish embryos is delayed by injecting morpholinos targeted to the mitfa gene |
| GO:0030318 melanocyte differentiation | IMP PMID:20862309 Differentiation of zebrafish melanophores depends on transcr... | ACCEPT | Summary: mitfa mutant genotype used in the Tfap2 melanophore study. Reason: Consistent with the established requirement for mitfa in melanophore differentiation. Supporting Evidence: PMID:20862309 Tfap2 activity, mediated redundantly by Tfap2a and Tfap2e, promotes melanophore differentiation in parallel with Mitf |
| GO:0030318 melanocyte differentiation | IMP PMID:21146516 mitfa is required at multiple stages of melanocyte different... | ACCEPT | Summary: Hypomorphic and temperature-sensitive mitfa alleles define multiple requirements. Reason: Strong allelic-series evidence for mitfa acting within melanocyte differentiation. Supporting Evidence: PMID:21146516 mitfa is required at several stages of melanocyte differentiation, including for expression of the early melanoblast marker dct |
| GO:0030318 melanocyte differentiation | IMP PMID:21146516 mitfa is required at multiple stages of melanocyte different... | ACCEPT | Summary: Second genotype from the same allelic series (temperature-sensitive allele). Reason: Same evidence as above. Supporting Evidence: PMID:21146516 again for maintenance of dendritic form following differentiation |
| GO:0030318 melanocyte differentiation | IMP PMID:23364329 On the embryonic origin of adult melanophores: the role of E... | ACCEPT | Summary: Mitfa morpholino depletes larval melanophores and prematurely activates embryonic melanophore progenitors. Reason: Consistent with mitfa's requirement for melanophore differentiation. Supporting Evidence: PMID:23364329 Upon depletion of larval melanophores by morpholino knockdown of Mitfa, the embryonic MPs are prematurely activated |
| GO:0030318 melanocyte differentiation | IMP PMID:25535837 Gap junctions composed of connexins 41.8 and 39.4 are essent... | ACCEPT | Summary: nacre/mitfa mutants lacking melanophores used in adult stripe-pattern analysis. Reason: The paper re-uses the melanophore-less nacre phenotype; consistent with the core role. Supporting Evidence: PMID:25535837 in mutants for nacre/mitfA melanophores are missing |
| GO:0030318 melanocyte differentiation | IMP PMID:28249010 TFAP2 paralogs regulate melanocyte differentiation in parall... | ACCEPT | Summary: mitfa allele combinations (w2/z25) with reduced melanocytes. Reason: Consistent with mitfa promoting melanocyte differentiation. Supporting Evidence: PMID:28249010 nor did it improve the quality or pigmentation of melanocytes in mitfaz25/z25 and mitfaw2/z25 mutants |
| GO:0043473 pigmentation | IGI PMID:28249010 TFAP2 paralogs regulate melanocyte differentiation in parall... | KEEP AS NON CORE | Summary: Broad pigmentation term from the mitfa;tfap2a interaction. Reason: Correct but general; the specific process (melanocyte differentiation) is already annotated from the same paper. |
| GO:0043473 pigmentation | IMP PMID:25214630 Local reorganization of xanthophores fine-tunes and colors t... | KEEP AS NON CORE | Summary: Xanthophore time-lapse study of adult stripe formation (abstract only); the nacre genotype was presumably used to remove melanophores. Reason: Broad but correct for mitfa (loss of melanophores alters the adult pigment pattern); deferring to the curator on the full-text details. Supporting Evidence: PMID:25214630 Thus, xanthophores, attracted by iridophores and repelling melanophores, sharpen and color the pattern. |
| GO:0045636 positive regulation of melanocyte differentiation | IMP PMID:33439865 The MITF paralog tfec is required in neural crest developmen... | ACCEPT | Summary: Petratou et al. show that Mitfa represses tfec in melanoblasts, contributing to the melanocyte versus iridophore fate choice. Reason: mitfa as master regulator promotes melanocyte fate; positive regulation of melanocyte differentiation is an appropriate description for a lineage-determining TF. Supporting Evidence: PMID:33439865 We show that Mitfa represses tfec expression, revealing a likely mechanism contributing to the decision between melanocyte and iridophore fate. |
| GO:0046983 protein dimerization activity | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO mapping from the HLH domain. bHLH-LZ factors bind DNA as dimers, so the mapping is correct, but it describes part of the TF mechanism. Reason: Correct domain-based inference; subsidiary to the transcription factor activity. |
| GO:0061386 closure of optic fissure | IGI PMID:32541011 Mitf-family transcription factor function is required within... | KEEP AS NON CORE | Summary: mitfa;tfec double mutants have colobomas; Mitf activity is needed in cranial neural crest cells for choroid fissure closure. mitfa single mutants close the fissure normally. Reason: Real but redundant (with tfec) role in eye morphogenesis; not the primary function of mitfa. Supporting Evidence: PMID:32541011 mitfa;tfec mutants possess severe colobomas and our data demonstrate that Mitf activity is required within cranial neural crest cells (cNCCs) during CF closure |
| GO:0071228 cellular response to tumor cell | IMP PMID:35929478 Fate mapping melanoma persister cells through regression and... | REMOVE | Summary: Travnickova-style conditional melanoma model in which a temperature-sensitive mitfa splicing allele switches MITF activity in the tumour cells, driving tumour regression and recurrence. The full text was read. Reason: GO:0071228 is defined as a change in a cell as a result of a stimulus from a tumor cell. In this paper mitfa is the oncogenic driver acting within the melanoma cells themselves; nothing is shown about mitfa mediating a response of cells to tumour cells. The experiment is valid, but the term does not describe it. Supporting Evidence: PMID:35929478 At the lower permissive temperature, MITF activity is on and promotes tumourigenesis |
| GO:0050936 xanthophore differentiation | IGI PMID:37823232 A gene regulatory network combining Pax3/7, Sox10 and Mitf g... | NEW | Summary: NEW (proposed). mitfa contributes, redundantly with mitfb and tfec, to xanthophore development. mitfa;mitfb double nulls have fewer xanthophores than mitfa single mutants in two independent studies, and a dominant-negative DNA-binding-domain mitfa allele eliminates xanthophores through interference with Tfec. Reason: Participation: MiT factors directly activate xanthophore pigment genes (gch2) in the lineage, so mitfa does part of the work as a transcription factor, not merely as a prerequisite. Proposed equally for mitfb, since the evidence is from double mutants and applies to both copies. Supporting Evidence: PMID:37823232 the results suggest that in zebrafish xanthophore development may be partially dependent on Mitf function PMID:40123122 Our findings point to collaborative roles for Mitfa and Tfec in promoting chromatophore development, particularly in xanthophore lineages file:DANRE/mitfa/mitfa-deep-research-falcon.md Genetic evidence also supports partial redundancy with **Tfec**. |
Loading supporting content…
Download this section (compressed HTML)Q: Is mitfa's contribution to xanthophore development direct (cell-autonomous activation of pteridine-pathway genes such as gch2 in xanthoblasts, as shown in medaka) or indirect through tfec cross-regulation?
Q: Does the IDA circadian rhythm annotation from PMID:26278158 rest on anything beyond diurnal variation of mitfa transcript levels?
Q: Since mitfa, mitfb and tfec are jointly required for RPE pigmentation (PMID:42663426), which of the three normally carries most of the RPE melanogenic transcription in wild type?
Experiment: Lineage-restricted CUT&RUN or ChIP-seq for tagged Mitfa in sorted xanthoblasts, combined with RNA-seq of mitfa;mitfb double mutant xanthophores, to test direct binding at gch2 and other pteridine-pathway loci.
Hypothesis: mitfa directly regulates xanthophore pigment-synthesis genes in zebrafish.
Type: genomics
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)