MITF (melanocyte inducing transcription factor) is a basic helix-loop-helix leucine-zipper (bHLH-Zip) transcription factor of the MiT/TFE family (with TFE3, TFEB and TFEC). It binds E-box (CACGTG) and M-box (TCATGTG) elements as a homodimer or as a heterodimer with other MiT/TFE members, and activates RNA polymerase II transcription of pigmentation genes such as TYR and TYRP1. It is the master regulator of melanocyte survival, differentiation and melanosome biogenesis, and also controls differentiation of retinal pigment epithelium, mast cells and osteoclasts. Its nuclear activity is controlled by nutrient signalling: in nutrient-replete cells active Rag GTPases recruit MITF to lysosomes, where mTORC1 phosphorylation promotes 14-3-3 binding and cytoplasmic retention, whereas mTORC1 inhibition or starvation promotes nuclear accumulation. Alternative promoters and first exons generate several isoforms (A, B, C, H, M and others) that share the bHLH-Zip and C-terminal regions. The donkey gene product described here (610 aa) is an isoform A-type product with an unusual 115-residue N-terminal extension; its bHLH domain is identical to that of human MITF.
Existing Annotations Review
GO Term
Evidence
Action
Reason
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding
IEA GO_REF:0000118
ACCEPT
Summary: Sequence-specific binding to RNA polymerase II cis-regulatory regions, transferred by TreeGrafter within the MITF subfamily.
Reason: TreeGrafter places this donkey model in PANTHER PTHR45776:SF4 (MICROPHTHALMIA-ASSOCIATED TRANSCRIPTION FACTOR), the subfamily containing human O75030 and mouse Q08874, and transfers the term from node PTN000000842. The PAINT family file places GO:0000978 at the MiT/TFE root node PTN005248237 (IBD seeded by human MITF and mouse Mitf, Tfe3, Tfeb among others), so the function is ancestral to the whole family. Human MITF binds E-box and M-box elements in pigmentation-gene promoters, and the donkey bHLH domain is identical to the human one. Accept as core.
Binds to M-boxes (5'-TCATGTG-3') and symmetrical DNA sequences (E-boxes) (5'-CACGTG-3') found in the promoter of pigmentation genes, such as tyrosinase (TYR)
file:EQUAS/MITF/MITF-bioinformatics/RESULTS.md
DOMAIN bHLH: human [311, 364] QL -> donkey [395, 448] QL; 54 of 54 human residues in this span are identical
Reason: TreeGrafter places this donkey model in PANTHER PTHR45776:SF4 (MICROPHTHALMIA-ASSOCIATED TRANSCRIPTION FACTOR), the subfamily containing human O75030 and mouse Q08874, and transfers the term from node PTN000000842. GO:0000981 is an IBD at the family root node PTN005248237, seeded by many MiT/TFE members including human MITF. Human and mouse MITF-A activate TYR and TYRP1 transcription; this donkey model is an isoform A-type product from residue 116 onwards, and the bHLH-Zip and transactivation regions are conserved. Core activity.
Reason: Nucleus is the site of MITF's transcription factor activity and is an IBD at the MiT/TFE root node PTN005248237. Experimentally, MITF shuttles into the nucleus when mTORC1 is inhibited, and inactive Rag GTPases cause nuclear accumulation of MITF. Accept as core location.
Reason: Correct: human and mouse MITF hold a regulated, inactive cytoplasmic pool. Phosphorylation promotes 14-3-3 binding and cytosolic retention, and in nutrient-replete cells active Rag GTPases recruit MITF to the lysosome surface. The UniProt subcellular-location line on this entry is ARBA-derived, so the support here is the experimental orthologue evidence. This is a regulatory sequestration site, not where the core activity occurs, so keep as non-core.
MITF can shuttle from cytoplasm to nucleus dependent upon RANKL/CSF-1 action
GO:0006355 regulation of DNA-templated transcription
IEA GO_REF:0000002
MODIFY
Summary: Regulation of DNA-templated transcription (InterPro2GO, MiT/TFE C-terminal domain).
Reason: True but too general. MITF regulates transcription by RNA polymerase II, and for its defining targets (TYR, TYRP1) it is an activator. Replace with positive regulation of transcription by RNA polymerase II (GO:0045944), the term used in core_functions; the same replacement is proposed for the GO:0006357 row.
transient cotransfection assays suggested that MITF-A activated transcription of the tyrosinase and tyrosinase-related protein 1 genes
GO:0006357 regulation of transcription by RNA polymerase II
IEA GO_REF:0000118
MODIFY
Summary: Regulation of transcription by RNA polymerase II (TreeGrafter; IBD at the MiT/TFE root node).
Reason: Correct and inherited from the family root node PTN005248237 (IBD). However, the evidence supports the more specific direction: MITF activates pigmentation, lysosomal and autophagy genes, and human MITF-A activates the TYR and TYRP1 promoters. Refine to positive regulation of transcription by RNA polymerase II (GO:0045944). Repression of some targets has been reported for human MITF but was not assessed here, so it is not proposed as a second replacement.
Reason: TreeGrafter places this donkey model in PANTHER PTHR45776:SF4 (MICROPHTHALMIA-ASSOCIATED TRANSCRIPTION FACTOR), the subfamily containing human O75030 and mouse Q08874, and transfers the term from node PTN000000842. In the PAINT family file, melanocyte differentiation is an IBD placed on the MITF lineage itself, not at the MiT/TFE root: PTN000000820 (Tetrapoda, seeded by mouse Mitf) and PTN000000863 (teleost mitfa/mitfb). It is therefore a subfamily-specific function that this donkey model inherits. MITF takes part directly, as the transcription factor that switches on the pigment-cell differentiation programme, so this is participation and not an indirect phenotype. Accept as core.
Summary: Protein dimerization activity (InterPro2GO, HLH domain).
Reason: Correct. MITF forms homodimers and heterodimers with TFE3, TFEB or TFEC through its HLH-leucine zipper, and efficient DNA binding requires dimerization. Homodimerization and heterodimerization with MiT/TFE partners are both documented, so the parent term is as precise as a single annotation can be. It supports DNA binding rather than being a separate core function, so keep as non-core.
Binds DNA in the form of homodimer or heterodimer with either TFE3, TFEB or TFEC
Core Functions
bHLH-Zip transcription factor that binds E-box/M-box elements as a MiT/TFE dimer and activates RNA polymerase II transcription of pigmentation genes, driving melanocyte differentiation.
Binds to M-boxes (5'-TCATGTG-3') and symmetrical DNA sequences (E-boxes) (5'-CACGTG-3') found in the promoter of pigmentation genes, such as tyrosinase (TYR)
Q: Is the 115-residue Arg/Pro/Gly-rich N-terminal extension of donkey model ENSEAST00005067024 (A0A9L0JBN5) translated in vivo, or is it a gene-model artefact from an upstream in-frame start in the exon 1A 5' untranslated region?
Q: Which of the five donkey MITF transcript models (A0A8C4PGB1, A0A9L0IUI7, A0A9L0JHX8, A0A9L0KEI8, A0A9L0JBN5) are expressed in donkey melanocytes and retinal pigment epithelium, and does the absence of the 25-residue segment matching human A1 138-162 reflect real alternative splicing?
External Prediction Reviews
These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
Assessment of the single ProtNLM2 GO prediction for donkey MITF (A0A9L0JBN5), a bHLH-Zip MiT/TFE transcription factor 98.4% identical to human MITF. Regulation of DNA-templated transcription is correct but less precise than the regulation of transcription by RNA polymerase II already in donkey GOA (LSP). ProtNLM2 emitted no function text or subcellular-location output for this accession.
Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.
GO:0006355 regulation of DNA-templated transcriptionGO_BP
LSP — Less precise than existing annotation Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-10-14
Review rationale: Human MITF is a sequence-specific transcription factor that binds E-box and M-box promoter elements and regulates RNA polymerase II transcription of TYR and TYRP1; the donkey bHLH domain is 54/54 identical and the protein is 98.4% identical over paired residues. The predicted term is correct and is already in donkey GOA (InterPro2GO), but donkey GOA also has the more specific regulation of transcription by RNA polymerase II (GO:0006357, a descendant), and the gene review refines both rows to positive regulation of transcription by RNA polymerase II (GO:0045944) because human MITF-A activates the TYR and TYRP1 promoters. The prediction is therefore correct, not novel, and less precise.