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Cited by 136melanin and skin pigmentationBioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

A curated gene list for expanding the horizons of pigmentation biology

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Baxter, Laura L., Watkins‐Chow, Dawn E., Pavan, William J., Loftus, Stacie K.·2019·Pigment Cell & Melanoma Research
DOI 10.1111/pcmr.12743PMC PMC10413850
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Abstract

Over the past century, studies of human pigmentary disorders along with mouse and zebrafish models have shed light on the many cellular functions associated with visible pigment phenotypes. This has led to numerous genes annotated with the ontology term “pigmentation” in independent human, mouse, and zebrafish databases. Comparisons among these datasets revealed that each is individually incomplete in documenting all genes involved in integument‐based pigmentation phenotypes. Additionally, each database contained inherent species‐specific biases in data annotation, and the term “pigmentation” did not solely reflect integument pigmentation phenotypes. This review presents a comprehensive, cross‐species list of 650 genes involved in pigmentation phenotypes that was compiled with extensive manual curation of genes annotated in OMIM, MGI, ZFIN, and GO. The resulting cross‐species list of genes both intrinsic and extrinsic to integument pigment cells provides a valuable tool that can be used to expand our knowledge of complex, pigmentation‐associated pathways.

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Research works printed but not linked: 58

  1. Abdel-Malek ZA, Kadekaro AL, & Swope VB (2010). Stepping up melanocytes to the challenge of UV exposure. Pigment Cell & Melanoma Research, 23(2), 171– 186. 10.1111/j.1755-148X.2010.00679.x. 20128873 · DOI · Paper page
  2. Amberger JS, & Hamosh A (2017). Searching online mendelian inheritance in man (OMIM): A knowledgebase of human genes and genetic phenotypes. Current Protocols in Bioinformatics, 58, 1.2.1– 1.2.12. 10.1002/cpbi.27. PMC5662200 28654725 · DOI
  3. Ammann S, Schulz A, Krägeloh-Mann I, Dieckmann NMG, Niethammer K, Fuchs S, … Ehl S (2016). Mutations in AP3D1 associated with immunodeficiency and seizures define a new type of Hermansky-Pudlak syndrome. Blood, 127(8), 997– 1006. 10.1182/blood-2015-09-671636. 26744459 PMC7611501 · DOI
  4. Arora H, Chacon AH, Choudhary S, McLeod MP, Meshkov L, Nouri K, & Izakovic J (2014). Bloom syndrome. International Journal of Dermatology, 53(7), 798– 802. 10.1111/ijd.12408. 24602044 · DOI
  5. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, … Sherlock G (2000). Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics, 25(1), 25– 29. 10.1038/75556. 10802651 PMC3037419 · DOI · Paper page
  6. Bagnara JT, & Matsumoto J (2006). Comparative anatomy and physiology of pigment cells in nonmammalian tissues. In Nordlund JJ, Boissy RE, Hearing VJ, King RA & Ortonne J-P (Eds.), The pigmentary system: Physiology and pathophysiology (2nd ed., pp. 11– 59). Oxford, UK: Wiley-Blackwell.
  7. Ballew BJ, & Savage SA (2013). Updates on the biology and management of dyskeratosis congenita and related telomere biology disorders. Expert Review of Hematology, 6(3), 327– 337. 10.1586/ehm.13.23. 23782086 · DOI
  8. Bellono NW, Escobar IE, Lefkovith AJ, Marks MS, & Oancea E (2014). An intracellular anion channel critical for pigmentation. eLife, 3, e04543. 10.7554/eLife.04543. 25513726 PMC4270065 · DOI
  9. Bellono NW, & Oancea EV (2014). Ion transport in pigmentation. Archives of Biochemistry and Biophysics, 563, 35– 41. 10.1016/j.abb.2014.06.020. 25034214 PMC4497562 · DOI
  10. Bennett DC, & Lamoreux ML (2003). The color loci of mice–a genetic century. Pigment Cell Research, 16(4), 333– 344. 10.1034/j.1600-0749.2003.00067.x. 12859616 · DOI
  11. Bin B-H, Bhin J, Yang SH, Shin M, Nam Y-J, Choi D-H, … Lee TR (2015). Membrane-associated transporter protein (MATP) regulates melanosomal ph and influences tyrosinase activity. PLoS ONE, 10(6), e0129273. 10.1371/journal.pone.0129273. 26057890 PMC4461305 · DOI
  12. Blake JA, Eppig JT, Kadin JA, Richardson JE, Smith CL, Bult CJ,& the Mouse Genome Database Group (2017). Mouse Genome Database (MGD)-2017: Community knowledge resource for the laboratory mouse. Nucleic Acids Research, 45(D1), D723– D729. 10.1093/nar/gkw1040. 27899570 PMC5210536 · DOI
  13. Bondurand N, & Sham MH (2013). The role of SOX10 during enteric nervous system development. Developmental Biology, 382(1), 330– 343. 10.1016/j.ydbio.2013.04.024. 23644063 · DOI
  14. Carrero D, Soria-Valles C, & López-Otín C (2016). Hallmarks of progeroid syndromes: Lessons from mice and reprogrammed cells. Disease Models & Mechanisms, 9(7), 719– 735. 10.1242/dmm.024711. 27482812 PMC4958309 · DOI · Paper page
  15. Chu G, & Chang E (1988). Xeroderma pigmentosum group E cells lack a nuclear factor that binds to damaged DNA. Science, 242(4878), 564– 567. 3175673
  16. Cooper CD (2017). Insights from zebrafish on human pigment cell disease and treatment. Developmental Dynamics, 246(11), 889– 896. 10.1002/dvdy.24550. 28710811 · DOI
  17. Crawford NG, Kelly DE, Hansen MEB, Beltrame MH, Fan S, Bowman SL, … Tishkoff SA (2017). Loci associated with skin pigmentation identified in African populations. Science, 358(6365), eaan8433. 10.1126/science.aan8433. 29025994 PMC5759959 · DOI
  18. de Boer J, Andressoo JO, de Wit J, Huijmans J, Beems RB, van Steeg H, … … J. H. (2002). Premature aging in mice deficient in DNA repair and transcription. Science, 296(5571), 1276– 1279. 10.1126/science.1070174. 11950998 · DOI · Paper page
  19. Dias MF, Joo K, Kemp JA, Fialho SL, da Silva Cunha A, Woo SJ, & Kwon YJ (2018). Molecular genetics and emerging therapies for retinitis pigmentosa: Basic research and clinical perspectives. Progress in Retinal and Eye Research, 63, 107– 131. 10.1016/j.preteyeres.2017.10.004. 29097191 · DOI
  20. Dooley CM, Schwarz H, Mueller KP, Mongera A, Konantz M, Neuhauss SCF, … Geisler R (2013). Slc45a2 and V-ATPase are regulators of melanosomal pH homeostasis in zebrafish, providing a mechanism for human pigment evolution and disease. Pigment Cell & Melanoma Research, 26(2), 205– 217. 10.1111/pcmr.12053. 23205854 · DOI · Paper page
  21. Harris ML, Fufa TD, Palmer JW, Joshi SS, Larson DM, Incao A, … Pavan WJ (2018). A direct link between MITF, innate immunity, and hair graying. PLoS Biology, 16(5), e2003648. 10.1371/journal.pbio.2003648. 29723194 PMC5933715 · DOI
  22. Hernandez-Pacheco N, Flores C, Alonso S, Eng C, Mak ACY, Hunstman S, … Pino-Yanes M (2017). Identification of a novel locus associated with skin colour in African-admixed populations. Scientific Reports, 7, 44548. 10.1038/srep44548. 28300201 PMC5353593 · DOI
  23. Hoki Y, Araki R, Fujimori A, Ohhata T, Koseki H, Fukumura R, … … M. (2003). Growth retardation and skin abnormalities of the Recql4-deficient mouse. Human Molecular Genetics, 12(18), 2293– 2299. 10.1093/hmg/ddg254. 12915449 · DOI
  24. Howe DG, Bradford YM, Conlin T, Eagle AE, Fashena D, Frazer K, … Westerfield M (2013). ZFIN, the Zebrafish model organism database: Increased support for mutants and transgenics. Nucleic Acids Research, 41(D1), D854– D860. 10.1093/nar/gks938. 23074187 PMC3531097 · DOI
  25. Huizing M, Helip-Wooley A, Westbroek W, Gunay-Aygun M, & Gahl WA (2008). Disorders of lysosome-related organelle biogenesis: Clinical and molecular genetics. Annual Review of Genomics and Human Genetics, 9, 359– 386. 10.1146/annurev.genom.9.081307.164303. PMC2755194 18544035 · DOI
  26. Irion U, Singh AP, & Nüsslein-Volhard C (2016). The developmental genetics of vertebrate color pattern formation: Lessons from zebrafish. Current Topics in Developmental Biology, 117, 141– 169. 10.1016/bs.ctdb.2015.12.012. 26969976 · DOI · Paper page
  27. Kelsh RN (2004). Genetics and evolution of pigment patterns in fish. Pigment Cell Research, 17(4), 326– 336. 10.1111/j.1600-0749.2004.00174.x. 15250934 · DOI
  28. Kelsh RN, Harris ML, Colanesi S, & Erickson CA (2009). Stripes and belly-spots – A review of pigment cell morphogenesis in vertebrates. Seminars in Cell & Developmental Biology, 20(1), 90– 104. 10.1016/j.semcdb.2008.10.001. 18977309 PMC2744437 · DOI · Paper page
  29. Koch SC, Simon N, Ebert C, & Carell T (2016). Molecular mechanisms of xeroderma pigmentosum (XP) proteins. Quarterly Reviews of Biophysics, 49, e5. 10.1017/S0033583515000268. 27660069 · DOI
  30. Lebel M, & Monnat RJ (2017). Werner syndrome (WRN) gene variants and their association with altered function and age-associated diseases. Ageing Research Reviews, 41, 82– 97. 10.1016/j.arr.2017.11.003. 29146545 · DOI
  31. Lloyd-Jones LR, Robinson MR, Moser G, Zeng J, Beleza S, Barsh GS, … Visscher PM (2017). Inference on the genetic basis of eye and skin color in an admixed population via bayesian linear mixed models. Genetics, 206(2), 1113– 1126. 10.1534/genetics.116.193383. 28381588 PMC5499166 · DOI
  32. Lu L, Jin W, & Wang LL (2017). Aging in Rothmund-Thomson syndrome and related RECQL4 genetic disorders. Ageing Research Reviews, 33, 30– 35. 10.1016/j.arr.2016.06.002. 27287744 · DOI
  33. Mahalwar P, Singh AP, Fadeev A, Nüsslein-Volhard C, & Irion U (2016). Heterotypic interactions regulate cell shape and density during color pattern formation in zebrafish. Biology Open, 5(11), 1680– 1690. 10.1242/bio.022251. 27742608 PMC5155543 · DOI · Paper page
  34. Mann MB, Hodges CA, Barnes E, Vogel H, Hassold TJ, & Luo G (2005). Defective sister-chromatid cohesion, aneuploidy and cancer predisposition in a mouse model of type II Rothmund-Thomson syndrome. Human Molecular Genetics, 14(6), 813– 825. 10.1093/hmg/ddi075. 15703196 · DOI
  35. Marks MS, Heijnen HFG, & Raposo G (2013). Lysosome-related organelles: Unusual compartments become mainstream. Current Opinion in Cell Biology, 25(4), 495– 505. 10.1016/j.ceb.2013.04.008. 23726022 PMC3729921 · DOI
  36. Meehan TF, Conte N, West DB, Jacobsen JO, Mason J, Warren J, … Smedley D (2017). Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium. Nature Genetics, 49(8), 1231– 1238. 10.1038/ng.3901. 28650483 PMC5546242 · DOI
  37. Mi H, Huang X, Muruganujan A, Tang H, Mills C, Kang D, & Thomas PD (2017). PANTHER version 11: Expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements. Nucleic Acids Research, 45(D1), D183– D189. 10.1093/nar/gkw1138. 27899595 PMC5210595 · DOI
  38. Montoliu L, & Marks MS (2017). A new type of syndromic albinism associated with mutations in AP3D1. Pigment Cell & Melanoma Research, 30(1), 5– 7. 10.1111/pcmr.12543. 27900855 PMC5555751 · DOI
  39. Mort RL, Jackson IJ, & Patton EE (2015). The melanocyte lineage in development and disease. Development, 142(4), 620– 632. 10.1242/dev.106567. 25670789 PMC4325379 · DOI · Paper page
  40. Palomera-Sanchez Z, & Zurita M (2011). Open, repair and close again: Chromatin dynamics and the response to UV-induced DNA damage. DNA Repair, 10(2), 119– 125. 10.1016/j.dnarep.2010.10.010. 21130713 · DOI
  41. Parichy DM, & Spiewak JE (2015). Origins of adult pigmentation: Diversity in pigment stem cell lineages and implications for pattern evolution. Pigment Cell & Melanoma Research, 28(1), 31– 50. 10.1111/pcmr.12332. 25421288 PMC4276524 · DOI
  42. Pruitt SC, Bailey KJ, & Freeland A (2007). Reduced Mcm2 expression results in severe stem/progenitor cell deficiency and cancer. Stem Cells, 25(12), 3121– 3132. 10.1634/stemcells.2007-0483. 17717065 · DOI
  43. Rawofi L, Edwards M, Krithika S, Le P, Cha D, Yang Z, … Parra EJ (2017). Genome-wide association study of pigmentary traits (skin and iris color) in individuals of East Asian ancestry. PeerJ, 5, e3951. 10.7717/peerj.3951. 29109912 PMC5671666 · DOI
  44. Reissmann M, & Ludwig A (2013). Pleiotropic effects of coat colour-associated mutations in humans, mice and other mammals. Seminars in Cell & Developmental Biology, 24(6–7), 576– 586. 10.1016/j.semcdb.2013.03.014. 23583561 · DOI · Paper page
  45. Ruzicka L, Bradford YM, Frazer K, Howe DG, Paddock H, Ramachandran S, … Westerfield M (2015). ZFIN, The zebrafish model organism database: Updates and new directions. Genesis, 53(8), 498– 509. 10.1002/dvg.22868. 26097180 PMC4545674 · DOI
  46. Schartl M, Larue L, Goda M, Bosenberg MW, Hashimoto H, & Kelsh RN (2016). What is a vertebrate pigment cell? Pigment Cell & Melanoma Research, 29(1), 8– 14. 10.1111/pcmr.12409. 26247887 · DOI
  47. Setty SRG, Tenza D, Sviderskaya EV, Bennett DC, Raposo G, & Marks MS (2008). Cell-specific ATP7A transport sustains copper-dependent tyrosinase activity in melanosomes. Nature, 454(7208), 1142– 1146. 10.1038/nature07163. 18650808 PMC2812007 · DOI
  48. Sitaram A, & Marks MS (2012). Mechanisms of protein delivery to melanosomes in pigment cells. Physiology, 27(2), 85– 99. 10.1152/physiol.00043.2011. 22505665 PMC3345138 · DOI
  49. Slominski A, Tobin DJ, Shibahara S, & Wortsman J (2004). Melanin pigmentation in mammalian skin and its hormonal regulation. Physiological Reviews, 84(4), 1155– 1228. 10.1152/physrev.00044.2003. 15383650 · DOI · Paper page
  50. Teive HAG, Moro A, Moscovich M, Arruda WO, Munhoz RP, Raskin S, & Ashizawa T (2015). Ataxia-telangiectasia - A historical review and a proposal for a new designation: ATM syndrome. Journal of the Neurological Sciences, 355(1–2), 3– 6. 10.1016/j.jns.2015.05.022. 26050521 PMC5161405 · DOI
  51. The Gene Ontology Consortium (2017). Expansion of the gene ontology knowledgebase and resources. Nucleic Acids Research, 45(D1), D331– D338. 10.1093/nar/gkw1108. 27899567 PMC5210579 · DOI · Paper page
  52. Verbakel SK, van Huet RAC, Boon CJF, den Hollander AI, Collin RWJ, Klaver CCW, … Klevering BJ (2018). Non-syndromic retinitis pigmentosa. Progress in Retinal and Eye Research, 10.1016/j.preteyeres.2018.03.005. 29597005 · DOI · Paper page
  53. Vogel P, Read RW, Vance RB, Platt KA, Troughton K, & Rice DS (2008). Ocular albinism and hypopigmentation defects in Slc24a5−/− mice. Veterinary Pathology, 45(2), 264– 279. 10.1354/vp.45-2-264. 18424845 · DOI
  54. Wang Y, Viennet C, Robin S, Berthon J-Y, He L, & Humbert P (2017). Precise role of dermal fibroblasts on melanocyte pigmentation. Journal of Dermatological Science, 88(2), 159– 166. 10.1016/j.jdermsci.2017.06.018. 28711237 · DOI
  55. Weider M, & Wegner M (2017). SoxE factors: Transcriptional regulators of neural differentiation and nervous system development. Seminars in Cell & Developmental Biology, 63, 35– 42. 10.1016/j.semcdb.2016.08.013. 27552919 · DOI
  56. Wu X, & Hammer JA (2014). Melanosome transfer: It is best to give and receive. Current Opinion in Cell Biology, 29, 1– 7. 10.1016/j.ceb.2014.02.003. 24662021 PMC4130791 · DOI
  57. Yamaguchi Y, & Hearing VJ (2009). Physiological factors that regulate skin pigmentation. BioFactors (Oxford, England), 35(2), 193– 199. 10.1002/biof.29. 19449448 PMC2793097 · DOI
  58. Yamaguchi Y, & Hearing VJ (2014). Melanocytes and their diseases. Cold Spring Harbor Perspectives in Medicine, 4(5), a017046. 10.1101/cshperspect.a017046. 24789876 PMC3996377 · DOI

Cited by

Sorted by citations

Authors
Baxter, L. L., Watkins‐Chow, D. E., Pavan, W. J., & Loftus, S. K.
Affiliations
National Institutes of Health (US)
Corresponding author
Loftus, Stacie K.
ORCID
Venue
Pigment Cell & Melanoma Research
Publisher
Wiley
Published
2018-11-06
Volume
32
Issue
3
Pages
348-358
ISSN
  • 1755-1471 (ISSN-L)
  • 1755-148X
DOI
10.1111/pcmr.12743
PMC
PMC10413850
OpenAlex
W2896906082
Cited by
136
References
7
Citations by year
2026: 13 · 2025: 17 · 2024: 32 · 2023: 18 · 2022: 26 · 2021: 12 · 2020: 11 · 2019: 6 · 2018: 1
FWCI
0.85
Type
journal article
Language
en
Open access
Licence
onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Locations
  • Pigment Cell & Melanoma Research (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
National Institutes of Health (1ZIAHG000136‐18)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › melanin and skin pigmentation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
Keywords
pigmentation, pigmentation genes, melanocytes, skin pigmentation disorders, genome annotation, human pigmentation
MeSH terms
Animals, Genes, Humans, Mutation, Pigmentation, Polymorphism, Genetic, Genomics, Gene Regulatory Networks, Genetic Association Studies

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