Informatic and genomic analysis of melanocyte cDNA libraries as a resource for the study of melanocyte development and function

Pigment Cell Research

Volumn 20, Issue 3, 2007, Pages 201-209

  Baxter, Laura L ^a   Hsu, Benjamin J ^a   Umayam, Lowell ^a   Wolfsberg, Tyra G ^a   Larson, Denise M ^a   Frith, Martin C ^b,c   Kawai, Jun ^c,d   Hayashizaki, Yoshihide ^c,d   Carninci, Piero ^c,d   Pavan, William J ^a  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF QUEENSLAND   (Australia)

^c RIKEN YOKOHAMA INSTITUTE   (Japan)

^d Japan Science and Technology Agency   (Japan)

Author keywords

B16F10Y; cDNA library; Development; Melan c; Melanocyte

Indexed keywords

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; BIOINFORMATICS; CELL FUNCTION; DEVELOPMENTAL GENETICS; DNA LIBRARY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; GENE FUNCTION; GENE SEQUENCE; GENETIC CODE; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HUMAN; MELANOCYTE; MOLECULAR CLONING; NONHUMAN; TUMOR CELL;

ANIMALS; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETIC TECHNIQUES; GENOME; GENOMICS; MELANOCYTES; MELANOMA, EXPERIMENTAL; MICE; MODELS, BIOLOGICAL;

EID: 34248644020     PISSN: 08935785     EISSN: 16000749     Source Type: Journal    
DOI: 10.1111/j.1600-0749.2007.00372.x     Document Type: Article

References (39)

1. Baxter, L.L. Pavan, W.J. (2002). The oculocutaneous albinism type IV gene Matp is a new marker of pigment cell precursors during mouse embryonic development. Mech. Dev. 116, 209 212.
2. Baxter, L.L. Pavan, W.J. (2003). Pmel17 expression is Mitf-dependent and reveals cranial melanoblast migration during murine development. Gene Expr. Patterns. 3, 703 707.
3. Bennett, D.C. Lamoreux, M.L. (2003). The color loci of mice - a genetic century. Pigment Cell Res. 16, 333 344.
4. Bennett, D.C., Cooper, P.J., Dexter, T.J., Devlin, L.M., Heasman, J. Nester, B. (1989). Cloned mouse melanocyte lines carrying the germline mutations albino and brown: complementation in culture. Development 105, 379 385.
5. Bennett, D.C., Huszar, D., Laipis, P.J., Jaenisch, R. Jackson, I.J. (1990). Phenotypic rescue of mutant brown melanocytes by a retrovirus carrying a wild-type tyrosinase-related protein gene. Development 110, 471 475.
6. Carninci, P. Hayashizaki, Y. (1999). High-efficiency full-length cDNA cloning. Methods Enzymol. 303, 19 44.
7. Carninci, P., Kvam, C., Kitamura, A., et al. (1996). High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Genomics 37, 327 336.
8. Carninci, P., Westover, A., Nishiyama, Y. et al. (1997). High efficiency selection of full-length cDNA by improved biotinylated cap trapper. DNA Res. 4, 61 66.
9. Carninci, P., Shibata, Y., Hayatsu, N. et al. (2000). Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Res. 10, 1617 1630.
10. Carninci, P., Shibata, Y., Hayatsu, N. et al. (2001). Balanced-size and long-size cloning of full-length, cap-trapped cDNAs into vectors of the novel lambda-FLC family allows enhanced gene discovery rate and functional analysis. Genomics 77, 79 90.
11. Carninci, P., Waki, K., Shiraki, T. et al. (2003). Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Genome Res. 13, 1273 1289.
12. Carninci, P., Kasukawa, T., Katayama, S. et al. (2005). The transcriptional landscape of the mammalian genome. Science 309, 1559 1563.
13. Cook, A.L., Smith, A.G., Smit, D.J., Leonard, J.H. Sturm, R.A. (2005). Co-expression of SOX9 and SOX10 during melanocytic differentiation in vitro. Exp. Cell Res. 308, 222 235.
14. Dupin, E., Real, C., Glavieux-Pardanaud, C., Vaigot, P. Le Douarin, N.M. (2003). Reversal of developmental restrictions in neural crest lineages: transition from Schwann cells to glial-melanocytic precursors in vitro. Proc. Natl. Acad. Sci. U. S. A. 100, 5229 5233.
15. Fidler, I.J. (1973). Selection of successive tumour lines for metastasis. Nat. New Biol. 242, 148 149.
16. Goulding, M.D., Chalepakis, G., Deutsch, U., Erselius, J.R. Gruss, P. (1991). Pax-3, a novel murine DNA binding protein expressed during early neurogenesis. Embo J. 10, 1135 1147.
17. Hartley, J.L., Temple, G.F. Brasch, M.A. (2000). DNA cloning using in vitro site-specific recombination. Genome Res. 10, 1788 1795.
18. Henion, P.D. Weston, J.A. (1997). Timing and pattern of cell fate restrictions in the neural crest lineage. Development 124, 4351 4359.
19. Hill, R.P., Chambers, A.F., Ling, V. Harris, J.F. (1984). Dynamic heterogeneity: rapid generation of metastatic variants in mouse B16 melanoma cells. Science 224, 998 1001.
20. Hodgkinson, C.A., Moore, K.J., Nakayama, A., Steingrimsson, E., Copeland, N.G., Jenkins, N.A. Arnheiter, H. (1993). Mutations at the mouse microphthalmia locus are associated with defects in a gene encoding a novel basic-helix-loop-helix-zipper protein. Cell 74, 395 404.
21. Hughes, M.J., Lingrel, J.B., Krakowsky, J.M. Anderson, K.P. (1993). A helix-loop-helix transcription factor-like gene is located at the mi locus. J. Biol. Chem. 268, 20 687 20 690.
22. Huizing, M., Boissy, R.E. Gahl, W.A. (2002). Hermansky-Pudlak syndrome: vesicle formation from yeast to man. Pigment Cell Res. 15, 405 419.
23. Karlin, S. Altschul, S.F. (1990). Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. U. S. A. 87, 2264 2268.
24. Kawai, J., Shinagawa, A., Shibata, K. et al. (2001). Functional annotation of a full-length mouse cDNA collection. Nature 409, 685 690.
25. Loftus, S.K., Larson, D.M., Baxter, L.L. et al. (2002). Mutation of melanosome protein RAB38 in chocolate mice. Proc. Natl. Acad. Sci. U. S. A. 99, 4471 4476.
26. Mollaaghababa, R. Pavan, W.J. (2003). The importance of having your SOX on: role of SOX10 in the development of neural crest-derived melanocytes and glia. Oncogene 22, 3024 3034.
27. Nakayama, A., Nguyen, M.T., Chen, C.C., Opdecamp, K., Hodgkinson, C.A. Arnheiter, H. (1998). Mutations in microphthalmia, the mouse homolog of the human deafness gene MITF, affect neuroepithelial and neural crest-derived melanocytes differently. Mech. Dev. 70, 155 166.
28. Oetting, W.S. Bennett, D.C. (2007). International Federation of Pigment Cell Societies. Available at: http://ifpcs.med.umn.edu/micemut.htm.
29. Okazaki, Y., Furuno, M., Kasukawa, T. et al. (2002). Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420, 563 573.
30. Opdecamp, K., Nakayama, A., Nguyen, M.T., Hodgkinson, C.A., Pavan, W.J. Arnheiter, H. (1997). Melanocyte development in vivo and in neural crest cell cultures: crucial dependence on the Mitf basic-helix-loop-helix-zipper transcription factor. Development 124, 2377 2386.
31. Rendl, M., Lewis, L. Fuchs, E. (2005). Molecular dissection of mesenchymal-epithelial interactions in the hair follicle. PLoS Biol. 3, e331.
32. Shiflett, S.L., Kaplan, J. Ward, D.M. (2002). Chediak-Higashi Syndrome: a rare disorder of lysosomes and lysosome related organelles. Pigment Cell Res. 15, 251 257.
33. Silver, D.L., Hou, L. Pavan, W.J. (2006). The genetic regulation of pigment cell development. In Neural Crest Induction and Differentiation, J.-P. Saint-Jeannet, ed Austin, TX: Landes Bioscience pp. 157 171.
34. Southard-Smith, E.M., Kos, L. Pavan, W.J. (1998). Sox10 mutation disrupts neural crest development in Dom Hirschsprung mouse model. Nat. Genet. 18, 60 64.
35. Steel, K.P., Davidson, D.R. Jackson, I.J. (1992). TRP-2/DT, a new early melanoblast marker, shows that steel growth factor (c-kit ligand) is a survival factor. Development 115, 1111 1119.
36. Stemple, D.L. Anderson, D.J. (1992). Isolation of a stem cell for neurons and glia from the mammalian neural crest. Cell 71, 973 985.
37. Stemple, D.L. Anderson, D.J. (1993). Lineage diversification of the neural crest: in vitro investigations. Dev. Biol. 159, 12 23.
38. Tang, H. Lewontin, R.C. (1999). Locating regions of differential variability in DNA and protein sequences. Genetics 153, 485 495.
39. Wei, M.L. (2006). Hermansky-Pudlak syndrome: a disease of protein trafficking and organelle function. Pigment Cell Res. 19, 19 42.