Identification of CHD7 S as a novel splicing variant of CHD7 with functions similar and antagonistic to those of the full-length CHD7 L

Genes to Cells

Volumn 17, Issue 7, 2012, Pages 536-547

  Kita, Yasuyuki ^a,b   Nishiyama, Masaaki ^a,b   Nakayama, Keiichi I ^a,b  

^a KYUSHU UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; HELICASE; PROTEIN CHD7L; PROTEIN CHD7S; PROTEIN VARIANT; RNA PRECURSOR; TRANSCRIPTION FACTOR SOX2; UNCLASSIFIED DRUG; CHD7 PROTEIN, HUMAN; DNA BINDING PROTEIN; ISOPROTEIN; RIBOSOME RNA; RNA, RIBOSOMAL, 45S; SOX2 PROTEIN, HUMAN; TRANSCRIPTION FACTOR SOX;

ALTERNATIVE RNA SPLICING; ARTICLE; CELL PROLIFERATION; CHD 7 GENE; CONTROLLED STUDY; DNA BINDING; EXON; GENE; GENE LOCUS; GENE MUTATION; GENE OVEREXPRESSION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; NONHUMAN; NUCLEOLAR LOCALIZATION SIGNAL; NUCLEOLUS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DEPLETION; PROTEIN LOCALIZATION; RNA INTERFERENCE; SYNDROME CHARGE; TRANSCRIPTION REGULATION; ANTIBODY SPECIFICITY; CELL LINE; CHEMISTRY; GENE EXPRESSION REGULATION; GENE ORDER; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEAR LOCALIZATION SIGNAL; TRANSCRIPTION INITIATION;

ALTERNATIVE SPLICING; BASE SEQUENCE; CELL LINE; CELL NUCLEOLUS; DNA HELICASES; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION; GENE ORDER; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEAR LOCALIZATION SIGNALS; ORGAN SPECIFICITY; PROTEIN ISOFORMS; RNA, RIBOSOMAL; SOXB1 TRANSCRIPTION FACTORS; TRANSCRIPTIONAL ACTIVATION;

EID: 84862774918     PISSN: 13569597     EISSN: 13652443     Source Type: Journal    
DOI: 10.1111/j.1365-2443.2012.01606.x     Document Type: Article

References (46)

1. Ahmad, Y., Boisvert, F.M., Gregor, P., Cobley, A. & Lamond, A.I. (2009) NOPdb: nucleolar Proteome Database-2008 update. Nucleic Acids Res. 37, D181-D184.
2. Allen, M.D., Religa, T.L., Freund, S.M. & Bycroft, M. (2007) Solution structure of the BRK domains from CHD7. J. Mol. Biol. 371, 1135-1140.
3. Aramaki, M., Udaka, T., Kosaki, R., Makita, Y., Okamoto, N., Yoshihashi, H., Oki, H., Nanao, K., Moriyama, N., Oku, S., Hasegawa, T., Takahashi, T., Fukushima, Y., Kawame, H. & Kosaki, K. (2006) Phenotypic spectrum of CHARGE syndrome with CHD7 mutations. J. Pediatr. 148, 410-414.
4. Bajpai, R., Chen, D.A., Rada-Iglesias, A., Zhang, J., Xiong, Y., Helms, J., Chang, C.P., Zhao, Y., Swigut, T. & Wysocka, J. (2010) CHD7 cooperates with PBAF to control multipotent neural crest formation. Nature 463, 958-962.
5. Becker, P.B. (2005) Nucleosome remodelers on track. Nat. Struct. Mol. Biol. 12, 732-733.
6. Birchenall-Roberts, M.C., Fu, T., Kim, S.G., Huang, Y.K., Dambach, M., Resau, J.H. & Ruscetti, F.W. (2006) K-Ras4B proteins are expressed in the nucleolus: interaction with nucleolin. Biochem. Biophys. Res. Commun. 348, 540-549.
7. Bosman, E.A., Penn, A.C., Ambrose, J.C., Kettleborough, R., Stemple, D.L. & Steel, K.P. (2005) Multiple mutations in mouse Chd7 provide models for CHARGE syndrome. Hum. Mol. Genet. 14, 3463-3476.
8. Clapier, C.R. & Cairns, B.R. (2009) The biology of chromatin remodeling complexes. Annu. Rev. Biochem. 78, 273-304.
9. Colin, C., Tobaruella, F.S., Correa, R.G., Sogayar, M.C. & Demasi, M.A. (2010) Cloning and characterization of a novel alternatively spliced transcript of the human CHD7 putative helicase. BMC Res. Notes 3, 252.
10. Engelen, E., Akinci, U., Bryne, J.C., et al. (2011) Sox2 cooperates with Chd7 to regulate genes that are mutated in human syndromes. Nat. Genet. 43, 607-611.
11. Flanagan, J.F., Mi, L.Z., Chruszcz, M., Cymborowski, M., Clines, K.L., Kim, Y., Minor, W., Rastinejad, F. & Khorasanizadeh, S. (2005) Double chromodomains cooperate to recognize the methylated histone H3 tail. Nature 438, 1181-1185.
12. Gennery, A.R., Slatter, M.A., Rice, J., Hoefsloot, L.H., Barge, D., McLean-Tooke, A., Montgomery, T., Goodship, J.A., Burt, A.D., Flood, T.J., Abinun, M., Cant, A.J. & Johnson, D. (2008) Mutations in CHD7 in patients with CHARGE syndrome cause T-B + natural killer cell + severe combined immune deficiency and may cause Omenn-like syndrome. Clin. Exp. Immunol. 153, 75-80.
13. Gonzales, B., Henning, D., So, R.B., Dixon, J., Dixon, M.J. & Valdez, B.C. (2005) The Treacher Collins syndrome (TCOF1) gene product is involved in pre-rRNA methylation. Hum. Mol. Genet. 14, 2035-2043.
14. Hall, J.A. & Georgel, P.T. (2007) CHD proteins: a diverse family with strong ties. Biochem. Cell Biol. 85, 463-476.
15. Ho, L. & Crabtree, G.R. (2010) Chromatin remodelling during development. Nature 463, 474-484.
16. Hurd, E.A., Capers, P.L., Blauwkamp, M.N., Adams, M.E., Raphael, Y., Poucher, H.K. & Martin, D.M. (2007) Loss of Chd7 function in gene-trapped reporter mice is embryonic lethal and associated with severe defects in multiple developing tissues. Mamm. Genome 18, 94-104.
17. Hurd, E.A., Poucher, H.K., Cheng, K., Raphael, Y. & Martin, D.M. (2010) The ATP-dependent chromatin remodeling enzyme CHD7 regulates pro-neural gene expression and neurogenesis in the inner ear. Development 137, 3139-3150.
18. Iovino, N. & Cavalli, G. (2011) Rolling ES cells down the Waddington landscape with Oct4 and Sox2. Cell 145, 815-817.
19. Jongmans, M.C., van Ravenswaaij-Arts, C.M., Pitteloud, N., Ogata, T., Sato, N., Claahsen-van der Grinten, H.L., van der Donk, K., Seminara, S., Bergman, J.E., Brunner, H.G., Crowley, W.F. Jr & Hoefsloot, L.H. (2009) CHD7 mutations in patients initially diagnosed with Kallmann syndrome-the clinical overlap with CHARGE syndrome. Clin. Genet. 75, 65-71.
20. Kim, H.G., Kurth, I., Lan, F., et al. (2008) Mutations in CHD7, encoding a chromatin-remodeling protein, cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome. Am. J. Hum. Genet. 83, 511-519.
21. Kobayashi, M., Kishida, S., Fukui, A., Michiue, T., Miyamoto, Y., Okamoto, T., Yoneda, Y., Asashima, M. & Kikuchi, A. (2002) Nuclear localization of Duplin, a β-catenin-binding protein, is essential for its inhibitory activity on the Wnt signaling pathway. J. Biol. Chem. 277, 5816-5822.
22. Kopan, R. & Ilagan, M.X. (2009) The canonical Notch signaling pathway: unfolding the activation mechanism. Cell 137, 216-233.
23. Lalani, S.R., Safiullah, A.M., Fernbach, S.D., et al. (2006) Spectrum of CHD7 mutations in 110 individuals with CHARGE syndrome and genotype-phenotype correlation. Am. J. Hum. Genet. 78, 303-314.
24. Layman, W.S., McEwen, D.P., Beyer, L.A., Lalani, S.R., Fernbach, S.D., Oh, E., Swaroop, A., Hegg, C.C., Raphael, Y., Martens, J.R. & Martin, D.M. (2009) Defects in neural stem cell proliferation and olfaction in Chd7 deficient mice indicate a mechanism for hyposmia in human CHARGE syndrome. Hum. Mol. Genet. 18, 1909-1923.
25. Lusser, A., Urwin, D.L. & Kadonaga, J.T. (2005) Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly. Nat. Struct. Mol. Biol. 12, 160-166.
26. Marfella, C.G. & Imbalzano, A.N. (2007) The Chd family of chromatin remodelers. Mutat. Res. 618, 30-40.
27. Marsh, K.L., Dixon, J. & Dixon, M.J. (1998) Mutations in the Treacher Collins syndrome gene lead to mislocalization of the nucleolar protein treacle. Hum. Mol. Genet. 7, 1795-1800.
28. Mongelard, F. & Bouvet, P. (2007) Nucleolin: a multiFACeTed protein. Trends Cell Biol. 17, 80-86.
29. Kip1 display increased body size, multiple organ hyperplasia, retinal dysplasia, and pituitary tumors. Cell 85, 707-720.
30. Nishimoto, M., Fukushima, A., Okuda, A. & Muramatsu, M. (1999) The gene for the embryonic stem cell coactivator UTF1 carries a regulatory element which selectively interacts with a complex composed of Oct-3/4 and Sox-2. Mol. Cell. Biol. 19, 5453-5465.
31. Nishiyama, M., Nakayama, K., Tsunematsu, R., Tsukiyama, T., Kikuchi, A. & Nakayama, K.I. (2004) Early embryonic death in mice lacking the β-catenin-binding protein Duplin. Mol. Cell. Biol. 24, 8386-8394.
32. Nishiyama, M., Oshikawa, K., Tsukada, Y., Nakagawa, T., Iemura, S., Natsume, T., Fan, Y., Kikuchi, A., Skoultchi, A.I. & Nakayama, K.I. (2009) CHD8 suppresses p53-mediated apoptosis through histone H1 recruitment during early embryogenesis. Nat. Cell Biol. 11, 172-182.
33. Nishiyama, M., Skoultchi, A.I. & Nakayama, K.I. (2012) Histone H1 recruitment by CHD8 is essential for suppression of the Wnt-β-catenin signaling pathway. Mol. Cell. Biol. 32, 501-512.
34. Sanlaville, D. & Verloes, A. (2007) CHARGE syndrome: an update. Eur. J. Hum. Genet. 15, 389-399.
35. Schnetz, M.P., Bartels, C.F., Shastri, K., Balasubramanian, D., Zentner, G.E., Balaji, R., Zhang, X., Song, L., Wang, Z., Laframboise, T., Crawford, G.E. & Scacheri, P.C. (2009) Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns. Genome Res. 19, 590-601.
36. Schnetz, M.P., Handoko, L., Akhtar-Zaidi, B., Bartels, C.F., Pereira, C.F., Fisher, A.G., Adams, D.J., Flicek, P., Crawford, G.E., Laframboise, T., Tesar, P., Wei, C.L. & Scacheri, P.C. (2010) CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet. 6, e1001023.
37. Srinivasan, S., Dorighi, K.M. & Tamkun, J.W. (2008) Drosophila Kismet regulates histone H3 lysine 27 methylation and early elongation by RNA polymerase II. PLoS Genet. 4, e1000217.
38. Takada, I., Mihara, M., Suzawa, M., et al. (2007) A histone lysine methyltransferase activated by non-canonical Wnt signalling suppresses PPAR-gamma transactivation. Nat. Cell Biol. 9, 1273-1285.
39. Thomson, M., Liu, S.J., Zou, L.N., Smith, Z., Meissner, A. & Ramanathan, S. (2011) Pluripotency factors in embryonic stem cells regulate differentiation into germ layers. Cell 145, 875-889.
40. Valdez, B.C., Henning, D., So, R.B., Dixon, J. & Dixon, M.J. (2004) The Treacher Collins syndrome (TCOF1) gene product is involved in ribosomal DNA gene transcription by interacting with upstream binding factor. Proc. Natl Acad. Sci. USA 101, 10709-10714.
41. Vissers, L.E., van Ravenswaaij, C.M., Admiraal, R., Hurst, J.A., de Vries, B.B., Janssen, I.M., van der Vliet, W.A., Huys, E.H., de Jong, P.J., Hamel, B.C., Schoenmakers, E.F., Brunner, H.G., Veltman, J.A. & van Kessel, A.G. (2004) Mutations in a new member of the chromodomain gene family cause CHARGE syndrome. Nat. Genet. 36, 955-957.
42. Wang, Y., Chen, B., Li, Y., Zhou, D. & Chen, S. (2011) PNRC accumulates in the nucleolus by interaction with B23/nucleophosmin via its nucleolar localization sequence. Biochim. Biophys. Acta 1813, 109-119.
43. Winokur, S.T. & Shiang, R. (1998) The Treacher Collins syndrome (TCOF1) gene product, treacle, is targeted to the nucleolus by signals in its C-terminus. Hum. Mol. Genet. 7, 1947-1952.
44. Wise, C.A., Chiang, L.C., Paznekas, W.A., Sharma, M., Musy, M.M., Ashley, J.A., Lovett, M. & Jabs, E.W. (1997) TCOF1 gene encodes a putative nucleolar phosphoprotein that exhibits mutations in Treacher Collins Syndrome throughout its coding region. Proc. Natl Acad. Sci. USA 94, 3110-3115.
45. Yuan, H., Corbi, N., Basilico, C. & Dailey, L. (1995) Developmental-specific activity of the FGF-4 enhancer requires the synergistic action of Sox2 and Oct-3. Genes Dev. 9, 2635-2645.
46. Zentner, G.E., Hurd, E.A., Schnetz, M.P., Handoko, L., Wang, C., Wang, Z., Wei, C., Tesar, P.J., Hatzoglou, M., Martin, D.M. & Scacheri, P.C. (2010) CHD7 functions in the nucleolus as a positive regulator of ribosomal RNA biogenesis. Hum. Mol. Genet. 19, 3491-3501.