[en] The human genome contains hundreds of repeats of the 3.3 kb family in regions associated with heterochromatin. We have previously isolated a 3.3 kb-like cDNA encoding a double homeodomain protein (DUX1). Demonstration that the protein was expressed in human rhabdomyosarcoma TE671 cells, and characterization of a homologous promoter suggested that functional DUX genes might be present in 3.3 kb elements. In the present study, we describe two nearly identical 3.3 kb/DUX genes derived from PAC 137F16 (DUX3), and TE671 genomic DNA (DUX5), both mapping to all the acrocentric chromosomes. Their promoters harbor a GC and a TATAA box, and the open reading frame of the intronless structural part encodes two DUX proteins differing by alternative translation initiation. The shorter protein of the DUX5 gene is identical to DUX1. Using a protein truncation test, we could show that these two proteins are encoded by total RNA, but not by poly (A)(+) RNA, from different human tissues and cell lines. Our results indicate that active genes of unusual structure are present in chromosome regions characterized by large amounts of heterochromatic repetitive DNA.
Disciplines :
General & internal medicine Biotechnology
Author, co-author :
Beckers, Marie-claire
Gabriëls, Jan
van der Maarel, Silvère
De Vriese, Astrid
R. Frants, Rune
Collen, Désiré
Belayew, Alexandra ; Université de Mons > Faculté de Médecine et de Pharmacie > Biochimie métabolique et moléculaire
Language :
English
Title :
Active genes in junk DNA? Characterization of DUX genes embedded within 3.3 kb repeated elements
Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
Birnboim H.C., Doly J. (1979) A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 7:1513-1523.
Clark L.N., Koehler U., Ward D.C., Wienberg J., Hewitt J.E. (1996) Analysis of the organisation and localisation of the FSHD-associated tandem array in primates: Implications for the origin and evolution of the 3.3 kb repeat family. Chromosoma 105:180-189.
Den Dunnen J.T., Van Ommen G.J. (1999) The protein truncation test: A review. Hum. Mutat. 14:95-102.
Devereux J., Haeberli P., Smithies O. (1984) A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12:387-395.
Ding H., Beckers M.C., Plaisance S., Marynen P., Collen D., Belayew A. (1998) Characterization of a double homeodomain protein (DUX1) encoded by a cDNA homologous to 3.3 kb dispersed repeated elements. Hum. Mol. Genet. 7:1681-1694.
Dominski Z., Marzluff W.F. (1999) Formation of the 3′ end of histone mRNA. Gene 239:1-14.
Gabriëls J., Beckers M.C., Ding H., De Vriese A., Plaisance S., Van der Maarel S.M., Padberg G.W., Frants R.R., Hewitt J.E., Collen D., Belayew A. (1999) Nucleotide sequence of the partially deleted D4Z4 locus in a patient with FSHD identifies a putative gene within each 3.3 kb element. Gene 236:25-32.
Hewitt J.E., Lyle R., Clark L.N., Valleley E.M., Wright T.J., Wijmenga C., Van Deutekom J.C., Francis F., Sharpe P.T., Hofker M. (1994) Analysis of the tandem repeat locus D4Z4 associated with facioscapulohumeral muscular dystrophy. Hum. Mol. Genet. 3:1287-1295.
Kozak M. (1996) Interpreting cDNA sequences: Some insights from studies on translation. Mamm. Genome 7:563-574.
Lee J.H., Goto K., Matsuda C., Arahata K. (1995) Characterization of a tandemly repeated 3.3 kb Kpnl unit in the facioscapulohumeral muscular dystrophy (FSHD) gene region on chromosome 4q35. Muscle Nerve 2.
Lyle R., Wright T.J., Clark L.N., Hewitt J.E. (1995) The FSHD-associated repeat, D4Z4, is a member of a dispersed family of homeobox-containing repeats, subsets of which are clustered on the short arms of the acrocentric chromosomes. Genomics 28:389-397.
Ochman H., Gerber A.S., Hartl D.L. (1988) Genetic applications of an inverse polymerase chain reaction. Genetics 120:621-623.
Triglia T., Peterson M.G., Kemp D.J. (1988) A procedure for in vitro amplification of DNA segments that lie outside the boundaries of known sequences. Nucleic Acids Res. 16:8186.
Van Deutekom J.C., Wijmenga C., Van Tienhoven E.A., Gruter A.M., Hewitt J.E., Padberg G.W., Van Ommen G.J., Hofker M.H., Frants R.R. (1993) FSHD associated DNA rearrangements are due to deletions of integral copies of a 3.2 kb tandemly repeated unit. Hum. Mol. Genet. 2:2037-2042.
Wang S.Y., Cruts M., Del Favero J., Zhang Y., Tissir F., Potier M.C., Patterson D., Nizetic D., Bosch A., Chen H., Bennett L., Estivill X., Kessling A., Antonarakis S.E., Van Broeckhoven C. (1999) A high-resolution physical map of human chromosome 21p using yeast artificial chromosomes. Genome Res. 9:1059-1073.
Wijmenga C., Hewitt J.E., Sandkuijl L.A., Clark L.N., Wright T.J., Dauwerse H.G., Gruter A.M., Hofker M.H., Moerer P., Williamson R. (1992) Chromosome 4q DNA rearrangements associated with facioscapulohumeral muscular dystrophy. Nat. Genet. 2:26-30.
Winokur S.T., Bengtsson U., Feddersen J., Mathews K.D., Weiffenbach B., Bailey H., Markovich R.P., Murray J.C., Wasmuth J.J., Altherr M.R. (1994) The DNA rearrangement associated with facioscapulohumeral muscular dystrophy involves a heterochromatin-associated repetitive element: Implications for a role of chromatin structure in the pathogenesis of the disease. Chromosome. Res. 2:225-234.
Winokur S.T., Bengtsson U., Vargas J.C., Wasmuth J.J., Altherr M.R., Weiffenbach B., Jacobsen S.J. (1996) The evolutionary distribution and structural organization of the homeobox-containing repeat D4Z4 indicates a functional role for the ancestral copy in the FSHD region. Hum. Mol. Genet. 5:1567-1575.