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EPIGENETIC ASPECTS OF MALE INFERTILITY RESEARCH ARTICLE

Interrogating the transgenic genome: development of an interspecies tiling array

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Pages 54-62 | Received 23 Mar 2010, Accepted 18 May 2010, Published online: 10 Jan 2011

References

  • Aoki, V.W., Liu, L. and Carrell, D.T. (2005) Identification and evaluation of a novel sperm protamine abnormality in a population of infertile males. Hum Reprod 20:1298–1306.
  • Arpanahi, A., Brinkworth, M., Iles, D., Krawetz, S.A., Paradowska, A., Platts, A.E., (2009) Endonuclease-sensitive regions of human spermatozoal chromatin are highly enriched in promoter and CTCF binding sequences. Genome Res 19:1338–1349.
  • Awe, S. and Renkawitz-Pohl, R. (2010) Histone H4 Acetylation is Essential to Proceed from a Histone- to a Protamine-based Chromatin Structure in Spermatid Nuclei of Drosophila melanogaster. Syst Biol Reprod Med 56:44–61.
  • Balhorn, R. (2007) The protamine family of sperm nuclear proteins. Genome Biol 8:227.
  • Balhorn, R., Reed, S. and Tanphaichitr, N. (1988) Aberrant protamine 1/protamine 2 ratios in sperm of infertile human males. Experientia 44:52–55.
  • Bar-Or, C., Czosnek, H. and Koltai, H. (2007) Cross-species microarray hybridizations: a developing tool for studying species diversity. Trends Genet 23:200–207.
  • Belokopytova, I.A., Kostyleva, E.I., Tomilin, A.N. and Vorob'ev, V.I. (1993a) Human male infertility may be due to a decrease of the protamine P2 content in sperm chromatin. Mol Reprod Dev 34:53–57.
  • Belokopytova, I.A., Kostyleva, E.I., Tomilin, A.N. and Vorob'ev, V.I. (1993b) Human male sterility can be caused by mutations in the protamine P2 gene. Tsitologiia 35:61–67.
  • Braun, R.E. (2001) Packaging paternal chromosomes with protamine. Nat Genet 28:10–12.
  • Brinster, R.L., Chen, H.Y., Trumbauer, M.E., Yagle, M.K. and Palmiter, R.D. (1985) Factors affecting the efficiency of introducing foreign DNA into mice by microinjecting eggs. Proc Natl Acad Sci USA 82:4438–4442.
  • Chen, H.H., Castanotto, D., LeBon, J.M., Rossi, J.J. and Riggs, A.D. (2000) In vivo, high-resolution analysis of yeast and mammalian RNA-protein interactions, RNA structure, RNA splicing and ribozyme cleavage by use of terminal transferase-dependent PCR. Nucleic Acids Res 28:1656–1664.
  • Chen, H.H., Kontaraki, J., Bonifer, C. and Riggs, A.D. (2001) Terminal transferase-dependent PCR (TDPCR) for in vivo UV photofootprinting of vertebrate cells. Sci STKE 2001:pl1.
  • Cho, C., Willis, W.D., Goulding, E.H., Jung-Ha, H., Choi, Y.C., Hecht, N.B., (2001) Haploinsufficiency of protamine-1 or 2 causes infertility in mice. Nat Genet 28:82–86.
  • Choudhary, S.K., Wykes, S.M., Kramer, J.A., Mohamed, A.N., Koppitch, F., Nelson, J.E., (1995) A haploid expressed gene cluster exists as a single chromatin domain in human sperm. J Biol Chem 270:8755–8762.
  • Churikov, D., Zalenskaya, I.A. and Zalensky, A.O. (2004) Male germline-specific histones in mouse and man. Cytogenet Genome Res 105:203–214.
  • de Yebra, L., Ballesca, J.L., Vanrell, J.A., Bassas, L. and Oliva, R. (1993) Complete selective absence of protamine P2 in humans. J Biol Chem 268:10553–10557.
  • de Yebra, L., Ballesca, J.L., Vanrell, J.A., Corzett, M., Balhorn, R. and Oliva, R. (1998) Detection of P2 precursors in the sperm cells of infertile patients who have reduced protamine P2 levels. Fertil Steril 69:755–759.
  • Deschamps, J. (2007) Ancestral and recently recruited global control of the Hox genes in development. Curr Opin Genet Dev 17:422–427.
  • Dumas, L., Kim, Y.H., Karimpour-Fard, A., Cox, M., Hopkins, J., Pollack, J.R., (2007) Gene copy number variation spanning 60 million years of human and primate evolution. Genome Res 17:1266–1277.
  • Erlich, H.A., Gelfand, D. and Sninsky, J.J. (1991) Recent advances in the polymerase chain reaction. Science 252:1643–1651.
  • Flynn, S.M. and Carr, S.M. (2007) Interspecies hybridization on DNA resequencing microarrays: efficiency of sequence recovery and accuracy of SNP detection in human, ape, and codfish mitochondrial DNA genomes sequenced on a human-specific MitoChip. BMC Genomics 8:339.
  • Gardiner-Garden, M., Ballesteros, M., Gordon, M. and Tam, P.P. (1998) Histone- and protamine-DNA association: conservation of different patterns within the beta-globin domain in human sperm. Mol Cell Biol 18:3350–3356.
  • Gatewood, J.M., Cook, G.R., Balhorn, R., Bradbury, E.M. and Schmid, C.W. (1987) Sequence-specific packaging of DNA in human sperm chromatin. Science 236:962–964.
  • Gilad, Y., Rifkin, S.A., Bertone, P., Gerstein, M. and White, K.P. (2005) Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res 15:674–680.
  • Goodrich, R.J., Ostermeier, G.C. and Krawetz, S.A. (2003) Multitasking with molecular dynamics Typhoon: quantifying nucleic acids and autoradiographs. Biotechnol Lett 25:1061–1065.
  • Graf, S., Nielsen, F.G., Kurtz, S., Huynen, M.A., Birney, E., Stunnenberg, H., (2007) Optimized design and assessment of whole genome tiling arrays. Bioinformatics 23:i 195–i204.
  • Grzmil, P., Boinska, D., Kleene, K.C., Adham, I., Schluter, G., Kamper, M., (2008) Prm3, the fourth gene in the mouse protamine gene cluster, encodes a conserved acidic protein that affects sperm motility. Biol Reprod 78:958–967.
  • Hammoud, S.S., Nix, D.A., Zhang, H., Purwar, J., Carrell, D.T. and Cairns, B.R. (2009) Distinctive chromatin in human sperm packages genes for embryo development. Nature 460:473–478.
  • Hecht, N.B. (1998) Molecular mechanisms of male germ cell differentiation. Bioessays 20:555–561.
  • Hecht, N.B. (1988) Post-meiotic gene expression during spermatogenesis. Prog Clin Biol Res 267:291–313.
  • Heng, H.H., Squire, J. and Tsui, L.C. (1992) High-resolution mapping of mammalian genes by in situ hybridization to free chromatin. Proc Natl Acad Sci USA 89:9509–9513.
  • Heng, H.H. and Tsui, L.C. (1993) Modes of DAPI banding and simultaneous in situ hybridization. Chromosoma 102:325–332.
  • Kashiwabara, S., Arai, Y., Kodaira, K. and Baba, T. (1990) Acrosin biosynthesis in meiotic and postmeiotic spermatogenic cells. Biochem Biophys Res Commun 173:240–245.
  • Kierszenbaum, A.L. and Tres, L.L. (1975) Structural and transcriptional features of the mouse spermatid genome. J Cell Biol 65:258–270.
  • Kleene, K.C. (1996) Patterns of translational regulation in the mammalian testis. Mol Reprod Dev 43:268–281.
  • Kramer, J.A., Adams, M.D., Singh, G.B., Doggett, N.A. and Krawetz, S.A. (1998a) Extended analysis of the region encompassing the PRM1→PRM2→TNP2 domain: genomic organization, evolution and gene identification. J Exp Zool 282:245–253.
  • Kramer, J.A. and Krawetz, S.A. (1996) Nuclear matrix interactions within the sperm genome. J Biol Chem 271:11619–11622.
  • Kramer, J.A., McCarrey, J.R., Djakiew, D. and Krawetz, S.A. (1998b) Differentiation: the selective potentiation of chromatin domains. Development 125:4749–4755.
  • Kramer, J.A., McCarrey, J.R., Djakiew, D. and Krawetz, S.A. (2000) Human spermatogenesis as a model to examine gene potentiation. Mol Reprod Dev 56:254–258.
  • Kramer, J.A., Zhang, S., Yaron, Y., Zhao, Y. and Krawetz, S.A. (1997) Genetic testing for male infertility: a postulated role for mutations in sperm nuclear matrix attachment regions. Genet Test 1:125–129.
  • Krawetz, S.A. and Dixon, G.H. (1988) Sequence similarities of the protamine genes: implications for regulation and evolution. J Mol Evol 27:291–297.
  • Krawetz, S.A., Kramer, J.A. and McCarrey, J.R. (1999) Reprogramming the male gamete genome: a window to successful gene therapy. Gene 234:1–9.
  • Kurtz, K., Martinez-Soler, F., Ausio, J. and Chiva, M. (2007) Acetylation of histone H4 in complex structural transitions of spermiogenic chromatin. J Cell Biochem 102:1432–1441.
  • Li, L., He, H., Zhang, J., Wang, X., Bai, S., Stolc, V., (2008) Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays. Genome Biol 9:R57.
  • Martins, R.P., Ostermeier, G.C. and Krawetz, S.A. (2004) Nuclear matrix interactions at the human protamine domain: a working model of potentiation. J Biol Chem 279:51862–51868.
  • McCarrey, J.R., Berg, W.M., Paragioudakis, S.J., Zhang, P.L., Dilworth, D.D., Arnold, B.L., (1992) Differential transcription of Pgk genes during spermatogenesis in the mouse. Dev Biol 154:160–168.
  • Meistrich, M.L., Trostle-Weige, P.K., Lin, R., Bhatnagar, Y.M. and Allis, C.D. (1992) Highly acetylated H4 is associated with histone displacement in rat spermatids. Mol Reprod Dev 31:170–181.
  • Miller, D., Brinkworth, M. and Iles, D. (2010) Paternal DNA packaging in spermatozoa: more than the sum of its parts? DNA, histones, protamines and epigenetics. Reproduction 139:287–301.
  • Nelson, J.E. and Krawetz, S.A. (1994) Characterization of a human locus in transition. J Biol Chem 269:31067–31073.
  • Nelson, J.E. and Krawetz, S.A. (1993) Linkage of human spermatid-specific basic nuclear protein genes. Definition and evolution of the P1→P2→TP2 locus. J Biol Chem 268:2932–2936.
  • Nelson, J.E. and Krawetz, S.A. (1995) Mapping the clonally unstable recombinogenic PRM1→PRM2→TNP2 region of human 16p13.2. DNA Seq 5:163–168.
  • Oliva, R. (2006) Protamines and male infertility. Hum Reprod Update 12:417–435.
  • Oliva, R. and Dixon, G.H. (1991) Vertebrate protamine genes and the histone-to-protamine replacement reaction. Prog Nucleic Acid Res Mol Biol 40:25–94.
  • Pivot-Pajot, C., Caron, C., Govin, J., Vion, A., Rousseaux, S. and Khochbin, S. (2003) Acetylation-dependent chromatin reorganization by BRDT, a testis-specific bromodomain-containing protein. Mol Cell Biol 23:5354–5365.
  • Platts, A.E., Johnson, G.D., Linnemann, A.K. and Krawetz, S.A. (2008) Real-time PCR quantification using a variable reaction efficiency model. Anal Biochem 380:315–322.
  • Reeves, R.H., Gearhart, J.D., Hecht, N.B., Yelick, P., Johnson, P. and O'Brien, S.J. (1989) Mapping of PRM1 to human chromosome 16 and tight linkage of Prm-1 and Prm-2 on mouse chromosome 16. J Hered 80:442–446.
  • Sambrook, J., Fritsch, E.F. and Maniatis, T. (1989) Molecular cloning: a laboratory manual.
  • Schmid, C., Heng, H.H., Rubin, C., Ye, C.J. and Krawetz, S.A. (2001) Sperm nuclear matrix association of the PRM1→PRM2→TNP2 domain is independent of Alu methylation. Mol Hum Reprod 7:903–911.
  • Steger, K. (1999) Transcriptional and translational regulation of gene expression in haploid spermatids. Anat Embryol (Berl) 199:471–487.
  • Steger, K., Klonisch, T., Gavenis, K., Behr, R., Schaller, V., Drabent, B., (1999) Round spermatids show normal testis-specific H1t but reduced cAMP-responsive element modulator and transition protein 1 expression in men with round-spermatid maturation arrest. J Androl 20:747–754.
  • Steger, K., Wilhelm, J., Konrad, L., Stalf, T., Greb, R., Diemer, T., (2008) Both protamine-1 to protamine-2 mRNA ratio and Bcl2 mRNA content in testicular spermatids and ejaculated spermatozoa discriminate between fertile and infertile men. Hum Reprod 23(1):11–16.
  • Su, A.I., Cooke, M.P., Ching, K.A., Hakak, Y., Walker, J.R., Wiltshire, T., (2002) Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci USA 99:4465–4470.
  • Wellik, D.M. (2009) Hox genes and vertebrate axial pattern. Curr Top Dev Biol 88:257–278.
  • Wykes, S.M. and Krawetz, S.A. (2003a) Conservation of the PRM1→PRM2→TNP2 domain. DNA Seq 14:359–367.
  • Wykes, S.M. and Krawetz, S.A. (2003b) The structural organization of sperm chromatin. J Biol Chem 278:29471–29477.
  • Yu, Y.E., Zhang, Y., Unni, E., Shirley, C.R., Deng, J.M., Russell, L.D., (2000) Abnormal spermatogenesis and reduced fertility in transition nuclear protein 1-deficient mice. Proc Natl Acad Sci USA 97:4683–4688.
  • Zalenskaya, I.A., Bradbury, E.M. and Zalensky, A.O. (2000) Chromatin structure of telomere domain in human sperm. Biochem Biophys Res Commun 279:213–218.
  • Zhao, M., Shirley, C.R., Yu, Y.E., Mohapatra, B., Zhang, Y., Unni, E., (2001) Targeted disruption of the transition protein 2 gene affects sperm chromatin structure and reduces fertility in mice. Mol Cell Biol 21:7243–7255.

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