Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster (original) (raw)

• Birchler, J.A., Riddle, N.C., Auger, D.L. & Veitia, R.A. Dosage balance in gene regulation: biological implications. Trends Genet. 21, 219–226 (2005).
  Article CAS Google Scholar
• Veitia, R.A., Bottani, S. & Birchler, J.A. Cellular reactions to gene dosage imbalance: genomic, transcriptomic and proteomic effects. Trends Genet. 24, 390–397 (2008).
  Article CAS Google Scholar
• Deng, X. & Disteche, C.M. Genomic responses to abnormal gene dosage: the X chromosome improved on a common strategy. PLoS Biol. 8, e1000318 (2010).
  Article Google Scholar
• Gelbart, M.E. & Kuroda, M.I. Drosophila dosage compensation: a complex voyage to the X chromosome. Development 136, 1399–1410 (2009).
  Article CAS Google Scholar
• Straub, T. & Becker, P.B. Dosage compensation: the beginning and end of generalization. Nat. Rev. Genet. 8, 47–57 (2007).
  Article CAS Google Scholar
• Lyon, M.F. Gene action in the X-chromosome of the mouse (Mus musculus L). Nature 190, 372–373 (1961).
  Article CAS Google Scholar
• Meyer, B.J. Targeting X chromosomes for repression. Curr. Opin. Genet. Dev. 20, 179–189 (2010).
  Article CAS Google Scholar
• Gupta, V. et al. Global analysis of X-chromosome dosage compensation. J. Biol. 5, 3 (2006).
  Article Google Scholar
• Nguyen, D.K. & Disteche, C.M. Dosage compensation of the active X chromosome in mammals. Nat. Genet. 38, 47–53 (2006).
  Article CAS Google Scholar
• Adler, D.A. et al. Evidence of evolutionary up-regulation of the single active X chromosome in mammals based on Clc4 expression levels in Mus spretus and Mus musculus. Proc. Natl. Acad. Sci. USA 94, 9244–9248 (1997).
  Article CAS Google Scholar
• Xiong, Y. et al. RNA sequencing shows no dosage compensation of the active X-chromosome. Nat. Genet. 42, 1043–1047 (2010).
  Article CAS Google Scholar
• Vicoso, B. & Charlesworth, B. Evolution on the X chromosome: unusual patterns and processes. Nat. Rev. Genet. 7, 645–653 (2006).
  Article CAS Google Scholar
• Kelly, W.G. et al. X-chromosome silencing in the germline of C. elegans. Development 129, 479–492 (2002).
  CAS PubMed PubMed Central Google Scholar
• Hense, W., Baines, J.F. & Parsch, J. X chromosome inactivation during Drosophila spermatogenesis. PLoS Biol. 5, e273 (2007).
  Article Google Scholar
• Turner, J.M. Meiotic sex chromosome inactivation. Development 134, 1823–1831 (2007).
  Article CAS Google Scholar
• Khil, P.P., Smirnova, N.A., Romanienko, P.J. & Camerini-Otero, R.D. The mouse X chromosome is enriched for sex-biased genes not subject to selection by meiotic sex chromosome inactivation. Nat. Genet. 36, 642–646 (2004).
  Article CAS Google Scholar
• Ross, M.T. et al. The DNA sequence of the human X chromosome. Nature 434, 325–337 (2005).
  Article CAS Google Scholar
• Mueller, J.L. et al. The mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression. Nat. Genet. 40, 794–799 (2008).
  Article CAS Google Scholar
• Pepke, S., Wold, B. & Mortazavi, A. Computation for ChIP-seq and RNA-seq studies. Nat. Methods 6, S22–S32 (2009).
  Article CAS Google Scholar
• Cheung, V.G. et al. Polymorphic cis- and trans-regulation of human gene expression. PLoS Biol. 8, e1000480 (2010).
  Article Google Scholar
• Saifi, G.M. & Chandra, H.S. An apparent excess of sex- and reproduction-related genes on the human X chromosome. Proc. Biol. Sci. 266, 203–209 (1999).
  Article CAS Google Scholar
• Hofmann, O. et al. Genome-wide analysis of cancer/testis gene expression. Proc. Natl. Acad. Sci. USA 105, 20422–20427 (2008).
  Article CAS Google Scholar
• Skuse, D.H. X-linked genes and mental functioning. Hum. Mol. Genet. 14 Spec No 1, R27–R32 (2005).
  Article Google Scholar
• Ropers, H.H. X-linked mental retardation: many genes for a complex disorder. Curr. Opin. Genet. Dev. 16, 260–269 (2006).
  Article CAS Google Scholar
• Stevenson, R.E. & Schwartz, C.E. X-linked intellectual disability: unique vulnerability of the male genome. Dev. Disabil. Res. Rev. 15, 361–368 (2009).
  Article Google Scholar
• Wang, P.J., McCarrey, J.R., Yang, F. & Page, D.C. An abundance of X-linked genes expressed in spermatogonia. Nat. Genet. 27, 422–426 (2001).
  Article Google Scholar
• Lin, H. et al. Dosage compensation in the mouse balances up-regulation and silencing of X-linked genes. PLoS Biol. 5, e326 (2007).
  Article Google Scholar
• Zvetkova, I. et al. Global hypomethylation of the genome in XX embryonic stem cells. Nat. Genet. 37, 1274–1279 (2005).
  Article CAS Google Scholar
• Mizuno, H., Okamoto, I. & Takagi, N. Developmental abnormalities in mouse embryos tetrasomic for chromosome 11: apparent similarity to embryos functionally disomic for the x chromosome. Genes Genet. Syst. 77, 269–276 (2002).
  Article Google Scholar
• Phatnani, H.P. & Greenleaf, A.L. Phosphorylation and functions of the RNA polymerase II CTD. Genes Dev. 20, 2922–2936 (2006).
  Article CAS Google Scholar
• Goldberg, A.D. et al. Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell 140, 678–691 (2010).
  Article CAS Google Scholar
• Byerly, L., Cassada, R.C. & Russell, R.L. The life cycle of the nematode Caenorhabditis elegans. I. Wild-type growth and reproduction. Dev. Biol. 51, 23–33 (1976).
  Article CAS Google Scholar
• Sulston, J.E., Schierenberg, E., White, J.G. & Thomson, J.N. The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev. Biol. 100, 64–119 (1983).
  Article CAS Google Scholar
• Lewis, J.A. et al. Cholinergic receptor mutants of the nematode Caenorhabditis elegans. J. Neurosci. 7, 3059–3071 (1987).
  Article CAS Google Scholar
• Wood, W.B. Determination of pattern and fate in early embryos of Caenorhabditis elegans. Dev. Biol. (N Y 1985) 5, 57–78 (1988).
  CAS Google Scholar
• Crittenden, S.L., Leonhard, K.A., Byrd, D.T. & Kimble, J. Cellular analyses of the mitotic region in the Caenorhabditis elegans adult germ line. Mol. Biol. Cell 17, 3051–3061 (2006).
  Article CAS Google Scholar
• Kislinger, T. et al. Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell 125, 173–186 (2006).
  Article CAS Google Scholar
• Parisi, M. et al. Paucity of genes on the Drosophila X chromosome showing male-biased expression. Science 299, 697–700 (2003).
  Article CAS Google Scholar
• Gan, Q. et al. Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq. Cell Res. 20, 763–783 (2010).
  Article CAS Google Scholar
• Rice, W.R. Sexually antagonistic genes: experimental evidence. Science 256, 1436–1439 (1992).
  Article CAS Google Scholar
• Zechner, U. et al. A high density of X-linked genes for general cognitive ability: a run-away process shaping human evolution? Trends Genet. 17, 697–701 (2001).
  Article CAS Google Scholar
• Hamada, F.N., Park, P.J., Gordadze, P.R. & Kuroda, M.I. Global regulation of X chromosomal genes by the MSL complex in Drosophila melanogaster. Genes Dev. 19, 2289–2294 (2005).
  Article CAS Google Scholar
• Gilfillan, G.D. et al. Chromosome-wide gene-specific targeting of the Drosophila dosage compensation complex. Genes Dev. 20, 858–870 (2006).
  Article CAS Google Scholar
• Zhang, Y. et al. Expression in aneuploid Drosophila S2 cells. PLoS Biol. 8, e1000320 (2010).
  Article Google Scholar
• Alekseyenko, A.A., Larschan, E., Lai, W.R., Park, P.J. & Kuroda, M.I. High-resolution ChIP-chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome. Genes Dev. 20, 848–857 (2006).
  Article CAS Google Scholar
• Larschan, E. et al. X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila. Nature 471, 115–118 (2011).
  Article CAS Google Scholar
• Ercan, S. et al. X chromosome repression by localization of the C. elegans dosage compensation machinery to sites of transcription initiation. Nat. Genet. 39, 403–408 (2007).
  Article CAS Google Scholar
• Carrel, L. & Willard, H.F. X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 434, 400–404 (2005).
  Article CAS Google Scholar
• Berletch, J.B., Yang, F. & Disteche, C.M. Escape from X inactivation in mice and humans. Genome Biol. 11, 213 (2010).
  Article Google Scholar
• Penny, G.D., Kay, G.F., Sheardown, S.A., Rastan, S. & Brockdorff, N. Requirement for Xist in X chromosome inactivation. Nature 379, 131–137 (1996).
  Article CAS Google Scholar
• Yang, F., Babak, T., Shendure, J. & Disteche, C.M. Global survey of escape from X inactivation by RNA-sequencing in mouse. Genome Res. 20, 614–622 (2010).
  Article CAS Google Scholar
• Mito, Y., Henikoff, J.G. & Henikoff, S. Genome-scale profiling of histone H3.3 replacement patterns. Nat. Genet. 37, 1090–1097 (2005).
  Article CAS Google Scholar
• Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009).
  Article CAS Google Scholar
• Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010).
  Article CAS Google Scholar
• Hosseini, P., Tremblay, A., Matthews, B.F. & Alkharouf, N.W. An efficient annotation and gene-expression derivation tool for Illumina Solexa datasets. BMC Res. Notes 3, 183 (2010).
  Article Google Scholar
• Gregg, C. et al. High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science 329, 643–648 (2010).
  Article CAS Google Scholar
• Hillier, L.W. et al. Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res. 19, 657–666 (2009).
  Article CAS Google Scholar
• Gerstein, M.B. et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330, 1775–1787 (2010).
  Article CAS Google Scholar
• Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
  Article Google Scholar
• Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
  Article CAS Google Scholar
• Davis, T.L. & Meyer, B.J. SDC-3 coordinates the assembly of a dosage compensation complex on the nematode X chromosome. Development 124, 1019–1031 (1997).
  CAS PubMed Google Scholar