Muller HJ: A factor for the fourth chromosome of Drosophila. Science. 1914, 39 (1016): 906-
Article
CAS
PubMed
Google Scholar
Charlesworth B: Model for evolution of Y chromosomes and dosage compensation. Proc Natl Acad Sci U S A. 1978, 75 (11): 5618-5622. 10.1073/pnas.75.11.5618.
Article
PubMed Central
CAS
PubMed
Google Scholar
Graves JA: Sex chromosome specialization and degeneration in mammals. Cell. 2006, 124 (5): 901-914. 10.1016/j.cell.2006.02.024.
Article
PubMed
Google Scholar
Larsson J, Meller VH: Dosage compensation, the origin and the afterlife of sex chromosomes. Chromosome Res. 2006, 14 (4): 417-431. 10.1007/s10577-006-1064-3.
Article
CAS
PubMed
Google Scholar
da Cunha PR, Granadino B, Perondini AL, Sanchez L: Dosage compensation in sciarids is achieved by hypertranscription of the single X chromosome in males. Genetics. 1994, 138 (3): 787-790.
PubMed Central
CAS
PubMed
Google Scholar
Meyer BJ: Targeting X chromosomes for repression. Curr Opin Genet Dev. 2011, 20 (2): 179-189.
Article
Google Scholar
Itoh Y, Melamed E, Yang X, Kampf K, Wang S, Yehya N, Van Nas A, Replogle K, Band M, Clayton D: Dosage compensation is less effective in birds than in mammals. J Biol. 2007, 6 (1): 2-10.1186/jbiol53.
Article
PubMed Central
PubMed
Google Scholar
Ellegren H, Hultin-Rosenberg L, Brunstrom B, Dencker L, Kultima K, Scholz B: Faced with inequality: chicken do not have a general dosage compensation of sex-linked genes. BMC Biol. 2007, 5: 40-10.1186/1741-7007-5-40.
Article
PubMed Central
PubMed
Google Scholar
Mank JE, Ellegren H: All dosage compensation is local: gene-by-gene regulation of sex-biased expression on the chicken Z chromosome. Heredity. 2009, 102 (3): 312-320. 10.1038/hdy.2008.116.
Article
CAS
PubMed
Google Scholar
Wolf J, Bryk J: General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq. BMC Genomics. 2011, 12 (1): 91-10.1186/1471-2164-12-91.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mank JE, Hosken DJ, Wedell N: Some inconvenient truths about sex chromosome dosage compensation and the role of sexual conflict. Evolution. 2011, 65 (8): 2133-2144. 10.1111/j.1558-5646.2011.01316.x.
Article
PubMed
Google Scholar
Lee JT: Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome. Genes Dev. 2009, 23 (16): 1831-1842. 10.1101/gad.1811209.
Article
PubMed Central
CAS
PubMed
Google Scholar
Escamilla-Del-Arenal M, da Rocha ST, Heard E: Evolutionary diversity and developmental regulation of X-chromosome inactivation. Hum Genet. 2011, 130 (2): 307-327. 10.1007/s00439-011-1029-2.
Article
PubMed Central
CAS
PubMed
Google Scholar
Grant J, Mahadevaiah SK, Khil P, Sangrithi MN, Royo H, Duckworth J, McCarrey JR, VandeBerg JL, Renfree MB, Taylor W: Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation. Nature. 2012, 487 (7406): 254-258. 10.1038/nature11171.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ohno S: Sex chromosomes and sex-linked genes. 1967, Berlin, New York [etc.]: Springer-Verlag
Book
Google Scholar
Nguyen DK, Disteche CM: Dosage compensation of the active X chromosome in mammals. Nat Genet. 2006, 38 (1): 47-53. 10.1038/ng1705.
Article
CAS
PubMed
Google Scholar
Gupta V, Parisi M, Sturgill D, Nuttall R, Doctolero M, Dudko OK, Malley JD, Eastman PS, Oliver B: Global analysis of X-chromosome dosage compensation. J Biol. 2006, 5 (1): 3-10.1186/jbiol30.
Article
PubMed Central
PubMed
Google Scholar
Lin H, Gupta V, VerMilyea MD, Falciani F, Lee JT, O'Neill LP, Turner BM: Dosage compensation in the mouse balances up-regulation and silencing of X-linked genes. PLoS Biol. 2007, 5 (12): 2809-2820.
Article
CAS
Google Scholar
Xiong YY, Chen XS, Chen ZD, Wang XZ, Shi SH, Wang XQ, Zhang JZ, He XL: RNA sequencing shows no dosage compensation of the active X-chromosome. Nat Genet. 2010, 42 (12): 1043-U1029. 10.1038/ng.711.
Article
CAS
PubMed
Google Scholar
Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR: Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nat Genet. 2011, 43 (12): 1179-1785. 10.1038/ng.948.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kharchenko PV, Xi R, Park PJ: Evidence for dosage compensation between the X chromosome and autosomes in mammals. Nat Genet. 2011, 43 (12): 1167-1169. 10.1038/ng.991. author reply 1171–1162
Article
CAS
PubMed
Google Scholar
Lin H, Halsall JA, Antczak P, O'Neill LP, Falciani F, Turner BM: Relative overexpression of X-linked genes in mouse embryonic stem cells is consistent with Ohno's hypothesis. Nat Genet. 2011, 43 (12): 1169-1170. 10.1038/ng.992. author reply 1171–1162
Article
CAS
PubMed
Google Scholar
Yildirim E, Sadreyev RI, Pinter SF, Lee JT: X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription. Nat Struct Mol Biol. 2012, 19 (1): 56-61.
Article
PubMed Central
CAS
Google Scholar
He X, Chen X, Xiong Y, Chen Z, Wang X, Shi S, Wang X, Zhang J: He et al. Reply. Nat Genet. 2011, 43 (12): 1171-1172. 10.1038/ng.1010.
Article
CAS
Google Scholar
Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, Cheung VG: Widespread RNA and DNA sequence differences in the human transcriptome. Science. 2011, 333 (6038): 53-58. 10.1126/science.1207018.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kleinman CL, Majewski J: Comment on "Widespread RNA and DNA sequence differences in the human transcriptome". Science. 2012, 335 (6074): 1302-author reply 1302
Article
CAS
PubMed
Google Scholar
Lin W, Piskol R, Tan MH, Li JB: Comment on "Widespread RNA and DNA sequence differences in the human transcriptome". Science. 2012, 335 (6074): 1302-author reply 1302
Article
CAS
PubMed
Google Scholar
Pickrell JK, Gilad Y, Pritchard JK: Comment on "Widespread RNA and DNA sequence differences in the human transcriptome". Science. 2012, 335 (6074): 1302-author reply 1302
Article
CAS
PubMed
Google Scholar
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008, 5 (7): 621-628. 10.1038/nmeth.1226.
Article
CAS
PubMed
Google Scholar
Wang ET, Sandberg R, Luo SJ, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB: Alternative isoform regulation in human tissue transcriptomes. Nature. 2008, 456 (7221): 470-476. 10.1038/nature07509.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cheung VG, Nayak RR, Wang IX, Elwyn S, Cousins SM, Morley M, Spielman RS: Polymorphic cis- and trans-regulation of human gene expression. PLoS Biol. 2010, 8 (9): e1000480. doi:10.1371/journal.pbio.1000480.
Tarazona S, Garcia-Alcalde F, Dopazo J, Ferrer A, Conesa A: Differential expression in RNA-seq: a matter of depth. Genome Res. 2011, 21 (12): 2213-2223. 10.1101/gr.124321.111.
Article
PubMed Central
CAS
PubMed
Google Scholar
Trapnell C, Pachter L, Salzberg SL: TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009, 25 (9): 1105-1111. 10.1093/bioinformatics/btp120.
Article
PubMed Central
CAS
PubMed
Google Scholar
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010, 28 (5): 511-U174. 10.1038/nbt.1621.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kondrashov FA, Koonin EV: A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends Genet. 2004, 20 (7): 287-290. 10.1016/j.tig.2004.05.001.
Article
CAS
PubMed
Google Scholar
Birchler JA, Veitia RA: The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution. New Phytol. 2010, 186 (1): 54-62. 10.1111/j.1469-8137.2009.03087.x.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pessia E, Makino T, Bailly-Bechet M, McLysaght A, Marais GA: Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome. Proc Natl Acad Sci U S A. 2012, 109 (14): 5346-5351. 10.1073/pnas.1116763109.
Article
PubMed Central
CAS
PubMed
Google Scholar
Deakin JE, Hore TA, Koina E, Graves JAM: The status of dosage compensation in the multiple X chromosomes of the platypus. PLoS Genet. 2008, 4 (7): 13-
Article
Google Scholar
Zha XF, Xia QY, Duan J, Wang CY, He NJ, Xiang ZH: Dosage analysis of Z chromosome genes using microarray in silkworm, Bombyx mori. Insect Biochem Mol Biol. 2009, 39 (5–6): 315-321.
Article
CAS
PubMed
Google Scholar
Leder EH, Cano JM, Leinonen T, O'Hara RB, Nikinmaa M, Primmer CR, Merila J: Female-biased expression on the X chromosome as a Key step in Sex chromosome evolution in threespine sticklebacks. Mol Biol Evol. 2010, 27 (7): 1495-1503. 10.1093/molbev/msq031.
Article
CAS
PubMed
Google Scholar
Prince EG, Kirkland D, Demuth JP: Hyperexpression of the X chromosome in both sexes results in extensive female bias of X-linked genes in the flour beetle. Genome Biol Evol. 2010, 2: 336-346. 10.1093/gbe/evq024.
Article
PubMed Central
PubMed
Google Scholar
Itoh Y, Replogle K, Kim YH, Wade J, Clayton DF, Arnold AP: Sex bias and dosage compensation in the zebra finch versus chicken genomes: general and specialized patterns among birds. Genome Res. 2010, 20 (4): 512-518. 10.1101/gr.102343.109.
Article
PubMed Central
CAS
PubMed
Google Scholar
Walters JR, Hardcastle TJ: Getting a full dose? Reconsidering sex chromosome dosage compensation in the silkworm, Bombyx mori. Genome Biol Evol. 2011, 3: 491-504. 10.1093/gbe/evr036.
Article
PubMed Central
CAS
PubMed
Google Scholar
Treangen TJ, Salzberg SL: Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet. 2012, 13 (1): 36-46.
CAS
Google Scholar
Roberts A, Pimentel H, Trapnell C, Pachter L: Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics. 2011, 27 (17): 2325-2329. 10.1093/bioinformatics/btr355.
Article
CAS
PubMed
Google Scholar
Tarazona S, GarcÃ-a-Alcalde F, Dopazo J, Ferrer A, Conesa A: Differential expression in RNA-seq: A matter of depth. Genome Res. 2011, 21 (12): 2213-2223. 10.1101/gr.124321.111.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hebenstreit D, Fang M, Gu M, Charoensawan V, van Oudenaarden A, Teichmann SA: RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Mol Syst Biol. 2011, 7: 497-
Article
PubMed Central
PubMed
Google Scholar
Cui P, Lin QA, Ding F, Xin CQ, Gong W, Zhang LF, Geng JN, Zhang B, Yu XM, Yang J: A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing. Genomics. 2010, 96 (5): 259-265. 10.1016/j.ygeno.2010.07.010.
Article
CAS
PubMed
Google Scholar
Cloonan N, Forrest ARR, Kolle G, Gardiner BBA, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G: Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods. 2008, 5 (7): 613-619. 10.1038/nmeth.1223.
Article
CAS
PubMed
Google Scholar
Blencowe BJ, Ahmad S, Lee LJ: Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. Genes Dev. 2009, 23 (12): 1379-1386. 10.1101/gad.1788009.
Article
CAS
PubMed
Google Scholar
Toung JM, Morley M, Li MY, Cheung VG: RNA-sequence analysis of human B-cells. Genome Res. 2011, 21 (6): 991-998. 10.1101/gr.116335.110.
Article
PubMed Central
CAS
PubMed
Google Scholar
Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M: Mouse genomic variation and its effect on phenotypes and gene regulation. Nature. 2011, 477 (7364): 289-294. 10.1038/nature10413.
Article
PubMed Central
CAS
PubMed
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10 (3): R25-10.1186/gb-2009-10-3-r25.
Article
PubMed Central
PubMed
Google Scholar