Dosage compensation and DNA methylation landscape of the X chromosome in mouse liver

[1]  S. Mirarab,et al.  Sequence Analysis , 2020, Encyclopedia of Bioinformatics and Computational Biology.

[2]  D. Waxman,et al.  Feminization of Male Mouse Liver by Persistent Growth Hormone Stimulation: Activation of Sex-Biased Transcriptional Networks and Dynamic Changes in Chromatin States , 2017, Molecular and Cellular Biology.

[3]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[4]  C. Disteche,et al.  Allele-specific non-CG DNA methylation marks domains of active chromatin in female mouse brain , 2017, Proceedings of the National Academy of Sciences.

[5]  J. Parsch,et al.  Sex-Biased Gene Expression. , 2016, Annual review of genetics.

[6]  Howard Y. Chang,et al.  Structural organization of the inactive X chromosome in the mouse , 2016, Nature.

[7]  Carolyn J. Brown,et al.  Escape Artists of the X Chromosome. , 2016, Trends in genetics : TIG.

[8]  Hao Wu,et al.  Differential methylation analysis for BS-seq data under general experimental design , 2016, Bioinform..

[9]  Helene Kretzmer,et al.  metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data , 2016, Genome research.

[10]  William Stafford Noble,et al.  Bipartite structure of the inactive mouse X chromosome , 2015, Genome Biology.

[11]  René A. M. Dirks,et al.  Dynamics of gene silencing during X inactivation using allele-specific RNA-seq , 2015, Genome Biology.

[12]  Erika L. Moen,et al.  Characterization of CpG sites that escape methylation on the inactive human X-chromosome , 2015, Epigenetics.

[13]  Matthew D. Schultz,et al.  Human Body Epigenome Maps Reveal Noncanonical DNA Methylation Variation , 2015, Nature.

[14]  William Stafford Noble,et al.  Escape from X Inactivation Varies in Mouse Tissues , 2015, PLoS genetics.

[15]  Carolyn J. Brown,et al.  Landscape of DNA methylation on the X chromosome reflects CpG density, functional chromatin state and X-chromosome inactivation , 2014, Human molecular genetics.

[16]  Martin J. Aryee,et al.  Coverage recommendations for methylation analysis by whole genome bisulfite sequencing , 2014, Nature Methods.

[17]  E. Heard,et al.  Noncoding RNAs and epigenetic mechanisms during X-chromosome inactivation. , 2014, Annual review of cell and developmental biology.

[18]  Carolyn J. Brown,et al.  Variable escape from X-chromosome inactivation: Identifying factors that tip the scales towards expression , 2014, BioEssays : news and reviews in molecular, cellular and developmental biology.

[19]  Francis S Collins,et al.  Policy: NIH to balance sex in cell and animal studies , 2014, Nature.

[20]  L. Doyle,et al.  Human active X-specific DNA methylation events showing stability across time and tissues , 2014, European Journal of Human Genetics.

[21]  J. Nathans,et al.  Cellular Resolution Maps of X Chromosome Inactivation: Implications for Neural Development, Function, and Disease , 2014, Neuron.

[22]  V. Catania,et al.  Hormonal regulation of hepatic drug biotransformation and transport systems. , 2013, Comprehensive Physiology.

[23]  Matthew D. Schultz,et al.  Global Epigenomic Reconfiguration During Mammalian Brain Development , 2013, Science.

[24]  David J. Waxman,et al.  Genome-Wide Analysis of Chromatin States Reveals Distinct Mechanisms of Sex-Dependent Gene Regulation in Male and Female Mouse Liver , 2013, Molecular and Cellular Biology.

[25]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[26]  Matthew D. Schultz,et al.  'Leveling' the playing field for analyses of single-base resolution DNA methylomes. , 2012, Trends in genetics : TIG.

[27]  Wei Sun,et al.  Site-Specific Silencing of Regulatory Elements as a Mechanism of X Inactivation , 2012, Cell.

[28]  Philip Cayting,et al.  An encyclopedia of mouse DNA elements (Mouse ENCODE) , 2012, Genome Biology.

[29]  Peter A. Jones Functions of DNA methylation: islands, start sites, gene bodies and beyond , 2012, Nature Reviews Genetics.

[30]  Hanlin Gao,et al.  Transcriptome-Wide Survey of Mouse CNS-Derived Cells Reveals Monoallelic Expression within Novel Gene Families , 2012, PloS one.

[31]  Edith Heard,et al.  Fifty years of X-inactivation research , 2011, Development.

[32]  K. Gunderson,et al.  High density DNA methylation array with single CpG site resolution. , 2011, Genomics.

[33]  Andrew J Sharp,et al.  DNA methylation profiles of human active and inactive X chromosomes. , 2011, Genome research.

[34]  W. V. van IJcken,et al.  The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. , 2011, Genes & development.

[35]  Elphège P. Nora,et al.  Regulation of X-chromosome inactivation by the X-inactivation centre , 2011, Nature Reviews Genetics.

[36]  M. Esteller,et al.  Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome , 2011, Epigenetics.

[37]  Ian M. Wilson,et al.  Chromosome-wide DNA methylation analysis predicts human tissue-specific X inactivation , 2011, Human Genetics.

[38]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[39]  William N. Venables,et al.  Modern Applied Statistics with S , 2010 .

[40]  S. Salzberg,et al.  NIH Public Access Author Manuscript , 2006 .

[41]  J. Shendure,et al.  Global survey of escape from X inactivation by RNA-sequencing in mouse. , 2010, Genome research.

[42]  Michael P. Snyder,et al.  X chromosome-wide analyses of genomic DNA methylation states and gene expression in male and female neutrophils , 2010, Proceedings of the National Academy of Sciences.

[43]  Martin J. Aryee,et al.  Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts , 2009, Nature Genetics.

[44]  R. Maronpot Biological Basis of Differential Susceptibility to Hepatocarcinogenesis among Mouse Strains , 2009, Journal of toxicologic pathology.

[45]  Rafael A. Irizarry,et al.  Genome-wide methylation analysis of human colon cancer reveals similar hypo- and hypermethylation at conserved tissue-specific CpG island shores , 2008, Nature Genetics.

[46]  Michael B. Stadler,et al.  Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome , 2007, Nature Genetics.

[47]  A. Chess,et al.  Gene Body-Specific Methylation on the Active X Chromosome , 2007, Science.

[48]  D. Waxman,et al.  Growth hormone regulation of sex-dependent liver gene expression. , 2006, Molecular endocrinology.

[49]  C. Disteche,et al.  Dosage compensation in mammals: fine-tuning the expression of the X chromosome. , 2006, Genes & development.

[50]  J. Rinn,et al.  Sexual dimorphism in mammalian gene expression. , 2005, Trends in genetics : TIG.

[51]  U. Bunz How Are Alkynes Scrambled? , 2005, Science.

[52]  Daiya Takai,et al.  Comprehensive analysis of CpG islands in human chromosomes 21 and 22 , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[53]  V. Chapman,et al.  Escape from X inactivation of Smcx is preceded by silencing during mouse development , 1998, Nature Genetics.

[54]  A. Niveleau,et al.  DNA methylation of the X chromosomes of the human female: an in situ semi-quantitative analysis , 1996, Chromosoma.

[55]  E. Maestrini,et al.  Methylation and sequence analysis around EagI sites: identification of 28 new CpG islands in XQ24-XQ28. , 1992, Nucleic acids research.

[56]  T. Mohandas,et al.  Reactivation of an inactive human X chromosome: evidence for X inactivation by DNA methylation. , 1981, Science.

[57]  R Holliday,et al.  DNA modification mechanisms and gene activity during development , 1975, Science.

[58]  K. Rao,et al.  Development of broad spectrum of tumors by ethylnitrosourea in mice and the modifying role of age, sex, and strain. , 1974, Cancer research.

[59]  S. Vesselinovitch The sex-dependent difference in the development of liver tumors in mice administered dimethylnitrosamine. , 1969, Cancer research.

[60]  M. Lyon Gene Action in the X-chromosome of the Mouse (Mus musculus L.) , 1961, Nature.

[61]  W. Gardner,et al.  The incidence of spontaneous hepatomas in C3H, C3H (low milk factor), and CBA mice and the effect of estrogen and androgen on the occurrence of these tumors in C3H mice. , 1952, Cancer research.

[62]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[63]  M. Waters,et al.  How growth hormone controls growth, obesity and sexual dimorphism. , 2008, Trends in genetics : TIG.

[64]  A. Bird DNA methylation patterns and epigenetic memory. , 2002, Genes & development.

[65]  Alex E. Lash,et al.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..

[66]  P. Jones,et al.  The DNA methylation paradox. , 1999, Trends in genetics : TIG.

[67]  V. Chapman,et al.  Mechanisms of X-chromosome regulation. , 1988, Annual review of genetics.

[68]  Arthur D. Riggs,et al.  X inactivation, differentiation, and DNA methylation. , 1975, Cytogenetics and cell genetics.