-
1
-
-
84901029300
-
X chromosome regulation: diverse patterns in development, tissues and disease
-
Deng X, Berletch JB, Nguyen DK, Disteche CM, (2014) X chromosome regulation: diverse patterns in development, tissues and disease. Nat Rev Genet 15: 367–378. doi: 10.1038/nrg3687 24733023
-
(2014)
Nat Rev Genet
, vol.15
, pp. 367-378
-
-
Deng, X.1
Berletch, J.B.2
Nguyen, D.K.3
Disteche, C.M.4
-
2
-
-
84884331196
-
X chromosome inactivation and epigenetic responses to cellular reprogramming
-
Lessing D, Anguera MC, Lee JT, (2013) X chromosome inactivation and epigenetic responses to cellular reprogramming. Annu Rev Genomics Hum Genet 14: 85–110. doi: 10.1146/annurev-genom-091212-153530 23662665
-
(2013)
Annu Rev Genomics Hum Genet
, vol.14
, pp. 85-110
-
-
Lessing, D.1
Anguera, M.C.2
Lee, J.T.3
-
3
-
-
79961023530
-
Genes that escape from X inactivation
-
Berletch JB, Yang F, Xu J, Carrel L, Disteche CM, (2011) Genes that escape from X inactivation. Hum Genet 130: 237–245. doi: 10.1007/s00439-011-1011-z 21614513
-
(2011)
Hum Genet
, vol.130
, pp. 237-245
-
-
Berletch, J.B.1
Yang, F.2
Xu, J.3
Carrel, L.4
Disteche, C.M.5
-
4
-
-
84904060948
-
Variable escape from X-chromosome inactivation: Identifying factors that tip the scales towards expression
-
Peeters SB, Cotton AM, Brown CJ, (2014) Variable escape from X-chromosome inactivation: Identifying factors that tip the scales towards expression. Bioessays
-
(2014)
Bioessays
-
-
Peeters, S.B.1
Cotton, A.M.2
Brown, C.J.3
-
5
-
-
0036524026
-
Variability of X chromosome inactivation: effect on levels of TIMP1 RNA and role of DNA methylation
-
Anderson CL, Brown CJ, (2002) Variability of X chromosome inactivation: effect on levels of TIMP1 RNA and role of DNA methylation. Hum Genet 110: 271–278. 11935340
-
(2002)
Hum Genet
, vol.110
, pp. 271-278
-
-
Anderson, C.L.1
Brown, C.J.2
-
6
-
-
15244353967
-
X-inactivation profile reveals extensive variability in X-linked gene expression in females
-
Carrel L, Willard HF, (2005) X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 434: 400–404. 15772666
-
(2005)
Nature
, vol.434
, pp. 400-404
-
-
Carrel, L.1
Willard, H.F.2
-
7
-
-
84886735355
-
Analysis of expressed SNPs identifies variable extents of expression from the human inactive X chromosome
-
Cotton AM, Ge B, Light N, Adoue V, Pastinen T, et al. (2013) Analysis of expressed SNPs identifies variable extents of expression from the human inactive X chromosome. Genome Biol 14: R122. doi: 10.1186/gb-2013-14-11-r122 24176135
-
(2013)
Genome Biol
, vol.14
, pp. 122
-
-
Cotton, A.M.1
Ge, B.2
Light, N.3
Adoue, V.4
Pastinen, T.5
-
8
-
-
33846055706
-
Care of girls and women with Turner syndrome: a guideline of the Turner Syndrome Study Group
-
Bondy CA, (2007) Care of girls and women with Turner syndrome: a guideline of the Turner Syndrome Study Group. J Clin Endocrinol Metab 92: 10–25. 17047017
-
(2007)
J Clin Endocrinol Metab
, vol.92
, pp. 10-25
-
-
Bondy, C.A.1
-
9
-
-
0027475040
-
Turner syndrome: the case of the missing sex chromosome
-
Zinn AR, Page DC, Fisher EM, (1993) Turner syndrome: the case of the missing sex chromosome. Trends Genet 9: 90–93. 8488568
-
(1993)
Trends Genet
, vol.9
, pp. 90-93
-
-
Zinn, A.R.1
Page, D.C.2
Fisher, E.M.3
-
10
-
-
67849113929
-
Identification of the chromatin regions coated by non-coding Xist RNA
-
Murakami K, Ohhira T, Oshiro E, Qi D, Oshimura M, et al. (2009) Identification of the chromatin regions coated by non-coding Xist RNA. Cytogenet Genome Res 125: 19–25. doi: 10.1159/000207514 19617692
-
(2009)
Cytogenet Genome Res
, vol.125
, pp. 19-25
-
-
Murakami, K.1
Ohhira, T.2
Oshiro, E.3
Qi, D.4
Oshimura, M.5
-
11
-
-
84879642373
-
The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome
-
Engreitz JM, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, et al. (2013) The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 341: 1237973. doi: 10.1126/science.1237973 23828888
-
(2013)
Science
, vol.341
, pp. 1237973
-
-
Engreitz, J.M.1
Pandya-Jones, A.2
McDonel, P.3
Shishkin, A.4
Sirokman, K.5
-
12
-
-
84890549512
-
High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation
-
Simon MD, Pinter SF, Fang R, Sarma K, Rutenberg-Schoenberg M, et al. (2013) High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation. Nature 504: 465–469. doi: 10.1038/nature12719 24162848
-
(2013)
Nature
, vol.504
, pp. 465-469
-
-
Simon, M.D.1
Pinter, S.F.2
Fang, R.3
Sarma, K.4
Rutenberg-Schoenberg, M.5
-
13
-
-
0036337759
-
Differentially methylated forms of histone H3 show unique association patterns with inactive human X chromosomes
-
Boggs BA, Cheung P, Heard E, Spector DL, Chinault AC, et al. (2002) Differentially methylated forms of histone H3 show unique association patterns with inactive human X chromosomes. Nat Genet 30: 73–76. 11740495
-
(2002)
Nat Genet
, vol.30
, pp. 73-76
-
-
Boggs, B.A.1
Cheung, P.2
Heard, E.3
Spector, D.L.4
Chinault, A.C.5
-
14
-
-
84870009618
-
Site-specific silencing of regulatory elements as a mechanism of X inactivation
-
Calabrese JM, Sun W, Song L, Mugford JW, Williams L, et al. (2012) Site-specific silencing of regulatory elements as a mechanism of X inactivation. Cell 151: 951–963. doi: 10.1016/j.cell.2012.10.037 23178118
-
(2012)
Cell
, vol.151
, pp. 951-963
-
-
Calabrese, J.M.1
Sun, W.2
Song, L.3
Mugford, J.W.4
Williams, L.5
-
15
-
-
78649720674
-
Genome-wide distribution of macroH2A1 histone variants in mouse liver chromatin
-
Changolkar LN, Singh G, Cui K, Berletch JB, Zhao K, et al. (2010) Genome-wide distribution of macroH2A1 histone variants in mouse liver chromatin. Mol Cell Biol 30: 5473–5483. doi: 10.1128/MCB.00518-10 20937776
-
(2010)
Mol Cell Biol
, vol.30
, pp. 5473-5483
-
-
Changolkar, L.N.1
Singh, G.2
Cui, K.3
Berletch, J.B.4
Zhao, K.5
-
16
-
-
0033598745
-
Promoter-specific hypoacetylation of X-inactivated genes
-
Gilbert SL, Sharp PA, (1999) Promoter-specific hypoacetylation of X-inactivated genes. Proc Natl Acad Sci U S A 96: 13825–13830. 10570157
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 13825-13830
-
-
Gilbert, S.L.1
Sharp, P.A.2
-
17
-
-
38449089882
-
Trimethylation of histone H3 lysine 4 is an epigenetic mark at regions escaping mammalian X inactivation
-
Khalil AM, Driscoll DJ, (2007) Trimethylation of histone H3 lysine 4 is an epigenetic mark at regions escaping mammalian X inactivation. Epigenetics 2: 114–118. 17965609
-
(2007)
Epigenetics
, vol.2
, pp. 114-118
-
-
Khalil, A.M.1
Driscoll, D.J.2
-
18
-
-
77951794067
-
Global survey of escape from X inactivation by RNA-sequencing in mouse
-
Yang F, Babak T, Shendure J, Disteche CM, (2010) Global survey of escape from X inactivation by RNA-sequencing in mouse. Genome Res 20: 614–622. doi: 10.1101/gr.103200.109 20363980
-
(2010)
Genome Res
, vol.20
, pp. 614-622
-
-
Yang, F.1
Babak, T.2
Shendure, J.3
Disteche, C.M.4
-
19
-
-
79961022818
-
Chromosome-wide DNA methylation analysis predicts human tissue-specific X inactivation
-
Cotton AM, Lam L, Affleck JG, Wilson IM, Penaherrera MS, et al. (2011) Chromosome-wide DNA methylation analysis predicts human tissue-specific X inactivation. Hum Genet 130: 187–201. doi: 10.1007/s00439-011-1007-8 21597963
-
(2011)
Hum Genet
, vol.130
, pp. 187-201
-
-
Cotton, A.M.1
Lam, L.2
Affleck, J.G.3
Wilson, I.M.4
Penaherrera, M.S.5
-
20
-
-
84879663784
-
Global epigenomic reconfiguration during mammalian brain development
-
Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, et al. (2013) Global epigenomic reconfiguration during mammalian brain development. Science 341: 1237905. doi: 10.1126/science.1237905 23828890
-
(2013)
Science
, vol.341
, pp. 1237905
-
-
Lister, R.1
Mukamel, E.A.2
Nery, J.R.3
Urich, M.4
Puddifoot, C.A.5
-
21
-
-
11244258156
-
Boundaries between chromosomal domains of X inactivation and escape bind CTCF and lack CpG methylation during early development
-
Filippova GN, Cheng MK, Moore JM, Truong JP, Hu YJ, et al. (2005) Boundaries between chromosomal domains of X inactivation and escape bind CTCF and lack CpG methylation during early development. Dev Cell 8: 31–42. 15669143
-
(2005)
Dev Cell
, vol.8
, pp. 31-42
-
-
Filippova, G.N.1
Cheng, M.K.2
Moore, J.M.3
Truong, J.P.4
Hu, Y.J.5
-
22
-
-
55949099351
-
Escape from X chromosome inactivation is an intrinsic property of the Jarid1c locus
-
Li N, Carrel L, (2008) Escape from X chromosome inactivation is an intrinsic property of the Jarid1c locus. Proc Natl Acad Sci U S A 105: 17055–17060. doi: 10.1073/pnas.0807765105 18971342
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 17055-17060
-
-
Li, N.1
Carrel, L.2
-
23
-
-
0032014618
-
Escape from X inactivation of Smcx is preceded by silencing during mouse development
-
Lingenfelter PA, Adler DA, Poslinski D, Thomas S, Elliott RW, et al. (1998) Escape from X inactivation of Smcx is preceded by silencing during mouse development. Nat Genet 18: 212–213. 9500539
-
(1998)
Nat Genet
, vol.18
, pp. 212-213
-
-
Lingenfelter, P.A.1
Adler, D.A.2
Poslinski, D.3
Thomas, S.4
Elliott, R.W.5
-
24
-
-
84897575650
-
Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta
-
Finn EH, Smith CL, Rodriguez J, Sidow A, Baker JC, (2014) Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta. Dev Biol 390: 80–92. doi: 10.1016/j.ydbio.2014.02.020 24594094
-
(2014)
Dev Biol
, vol.390
, pp. 80-92
-
-
Finn, E.H.1
Smith, C.L.2
Rodriguez, J.3
Sidow, A.4
Baker, J.C.5
-
25
-
-
84891818179
-
Cellular resolution maps of x chromosome inactivation: implications for neural development, function, and disease
-
Wu H, Luo J, Yu H, Rattner A, Mo A, et al. (2014) Cellular resolution maps of x chromosome inactivation: implications for neural development, function, and disease. Neuron 81: 103–119. doi: 10.1016/j.neuron.2013.10.051 24411735
-
(2014)
Neuron
, vol.81
, pp. 103-119
-
-
Wu, H.1
Luo, J.2
Yu, H.3
Rattner, A.4
Mo, A.5
-
26
-
-
84876420573
-
Mammalian X Upregulation Is Associated with Enhanced Transcription Initiation, RNA Half-Life, and MOF-Mediated H4K16 Acetylation
-
Deng X, Berletch JB, Ma W, Nguyen DK, Hiatt JB, et al. (2013) Mammalian X Upregulation Is Associated with Enhanced Transcription Initiation, RNA Half-Life, and MOF-Mediated H4K16 Acetylation. Dev Cell S1534–5807(13)00101–9 [pii] 10.1016/j.devcel.2013.01.028.
-
(2013)
Dev Cell
, vol.S1534–5807
, Issue.13
, pp. 00101-109
-
-
Deng, X.1
Berletch, J.B.2
Ma, W.3
Nguyen, D.K.4
Hiatt, J.B.5
-
27
-
-
60749087716
-
A proximal conserved repeat in the Xist gene is essential as a genomic element for X-inactivation in mouse
-
Hoki Y, Kimura N, Kanbayashi M, Amakawa Y, Ohhata T, et al. (2009) A proximal conserved repeat in the Xist gene is essential as a genomic element for X-inactivation in mouse. Development 136: 139–146. doi: 10.1242/dev.026427 19036803
-
(2009)
Development
, vol.136
, pp. 139-146
-
-
Hoki, Y.1
Kimura, N.2
Kanbayashi, M.3
Amakawa, Y.4
Ohhata, T.5
-
28
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520–562. 12466850
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
Waterston, R.H.1
Lindblad-Toh, K.2
Birney, E.3
Rogers, J.4
Abril, J.F.5
-
29
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511–515. doi: 10.1038/nbt.1621 20436464
-
(2010)
Nat Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
-
30
-
-
84868515935
-
Abundance of female-biased and paucity of male-biased somatically expressed genes on the mouse X-chromosome
-
Reinius B, Johansson MM, Radomska KJ, Morrow EH, Pandey GK, et al. (2012) Abundance of female-biased and paucity of male-biased somatically expressed genes on the mouse X-chromosome. BMC Genomics 13: 607. doi: 10.1186/1471-2164-13-607 23140559
-
(2012)
BMC Genomics
, vol.13
, pp. 607
-
-
Reinius, B.1
Johansson, M.M.2
Radomska, K.J.3
Morrow, E.H.4
Pandey, G.K.5
-
31
-
-
79952254021
-
Clcn4–2 genomic structure differs between the X locus in Mus spretus and the autosomal locus in Mus musculus: AT motif enrichment on the X
-
Nguyen DK, Yang F, Kaul R, Alkan C, Antonellis A, et al. (2011) Clcn4–2 genomic structure differs between the X locus in Mus spretus and the autosomal locus in Mus musculus: AT motif enrichment on the X. Genome Res 21: 402–409. doi: 10.1101/gr.108563.110 21282478
-
(2011)
Genome Res
, vol.21
, pp. 402-409
-
-
Nguyen, D.K.1
Yang, F.2
Kaul, R.3
Alkan, C.4
Antonellis, A.5
-
32
-
-
84873721021
-
A critical role for the cholesterol-associated proteolipids PLP and M6B in myelination of the central nervous system
-
Werner HB, Kramer-Albers EM, Strenzke N, Saher G, Tenzer S, et al. (2013) A critical role for the cholesterol-associated proteolipids PLP and M6B in myelination of the central nervous system. Glia 61: 567–586. doi: 10.1002/glia.22456 23322581
-
(2013)
Glia
, vol.61
, pp. 567-586
-
-
Werner, H.B.1
Kramer-Albers, E.M.2
Strenzke, N.3
Saher, G.4
Tenzer, S.5
-
33
-
-
84882595827
-
X-linked intellectual disability-associated mutations in synaptophysin disrupt synaptobrevin II retrieval
-
Gordon SL, Cousin MA, (2013) X-linked intellectual disability-associated mutations in synaptophysin disrupt synaptobrevin II retrieval. J Neurosci 33: 13695–13700. doi: 10.1523/JNEUROSCI.0636-13.2013 23966691
-
(2013)
J Neurosci
, vol.33
, pp. 13695-13700
-
-
Gordon, S.L.1
Cousin, M.A.2
-
34
-
-
81955167470
-
Novel GDI1 mutation in a large family with nonsyndromic X-linked intellectual disability
-
Strobl-Wildemann G, Kalscheuer VM, Hu H, Wrogemann K, Ropers HH, et al. (2011) Novel GDI1 mutation in a large family with nonsyndromic X-linked intellectual disability. Am J Med Genet A 155A: 3067–3070. doi: 10.1002/ajmg.a.34291 22002931
-
(2011)
Am J Med Genet A
, vol.155A
, pp. 3067-3070
-
-
Strobl-Wildemann, G.1
Kalscheuer, V.M.2
Hu, H.3
Wrogemann, K.4
Ropers, H.H.5
-
35
-
-
79953274733
-
Impaired striatum-dependent behavior in GASP-1-knock-out mice
-
Mathis C, Bott JB, Candusso MP, Simonin F, Cassel JC, (2011) Impaired striatum-dependent behavior in GASP-1-knock-out mice. Genes Brain Behav 10: 299–308. doi: 10.1111/j.1601-183X.2010.00666.x 21091868
-
(2011)
Genes Brain Behav
, vol.10
, pp. 299-308
-
-
Mathis, C.1
Bott, J.B.2
Candusso, M.P.3
Simonin, F.4
Cassel, J.C.5
-
36
-
-
80054678987
-
Increased levels of thymosin beta4 in synovial fluid of patients with rheumatoid arthritis: association of thymosin beta4 with other factors that are involved in inflammation and bone erosion in joints
-
Choi HM, Lee YA, Yang HI, Yoo MC, Kim KS, (2011) Increased levels of thymosin beta4 in synovial fluid of patients with rheumatoid arthritis: association of thymosin beta4 with other factors that are involved in inflammation and bone erosion in joints. Int J Rheum Dis 14: 320–324. doi: 10.1111/j.1756-185X.2011.01652.x 22004227
-
(2011)
Int J Rheum Dis
, vol.14
, pp. 320-324
-
-
Choi, H.M.1
Lee, Y.A.2
Yang, H.I.3
Yoo, M.C.4
Kim, K.S.5
-
37
-
-
84874951084
-
CRIg signals induce anti-intracellular bacterial phagosome activity in a chloride intracellular channel 3-dependent manner
-
Kim KH, Choi BK, Song KM, Cha KW, Kim YH, et al. (2013) CRIg signals induce anti-intracellular bacterial phagosome activity in a chloride intracellular channel 3-dependent manner. Eur J Immunol 43: 667–678. doi: 10.1002/eji.201242997 23280470
-
(2013)
Eur J Immunol
, vol.43
, pp. 667-678
-
-
Kim, K.H.1
Choi, B.K.2
Song, K.M.3
Cha, K.W.4
Kim, Y.H.5
-
38
-
-
84880792563
-
Properdin in complement activation and tissue injury
-
Lesher AM, Nilsson B, Song WC, (2013) Properdin in complement activation and tissue injury. Mol Immunol 56: 191–198. doi: 10.1016/j.molimm.2013.06.002 23816404
-
(2013)
Mol Immunol
, vol.56
, pp. 191-198
-
-
Lesher, A.M.1
Nilsson, B.2
Song, W.C.3
-
39
-
-
78649856319
-
The proteoglycan biglycan regulates expression of the B cell chemoattractant CXCL13 and aggravates murine lupus nephritis
-
Moreth K, Brodbeck R, Babelova A, Gretz N, Spieker T, et al. (2010) The proteoglycan biglycan regulates expression of the B cell chemoattractant CXCL13 and aggravates murine lupus nephritis. J Clin Invest 120: 4251–4272. doi: 10.1172/JCI42213 21084753
-
(2010)
J Clin Invest
, vol.120
, pp. 4251-4272
-
-
Moreth, K.1
Brodbeck, R.2
Babelova, A.3
Gretz, N.4
Spieker, T.5
-
40
-
-
84864779894
-
Function of the sex chromosomes in mammalian fertility
-
Heard E, Turner J, (2011) Function of the sex chromosomes in mammalian fertility. Cold Spring Harbor perspectives in biology 3: a002675. doi: 10.1101/cshperspect.a002675 21730045
-
(2011)
Cold Spring Harbor perspectives in biology
, vol.3
, pp. 002675
-
-
Heard, E.1
Turner, J.2
-
41
-
-
79955550445
-
A user's guide to the encyclopedia of DNA elements (ENCODE)
-
Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE, Gingeras TR, Kent WJ, Birney E, ENCODE Project Consortium MR, et al. (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9: e1001046. doi: 10.1371/journal.pbio.1001046 21526222
-
(2011)
PLoS Biol
, vol.9
, pp. 1001046
-
-
Stamatoyannopoulos, J.1
Snyder, M.2
Dunham, I.3
Hardison, R.C.4
Bernstein, B.E.5
Gingeras, T.R.6
Kent, W.J.7
Birney, E.8
-
42
-
-
84893767092
-
Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre
-
Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, et al. (2014) Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol 21: 198–206. doi: 10.1038/nsmb.2764 24463464
-
(2014)
Nat Struct Mol Biol
, vol.21
, pp. 198-206
-
-
Hacisuleyman, E.1
Goff, L.A.2
Trapnell, C.3
Williams, A.4
Henao-Mejia, J.5
-
43
-
-
79959952919
-
The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA
-
Splinter E, de Wit E, Nora EP, Klous P, van de Werken HJ, et al. (2011) The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. Genes Dev 25: 1371–1383. doi: 10.1101/gad.633311 21690198
-
(2011)
Genes Dev
, vol.25
, pp. 1371-1383
-
-
Splinter, E.1
de Wit, E.2
Nora, E.P.3
Klous, P.4
van de Werken, H.J.5
-
44
-
-
84885060271
-
Genomewide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions
-
Prickett AR, Barkas N, McCole RB, Hughes S, Amante SM, et al. (2013) Genomewide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions. Genome Res gr.150136.112 [pii] 10.1101/gr.150136.112.
-
(2013)
Genome Res gr.150136.112
-
-
Prickett, A.R.1
Barkas, N.2
McCole, R.B.3
Hughes, S.4
Amante, S.M.5
-
45
-
-
55749094855
-
An integrated software system for analyzing ChIP-chip and ChIP-seq data
-
Ji H, Jiang H, Ma W, Johnson DS, Myers RM, et al. (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 26: 1293–1300. doi: 10.1038/nbt.1505 18978777
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1293-1300
-
-
Ji, H.1
Jiang, H.2
Ma, W.3
Johnson, D.S.4
Myers, R.M.5
-
46
-
-
79957448422
-
The analysis of ChIP-Seq data
-
Ma W, Wong WH, (2011) The analysis of ChIP-Seq data. Methods Enzymol 497: 51–73. doi: 10.1016/B978-0-12-385075-1.00003-2 21601082
-
(2011)
Methods Enzymol
, vol.497
, pp. 51-73
-
-
Ma, W.1
Wong, W.H.2
-
47
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137. doi: 10.1186/gb-2008-9-9-r137 18798982
-
(2008)
Genome Biol
, vol.9
, pp. 137
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
-
48
-
-
84899415536
-
CTCF: an architectural protein bridging genome topology and function
-
Ong CT, Corces VG, (2014) CTCF: an architectural protein bridging genome topology and function. Nat Rev Genet 15: 234–246. doi: 10.1038/nrg3663 24614316
-
(2014)
Nat Rev Genet
, vol.15
, pp. 234-246
-
-
Ong, C.T.1
Corces, V.G.2
-
49
-
-
84899473294
-
Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators
-
Bellott DW, Hughes JF, Skaletsky H, Brown LG, Pyntikova T, et al. (2014) Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature 508: 494–499. doi: 10.1038/nature13206 24759411
-
(2014)
Nature
, vol.508
, pp. 494-499
-
-
Bellott, D.W.1
Hughes, J.F.2
Skaletsky, H.3
Brown, L.G.4
Pyntikova, T.5
-
50
-
-
84899484057
-
Origins and functional evolution of Y chromosomes across mammals
-
Cortez D, Marin R, Toledo-Flores D, Froidevaux L, Liechti A, et al. (2014) Origins and functional evolution of Y chromosomes across mammals. Nature 508: 488–493. doi: 10.1038/nature13151 24759410
-
(2014)
Nature
, vol.508
, pp. 488-493
-
-
Cortez, D.1
Marin, R.2
Toledo-Flores, D.3
Froidevaux, L.4
Liechti, A.5
-
51
-
-
84897143694
-
Detection of chromosomal breakpoints in patients with developmental delay and speech disorders
-
Utami KH, Hillmer AM, Aksoy I, Chew EG, Teo AS, et al. (2014) Detection of chromosomal breakpoints in patients with developmental delay and speech disorders. PLoS One 9: e90852. doi: 10.1371/journal.pone.0090852 24603971
-
(2014)
PLoS One
, vol.9
, pp. 90852
-
-
Utami, K.H.1
Hillmer, A.M.2
Aksoy, I.3
Chew, E.G.4
Teo, A.S.5
-
52
-
-
6844261193
-
The mouse Mid1 gene: implications for the pathogenesis of Opitz syndrome and the evolution of the mammalian pseudoautosomal region
-
Dal Zotto L, Quaderi NA, Elliott R, Lingerfelter PA, Carrel L, et al. (1998) The mouse Mid1 gene: implications for the pathogenesis of Opitz syndrome and the evolution of the mammalian pseudoautosomal region. Hum Mol Genet 7: 489–499. 9467009
-
(1998)
Hum Mol Genet
, vol.7
, pp. 489-499
-
-
Dal Zotto, L.1
Quaderi, N.A.2
Elliott, R.3
Lingerfelter, P.A.4
Carrel, L.5
-
53
-
-
38149016903
-
Sexually dimorphic gene expression in the heart of mice and men
-
Isensee J, Witt H, Pregla R, Hetzer R, Regitz-Zagrosek V, et al. (2008) Sexually dimorphic gene expression in the heart of mice and men. J Mol Med (Berl) 86: 61–74. 17646949
-
(2008)
J Mol Med (Berl)
, vol.86
, pp. 61-74
-
-
Isensee, J.1
Witt, H.2
Pregla, R.3
Hetzer, R.4
Regitz-Zagrosek, V.5
-
54
-
-
84901440197
-
The number of X chromosomes influences protection from cardiac ischaemia/reperfusion injury in mice: one X is better than two
-
Li J, Chen X, McClusky R, Ruiz-Sundstrom M, Itoh Y, et al. (2014) The number of X chromosomes influences protection from cardiac ischaemia/reperfusion injury in mice: one X is better than two. Cardiovasc Res 102: 375–384. doi: 10.1093/cvr/cvu064 24654234
-
(2014)
Cardiovasc Res
, vol.102
, pp. 375-384
-
-
Li, J.1
Chen, X.2
McClusky, R.3
Ruiz-Sundstrom, M.4
Itoh, Y.5
-
55
-
-
71749101705
-
Sex differences in sex chromosome gene expression in mouse brain
-
Xu J, Burgoyne PS, Arnold AP, (2002) Sex differences in sex chromosome gene expression in mouse brain. Hum Mol Genet 11: 1409–1419. 12023983
-
(2002)
Hum Mol Genet
, vol.11
, pp. 1409-1419
-
-
Xu, J.1
Burgoyne, P.S.2
Arnold, A.P.3
-
56
-
-
49749114829
-
Sex-specific expression of the X-linked histone demethylase gene Jarid1c in brain
-
Xu J, Deng X, Disteche CM, (2008) Sex-specific expression of the X-linked histone demethylase gene Jarid1c in brain. PLoS One 3: e2553. doi: 10.1371/journal.pone.0002553 18596936
-
(2008)
PLoS One
, vol.3
, pp. 2553
-
-
Xu, J.1
Deng, X.2
Disteche, C.M.3
-
57
-
-
43749094750
-
Sex-specific differences in expression of histone demethylases Utx and Uty in mouse brain and neurons
-
Xu J, Deng X, Watkins R, Disteche CM, (2008) Sex-specific differences in expression of histone demethylases Utx and Uty in mouse brain and neurons. J Neurosci 28: 4521–4527. doi: 10.1523/JNEUROSCI.5382-07.2008 18434530
-
(2008)
J Neurosci
, vol.28
, pp. 4521-4527
-
-
Xu, J.1
Deng, X.2
Watkins, R.3
Disteche, C.M.4
-
58
-
-
80054976678
-
The evolution of gene expression levels in mammalian organs
-
Brawand D, Soumillon M, Necsulea A, Julien P, Csardi G, et al. (2011) The evolution of gene expression levels in mammalian organs. Nature 478: 343–348. doi: 10.1038/nature10532 22012392
-
(2011)
Nature
, vol.478
, pp. 343-348
-
-
Brawand, D.1
Soumillon, M.2
Necsulea, A.3
Julien, P.4
Csardi, G.5
-
59
-
-
84859746595
-
Turner syndrome: advances in understanding altered cognition, brain structure and function
-
Knickmeyer RC, (2012) Turner syndrome: advances in understanding altered cognition, brain structure and function. Curr Opin Neurol 25: 144–149. doi: 10.1097/WCO.0b013e3283515e9e 22322416
-
(2012)
Curr Opin Neurol
, vol.25
, pp. 144-149
-
-
Knickmeyer, R.C.1
-
60
-
-
77649137263
-
Autoimmune diseases in women with Turner's syndrome
-
Jorgensen KT, Rostgaard K, Bache I, Biggar RJ, Nielsen NM, et al. (2010) Autoimmune diseases in women with Turner's syndrome. Arthritis Rheum 62: 658–666. doi: 10.1002/art.27270 20187158
-
(2010)
Arthritis Rheum
, vol.62
, pp. 658-666
-
-
Jorgensen, K.T.1
Rostgaard, K.2
Bache, I.3
Biggar, R.J.4
Nielsen, N.M.5
-
61
-
-
0016692463
-
Preferential inactivation of the paternally derived X chromosome in the extraembryonic membranes of the mouse
-
Takagi N, Sasaki M, (1975) Preferential inactivation of the paternally derived X chromosome in the extraembryonic membranes of the mouse. Nature 256: 640–642. 1152998
-
(1975)
Nature
, vol.256
, pp. 640-642
-
-
Takagi, N.1
Sasaki, M.2
-
62
-
-
84894051999
-
Spread of X-chromosome inactivation into autosomal sequences: role for DNA elements, chromatin features and chromosomal domains
-
Cotton AM, Chen CY, Lam LL, Wasserman WW, Kobor MS, et al. (2014) Spread of X-chromosome inactivation into autosomal sequences: role for DNA elements, chromatin features and chromosomal domains. Hum Mol Genet 23: 1211–1223. doi: 10.1093/hmg/ddt513 24158853
-
(2014)
Hum Mol Genet
, vol.23
, pp. 1211-1223
-
-
Cotton, A.M.1
Chen, C.Y.2
Lam, L.L.3
Wasserman, W.W.4
Kobor, M.S.5
-
63
-
-
84859766038
-
A cross-species comparison of escape from X inactivation in Eutheria: implications for evolution of X chromosome inactivation
-
Al Nadaf S, Deakin JE, Gilbert C, Robinson TJ, Graves JA, et al. (2012) A cross-species comparison of escape from X inactivation in Eutheria: implications for evolution of X chromosome inactivation. Chromosoma 121: 71–78. doi: 10.1007/s00412-011-0343-8 21947602
-
(2012)
Chromosoma
, vol.121
, pp. 71-78
-
-
Al Nadaf, S.1
Deakin, J.E.2
Gilbert, C.3
Robinson, T.J.4
Graves, J.A.5
-
64
-
-
84885001955
-
DNA methylation and differentiation: silencing, upregulation and modulation of gene expression
-
Ehrlich M, Lacey M, (2013) DNA methylation and differentiation: silencing, upregulation and modulation of gene expression. Epigenomics 5: 553–568. doi: 10.2217/epi.13.43 24059801
-
(2013)
Epigenomics
, vol.5
, pp. 553-568
-
-
Ehrlich, M.1
Lacey, M.2
-
65
-
-
84882245890
-
Genetic and epigenetic stability of human pluripotent stem cells
-
Lund RJ, Narva E, Lahesmaa R, (2012) Genetic and epigenetic stability of human pluripotent stem cells. Nat Rev Genet 13: 732–744. doi: 10.1038/nrg3271 22965355
-
(2012)
Nat Rev Genet
, vol.13
, pp. 732-744
-
-
Lund, R.J.1
Narva, E.2
Lahesmaa, R.3
-
66
-
-
80053135073
-
Allele-specific distribution of RNA polymerase II on female X chromosomes
-
Kucera KS, Reddy TE, Pauli F, Gertz J, Logan JE, et al. (2011) Allele-specific distribution of RNA polymerase II on female X chromosomes. Hum Mol Genet 20: 3964–3973. doi: 10.1093/hmg/ddr315 21791549
-
(2011)
Hum Mol Genet
, vol.20
, pp. 3964-3973
-
-
Kucera, K.S.1
Reddy, T.E.2
Pauli, F.3
Gertz, J.4
Logan, J.E.5
-
67
-
-
84912078506
-
Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association
-
Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, et al. (2014) Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. PLoS Genet 10: e1004798. doi: 10.1371/journal.pgen.1004798 25411781
-
(2014)
PLoS Genet
, vol.10
, pp. 1004798
-
-
Ding, Z.1
Ni, Y.2
Timmer, S.W.3
Lee, B.K.4
Battenhouse, A.5
-
68
-
-
84921539874
-
Locus-Specific Targeting to the X Chromosome Revealed by the RNA Interactome of CTCF
-
Kung JT, Kesner B, An JY, Ahn JY, Cifuentes-Rojas C, et al. (2015) Locus-Specific Targeting to the X Chromosome Revealed by the RNA Interactome of CTCF. Mol Cell
-
(2015)
Mol Cell
-
-
Kung, J.T.1
Kesner, B.2
An, J.Y.3
Ahn, J.Y.4
Cifuentes-Rojas, C.5
-
69
-
-
65649115253
-
CTCF and its protein partners: divide and rule?
-
Zlatanova J, Caiafa P, (2009) CTCF and its protein partners: divide and rule? J Cell Sci 122: 1275–1284. doi: 10.1242/jcs.039990 19386894
-
(2009)
J Cell Sci
, vol.122
, pp. 1275-1284
-
-
Zlatanova, J.1
Caiafa, P.2
-
70
-
-
84919949716
-
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
-
Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, et al. (2014) A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell 159: 1665–1680. doi: 10.1016/j.cell.2014.11.021 25497547
-
(2014)
Cell
, vol.159
, pp. 1665-1680
-
-
Rao, S.S.1
Huntley, M.H.2
Durand, N.C.3
Stamenova, E.K.4
Bochkov, I.D.5
-
71
-
-
84861095603
-
Topological domains in mammalian genomes identified by analysis of chromatin interactions
-
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, et al. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485: 376–380. doi: 10.1038/nature11082 22495300
-
(2012)
Nature
, vol.485
, pp. 376-380
-
-
Dixon, J.R.1
Selvaraj, S.2
Yue, F.3
Kim, A.4
Li, Y.5
-
72
-
-
84890504911
-
Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments
-
Seitan VC, Faure AJ, Zhan Y, McCord RP, Lajoie BR, et al. (2013) Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments. Genome Res 23: 2066–2077. doi: 10.1101/gr.161620.113 24002784
-
(2013)
Genome Res
, vol.23
, pp. 2066-2077
-
-
Seitan, V.C.1
Faure, A.J.2
Zhan, Y.3
McCord, R.P.4
Lajoie, B.R.5
-
73
-
-
84892934183
-
Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells
-
Zuin J, Dixon JR, van der Reijden MI, Ye Z, Kolovos P, et al. (2014) Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. Proc Natl Acad Sci U S A 111: 996–1001. doi: 10.1073/pnas.1317788111 24335803
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, pp. 996-1001
-
-
Zuin, J.1
Dixon, J.R.2
van der Reijden, M.I.3
Ye, Z.4
Kolovos, P.5
-
74
-
-
84888273443
-
Deletion of an x-inactivation boundary disrupts adjacent gene silencing
-
Horvath LM, Li N, Carrel L, (2013) Deletion of an x-inactivation boundary disrupts adjacent gene silencing. PLoS Genet 9: e1003952. doi: 10.1371/journal.pgen.1003952 24278033
-
(2013)
PLoS Genet
, vol.9
, pp. 1003952
-
-
Horvath, L.M.1
Li, N.2
Carrel, L.3
-
75
-
-
84868335552
-
Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains
-
Van Bortle K, Ramos E, Takenaka N, Yang J, Wahi JE, et al. (2012) Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains. Genome Res 22: 2176–2187. doi: 10.1101/gr.136788.111 22722341
-
(2012)
Genome Res
, vol.22
, pp. 2176-2187
-
-
Van Bortle, K.1
Ramos, E.2
Takenaka, N.3
Yang, J.4
Wahi, J.E.5
-
76
-
-
84916880365
-
Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes
-
Dowen JM, Fan ZP, Hnisz D, Ren G, Abraham BJ, et al. (2014) Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell 159: 374–387. doi: 10.1016/j.cell.2014.09.030 25303531
-
(2014)
Cell
, vol.159
, pp. 374-387
-
-
Dowen, J.M.1
Fan, Z.P.2
Hnisz, D.3
Ren, G.4
Abraham, B.J.5
-
77
-
-
84861100147
-
Spatial partitioning of the regulatory landscape of the X-inactivation centre
-
Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, et al. (2012) Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485: 381–385. doi: 10.1038/nature11049 22495304
-
(2012)
Nature
, vol.485
, pp. 381-385
-
-
Nora, E.P.1
Lajoie, B.R.2
Schulz, E.G.3
Giorgetti, L.4
Okamoto, I.5
-
78
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754–1760. doi: 10.1093/bioinformatics/btp324 19451168
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
79
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25. doi: 10.1186/gb-2009-10-3-r25 19261174
-
(2009)
Genome Biol
, vol.10
, pp. 25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
|