Biology Reference
In-Depth Information
[44] Duan Z, et al. A three-dimensional model of the yeast genome.
Nature 2010;465(7296):363
[64] Vernimmen D, De Gobbi M, Sloane-Stanley JA, Wood WG,
Higgs DR. Long-range chromosomal interactions regulate the
timing of the transition between poised and active gene expression.
EMBO J 2007;26(8):2041
7.
[45] Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromo-
some conformation. Science 2002;295(5558):1306 e 11.
[46] de Wit E, de Laat W. A decade of 3C technologies: insights into
nuclear organization. Genes Dev 2012;26(1):11 e 24.
[47] Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E,
van Steensel B, de Laat W. Nuclear organization of active and
inactive chromatin domains uncovered by chromosome conforma-
tion capture-on-chip (4C). Nat Genet 2006;38(11):1348 e 54.
[48] Zhao Z, et al. Circular chromosome conformation capture (4C)
uncovers extensive networks of epigenetically regulated intra- and
interchromosomal interactions. Nat Genet 2006;38(11):1341 e 7.
[49] Dostie J, et al. Chromosome conformation capture carbon copy
(5C): a massively parallel solution for mapping interactions
between genomic elements. Genome Res 2006;16(10):1299 e 309.
[50] Fullwood MJ, et al. An oestrogen-receptor-alpha-bound human
chromatin interactome. Nature 2009;462(7269):58 e 64.
[51] Sanyal A, Ba ` D, Mart ยด -Renom MA, Dekker J. Chromatin glob-
ules: a common motif of higher order chromosome structure? Curr
Opin Cell Biol 2013;23(3):325 e 31.
[52] Miele A, Dekker J. Long-range chromosomal interactions and gene
regulation. Mol Biosyst 2008;4(11):1046 e 57.
[53] Dekker J. Gene regulation in the third dimension. Science
2008;319(5871):1793
e
51.
[65] Bau D, Sanyal A, Lajoie BR, Capriotti E, Byron M, Lawrence JB,
Dekker J, Marti-Renom MA. The three-dimensional folding of the
alpha-globin gene domain reveals formation of chromatin globules.
Nat Struct Mol Biol 2011;18(1):107 e 14.
[66] Spilianakis CG, Flavell RA. Long-range intrachromosomal inter-
actions in the T helper type 2 cytokine locus. Nat Immunol
2004;5(10):1017 e 27.
[67] Ferraiuolo MA, Rousseau M, Miyamoto C, Shenker S, Wang XQ,
Nadler M, Blanchette M, Dostie J. The three-dimensional archi-
tecture
e
of Hox
cluster
silencing. Nucleic Acids Res
2010;38(21):7472 e 84.
[68] Wang KC, et al. A long noncoding RNA maintains active chro-
matin
to
coordinate
homeotic
gene
expression. Nature
2011;472(7341):120 e 4.
[69] Montavon T, Soshnikova N, Mascrez B, Joye E, Thevenet L,
Splinter E, de Laat W, Spitz F, Duboule D. A regulatory archi-
pelago
controls Hox
genes
transcription
in
digits. Cell
2011;147(5):1132 e 45.
[70] Tan-Wong SM, French JD, Proudfoot NJ, Brown MA. Dynamic
interactions between the promoter and terminator regions of the
mammalian BRCA1
4.
[54] Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction
landscape of gene promoters. Nature 2012;489:109
gene.
Proc Natl Acad
Sci USA
e
5.
[71] Wright JB, Brown SJ, Cole MD. Upregulation of c-MYC in cis
through a large chromatin loop linked to a cancer risk-associated
single-nucleotide polymorphism in colorectal cancer cells. Mol
Cell Biol 2010;30(6):1411 e 20.
[72] Ott CJ, Blackledge NP, Kerschner JL, Leir SH, Crawford GE,
Cotton CU, Harris A. Intronic enhancers coordinate epithelial-
specific looping of the active CFTR locus. Proc Natl Acad Sci USA
2009;106(47):19934 e 9.
[73] Gheldof N, Smith EM, Tabuchi TM, Koch CM, Dunham I,
Stamatoyannopoulos JA, Dekker J. Cell-type-specific long-range
looping interactions identify distant regulatory elements of the
CFTR gene. Nucleic Acids Res 2010;38(13):4325 e 36.
[74] Noordermeer D, et al. Variegated gene expression caused by
cell-specific long-range DNA interactions. Nat Cell Biol 2011;
13(8):944 e 51.
[75] Kocanova S, Kerr EA, Rafique S, Boyle S, Katz E, Caze-Subra S,
Bickmore WA, Bystricky K. Activation of estrogen-responsive
genes does not require their nuclear co-localization. PLoS Genet
2010;6(4):e1000922.
[76] Hakim O, et al. Diverse gene reprogramming events occur in the
same spatial clusters of distal regulatory elements. Genome Res
2011;21(5):697 e 706.
[77] Marshall WF, Straight A, Marko JF, Swedlow J, Dernburg A,
Belmont A, Murray AW, Agard DA, Sedat JW. Interphase chro-
mosomes undergo constrained diffusional motion in living cells.
Curr Biol 1997;7(12):930
2008;105(13):5160
e
13.
[55] Mateos-Langerak J, et al. Spatially confined folding of chromatin
in the interphase nucleus. Proc Natl Acad Sci USA 2009;
106(10):3812 e 7.
[56] Bantignies F, Roure V, Comet I, Leblanc B, Schuettengruber B,
Bonnet J, Tixier V, Mas A, Cavalli G. Polycomb-dependent regu-
latory contacts between distant Hox loci
e
in Drosophila. Cell
2011;144(2):214 e 26.
[57] Tolhuis B, et al. Interactions among Polycomb domains are guided by
chromosome architecture. PLoS Genet 2011;7(3):e1001343.
[58] Osborne CS, et al. Active genes dynamically colocalize to shared
sites of ongoing transcription. Nat Genet 2004;36(10):1065 e 71.
[59] Brown JM, et al. Association between active genes occurs at
nuclear speckles and is modulated by chromatin environment.
J Cell Biol 2008;182(6):1083 e 97.
[60] Bulger M, Groudine M. Looping versus linking: toward a model
for long-distance gene activation. Genes Dev 1999;13(19):
2465 e 77.
[61] Tolhuis B, Palstra RJ, Splinter E, Grosveld F, de Laat W.
Looping and interaction between hypersensitive sites in the
active beta-globin locus. Mol Cell 2002;10(6):1453 e 65.
[62] Drissen R, Palstra RJ, Gillemans N, Splinter E, Grosveld F,
Philipsen S, de Laat W. The active spatial organization of the beta-
globin locus requires the transcription factor EKLF. Genes Dev
2004;18(20):2485
90.
[63] Vakoc CR, Letting DL, Gheldof N, Sawado T, Bender MA,
Groudine M, Weiss MJ, Dekker J, Blobel GA. Proximity
among distant regulatory elements at the beta-globin locus
requires GATA-1 and FOG-1. Mol Cell 2005;17(3):453 e 62.
e
9.
[78] Chubb JR, Boyle S, Perry P, Bickmore WA. Chromatin motion is
constrained by association with nuclear compartments in human
cells. Curr Biol 2002;12(6):439 e 45.
e
Search WWH ::




Custom Search