|
1
|
Siegel RL, Miller KD and Jemal A: Cancer
statistics, 2015. CA Cancer J Clin. 65:5–29. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
2
|
Hadjihannas MV, Brückner M, Jerchow B,
Birchmeier W, Dietmaier W and Behrens J: Aberrant Wnt/beta-catenin
signaling can induce chromosomal instability in colon cancer. Proc
Natl Acad Sci USA. 103:10747–10752. 2006. View Article : Google Scholar : PubMed/NCBI
|
|
3
|
Niehrs C: Function and biological roles of
the Dickkopf family of Wnt modulators. Oncogene. 25:7469–7481.
2006. View Article : Google Scholar : PubMed/NCBI
|
|
4
|
Yamabuki T, Takano A, Hayama S, Ishikawa
N, Kato T, Miyamoto M, Ito T, Ito H, Miyagi Y, Nakayama H, et al:
Dikkopf-1 as a novel serologic and prognostic biomarker for lung
and esophageal carcinomas. Cancer Res. 67:2517–2525. 2007.
View Article : Google Scholar : PubMed/NCBI
|
|
5
|
Forget MA, Turcotte S, Beauseigle D,
Godin-Ethier J, Pelletier S, Martin J, Tanguay S and Lapointe R:
The Wnt pathway regulator DKK1 is preferentially expressed in
hormone-resistant breast tumours and in some common cancer types.
Br J Cancer. 96:646–653. 2007. View Article : Google Scholar : PubMed/NCBI
|
|
6
|
Xu R, Guo LJ, Xin J, Li WM, Gao Y, Zheng
YX, Guo YH, Lin YJ, Xie YH, Wu YQ and Xu RA: Luciferase assay to
screen tumour-specific promoters in lung cancer. Asian Pac J Cancer
Prev. 14:6557–6562. 2013. View Article : Google Scholar
|
|
7
|
Zhang C, Dai H and de Crombrugghe B:
Characterization of Dkk1 gene regulation by the osteoblast-specific
transcription factor Osx. Biochem Biophys Res Commun. 420:782–786.
2012. View Article : Google Scholar : PubMed/NCBI
|
|
8
|
Chung JH, Bell AC and Felsenfeld G:
Characterization of the chicken beta-globin insulator. Proc Natl
Acad Sci USA. 94:575–580. 1997. View Article : Google Scholar : PubMed/NCBI
|
|
9
|
Niu J, Wang J, Hu H, Chen Y, An J, Cai J,
Sun R, Sheng Z, Liu X and Lin S: Cross-talk between freezing
response and signaling for regulatory transcriptions of MIR475b and
its targets by miR475b promoter in Populus suaveolens. Sci Rep.
6:206482016. View Article : Google Scholar : PubMed/NCBI
|
|
10
|
Naumova N, Smith EM, Zhan Y and Dekker J:
Analysis of long-range chromatin interactions using Chromosome
Conformation Capture. Methods. 58:192–203. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
11
|
Sanyal A, Lajoie BR, Jain G and Dekker J:
The long-range interaction landscape of gene promoters. Nature.
489:109–113. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
12
|
Ecker JR, Bickmore WA, Barroso I,
Pritchard JK, Gilad Y and Segal E: Genomics: ENCODE explained.
Nature. 489:52–55. 2012. View
Article : Google Scholar : PubMed/NCBI
|
|
13
|
Deng T, Zhu ZI, Zhang S, Postnikov Y,
Huang D, Horsch M, Furusawa T, Beckers J, Rozman J, Klingenspor M,
et al: Functional compensation among HMGN variants modulates the
DNase I hypersensitive sites at enhancers. Genome Res.
25:1295–1308. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
14
|
Sherwood RI, Hashimoto T, O'Donnell CW,
Lewis S, Barkal AA, van Hoff JP, Karun V, Jaakkola T and Gifford
DK: Discovery of directional and nondirectional pioneer
transcription factors by modeling DNase profile magnitude and
shape. Nat Biotechnol. 32:171–178. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
15
|
Sotelo J, Esposito D, Duhagon MA, Banfield
K, Mehalko J, Liao H, Stephens RM, Harris TJ, Munroe DJ and Wu X:
Long-range enhancers on 8q24 regulate c-Myc. Proc Natl Acad Sci
USA. 107:3001–3005. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
16
|
Uslu VV, Petretich M, Ruf S, Langenfeld K,
Fonseca NA, Marioni JC and Spitz F: Long-range enhancers regulating
Myc expression are required for normal facial morphogenesis. Nat
Genet. 46:753–758. 2014. View
Article : Google Scholar : PubMed/NCBI
|
|
17
|
Khurana E, Fu Y, Chakravarty D, Demichelis
F, Rubin MA and Gerstein M: Role of non-coding sequence variants in
cancer. Nat Rev Genet. 17:93–108. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
18
|
Wang Z, Zang C, Rosenfeld JA, Schones DE,
Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ and Zhao K:
Combinatorial patterns of histone acetylations and methylations in
the human genome. Nat Genet. 40:897–903. 2008. View Article : Google Scholar : PubMed/NCBI
|
|
19
|
Schones DE and Zhao K: Genome-wide
approaches to studying chromatin modifications. Nat Rev Genet.
9:179–191. 2008. View
Article : Google Scholar : PubMed/NCBI
|
|
20
|
Zhou VW, Goren A and Bernstein BE:
Charting histone modifications and the functional organization of
mammalian genomes. Nat Rev Genet. 12:7–18. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
21
|
Ernst J and Kellis M: Large-scale
imputation of epigenomic datasets for systematic annotation of
diverse human tissues. Nat Biotechnol. 33:364–376. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
22
|
Gallo SM, Gerrard DT, Miner D, Simich M,
Des Soye B, Bergman CM and Halfon MS: REDfly v3.0: Toward a
comprehensive database of transcriptional regulatory elements in
Drosophila. Nucleic Acids Res. 39:(Database Issue). D118–D123.
2011. View Article : Google Scholar : PubMed/NCBI
|
|
23
|
ENCODE Project Consortium: A user's guide
to the encyclopedia of DNA elements (ENCODE). PLoS Biol.
9:e10010462011. View Article : Google Scholar : PubMed/NCBI
|
|
24
|
Bell AC, West AG and Felsenfeld G: The
protein CTCF is required for the enhancer blocking activity of
vertebrate insulators. Cell. 98:387–396. 1999. View Article : Google Scholar : PubMed/NCBI
|
|
25
|
Cuddapah S, Jothi R, Schones DE, Roh TY,
Cui K and Zhao K: Global analysis of the insulator binding protein
CTCF in chromatin barrier regions reveals demarcation of active and
repressive domains. Genome Res. 19:24–32. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
26
|
Petrykowska HM, Vockley CM and Elnitski L:
Detection and characterization of silencers and enhancer-blockers
in the greater CFTR locus. Genome Res. 18:1238–1246. 2008.
View Article : Google Scholar : PubMed/NCBI
|
|
27
|
Talbot D and Grosveld F: The 5′HS2 of the
globin locus control region enhances transcription through the
interaction of a multimeric complex binding at two functionally
distinct NF-E2 binding sites. EMBO J. 10:1391–1398. 1991.PubMed/NCBI
|
|
28
|
Elnitski L, Miller W and Hardison R:
Conserved E boxes function as part of the enhancer in
hypersensitive site 2 of the beta-globin locus control region role
of basic helix-loop-helix proteins. J Biol Chem. 272:369–378. 1997.
View Article : Google Scholar : PubMed/NCBI
|
|
29
|
Heintzman ND, Stuart RK, Hon G, Fu Y,
Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, et
al: Distinct and predictive chromatin signatures of transcriptional
promoters and enhancers in the human genome. Nat Genet. 39:311–318.
2007. View
Article : Google Scholar : PubMed/NCBI
|
|
30
|
Wu C, Chen Z, Dardalhon V, Xiao S,
Thalhamer T, Liao M, Madi A, Franca RF, Han T, Oukka M and Kuchroo
V: The transcription factor musculin promotes the unidirectional
development of peripheral Treg cells by suppressing the TH2
transcriptional program. Nat Immunol. 18:344–353. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
31
|
Fleetwood MR, Ho Y, Cooke NE and Liebhaber
SA: DNase I hypersensitive site II of the human growth hormone
locus control region mediates an essential and distinct long-range
enhancer function. J Biol Chem. 287:25454–25465. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
32
|
Jane SM, Ney PA, Vanin EF, Gumucio DL and
Nienhuis AW: Identification of a stage selector element in the
human gamma-globin gene promoter that fosters preferential
interaction with the 5′HS2 enhancer when in competition with the
beta-promoter. EMBO J. 11:2961–2969. 1992.PubMed/NCBI
|
|
33
|
Mina M, Magi S, Jurman G, Itoh M, Kawaji
H, Lassmann T, Arner E, Forrest AR, Carninci P, Hayashizaki Y, et
al: Promoter-level expression clustering identifies time
development of transcriptional regulatory cascades initiated by
ErbB receptors in breast cancer cells. Sci Rep. 5:119992015.
View Article : Google Scholar : PubMed/NCBI
|
|
34
|
Schoenfelder S, Furlan-Magaril M, Mifsud
B, Tavares-Cadete F, Sugar R, Javierre BM, Nagano T, Katsman Y,
Sakthidevi M, Wingett SW, et al: The pluripotent regulatory
circuitry connecting promoters to their long-range interacting
elements. Genome Res. 25:582–597. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
35
|
Wittkopp PJ and Kalay G: Cis-regulatory
elements: Molecular mechanisms and evolutionary processes
underlying divergence. Nat Rev Genet. 13:59–69. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
36
|
Barski A, Cuddapah S, Cui K, Roh TY,
Schones DE, Wang Z, Wei G, Chepelev I and Zhao K: High-resolution
profiling of histone methylations in the human genome. Cell.
129:823–837. 2007. View Article : Google Scholar : PubMed/NCBI
|
|
37
|
Visel A, Prabhakar S, Akiyama JA, Shoukry
M, Lewis KD, Holt A, Plajzer-Frick I, Afzal V, Rubin EM and
Pennacchio LA: Ultraconservation identifies a small subset of
extremely constrained developmental enhancers. Nat Genet.
40:158–160. 2008. View Article : Google Scholar : PubMed/NCBI
|
|
38
|
Blow MJ, McCulley DJ, Li Z, Zhang T,
Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F,
et al: ChIP-Seq identification of weakly conserved heart enhancers.
Nat Genet. 42:806–810. 2010. View
Article : Google Scholar : PubMed/NCBI
|
|
39
|
Heintzman ND, Hon GC, Hawkins RD,
Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW,
et al: Histone modifications at human enhancers reflect global
cell-type-specific gene expression. Nature. 459:108–112. 2009.
View Article : Google Scholar : PubMed/NCBI
|
|
40
|
Wendt KS, Yoshida K, Itoh T, Bando M, Koch
B, Schirghuber E, Tsutsumi S, Nagae G, Ishihara K, Mishiro T, et
al: Cohesin mediates transcriptional insulation by CCCTC-binding
factor. Nature. 451:796–801. 2008. View Article : Google Scholar : PubMed/NCBI
|
|
41
|
Ernst J, Kheradpour P, Mikkelsen TS,
Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M,
et al: Mapping and analysis of chromatin state dynamics in nine
human cell types. Nature. 473:43–49. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
42
|
Rada-Iglesias A, Bajpai R, Swigut T,
Brugmann SA, Flynn RA and Wysocka J: A unique chromatin signature
uncovers early developmental enhancers in humans. Nature.
470:279–283. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
43
|
Pougach K, Voet A, Kondrashov FA,
Voordeckers K, Christiaens JF, Baying B, Benes V, Sakai R, Aerts J,
Zhu B, et al: Duplication of a promiscuous transcription factor
drives the emergence of a new regulatory network. Nat Commun.
5:48682014. View Article : Google Scholar : PubMed/NCBI
|
|
44
|
Canver MC, Smith EC, Sher F, Pinello L,
Sanjana NE, Shalem O, Chen DD, Schupp PG, Vinjamur DS, Garcia SP,
et al: BCL11A enhancer dissection by Cas9-mediated in situ
saturating mutagenesis. Nature. 527:192–197. 2015. View Article : Google Scholar : PubMed/NCBI
|
