-
1
-
-
84930092058
-
Mapping long-range promoter contacts in human cells with highresolution capture Hi-C
-
Mifsud, B. et al. Mapping long-range promoter contacts in human cells with highresolution capture Hi-C. Nat. Genet. 47, 598-606 (2015).
-
(2015)
Nat. Genet.
, vol.47
, pp. 598-606
-
-
Mifsud, B.1
-
2
-
-
84971406209
-
Chromatin domains: The unit of chromosome organization
-
Dixon, J.R., Gorkin, D.U. & Ren, B. Chromatin domains: the unit of chromosome organization. Mol. Cell 62, 668-680 (2016).
-
(2016)
Mol. Cell
, vol.62
, pp. 668-680
-
-
Dixon, J.R.1
Gorkin, D.U.2
Ren, B.3
-
3
-
-
84923366733
-
Chromatin architecture reorganization during stem cell differentiation
-
Dixon, J.R. et al. Chromatin architecture reorganization during stem cell differentiation. Nature 518, 331-336 (2015).
-
(2015)
Nature
, vol.518
, pp. 331-336
-
-
Dixon, J.R.1
-
4
-
-
84927763931
-
The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements
-
Schoenfelder, S. et al. The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements. Genome Res. 25, 582-597 (2015).
-
(2015)
Genome Res.
, vol.25
, pp. 582-597
-
-
Schoenfelder, S.1
-
5
-
-
84925340676
-
A lncRNA-MAF:MAFB transcription factor network regulates epidermal differentiation
-
Lopez-Pajares, V. et al. A lncRNA-MAF:MAFB transcription factor network regulates epidermal differentiation. Dev. Cell 32, 693-706 (2015).
-
(2015)
Dev. Cell
, vol.32
, pp. 693-706
-
-
Lopez-Pajares, V.1
-
6
-
-
77957139539
-
Mediator and cohesin connect gene expression and chromatin architecture
-
Kagey, M.H. et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 467, 430-435 (2010).
-
(2010)
Nature
, vol.467
, pp. 430-435
-
-
Kagey, M.H.1
-
7
-
-
84957850407
-
3D chromosome regulatory landscape of human pluripotent cells
-
Ji, X. et al. 3D chromosome regulatory landscape of human pluripotent cells. Cell Stem Cell 18, 262-275 (2016).
-
(2016)
Cell Stem Cell
, vol.18
, pp. 262-275
-
-
Ji, X.1
-
8
-
-
84905593782
-
Enhancer loops appear stable during development and are associated with paused polymerase
-
Ghavi-Helm, Y. et al. Enhancer loops appear stable during development and are associated with paused polymerase. Nature 512, 96-100 (2014).
-
(2014)
Nature
, vol.512
, pp. 96-100
-
-
Ghavi-Helm, Y.1
-
9
-
-
84887620842
-
A high-resolution map of the three-dimensional chromatin interactome in human cells
-
Jin, F. et al. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 503, 290-294 (2013).
-
(2013)
Nature
, vol.503
, pp. 290-294
-
-
Jin, F.1
-
10
-
-
84878860751
-
Architectural protein subclasses shape 3D organization of genomes during lineage commitment
-
Phillips-Cremins, J.E. et al. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell 153, 1281-1295 (2013).
-
(2013)
Cell
, vol.153
, pp. 1281-1295
-
-
Phillips-Cremins, J.E.1
-
11
-
-
84919949716
-
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping
-
Rao, S.S.P. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680 (2014).
-
(2014)
Cell
, vol.159
, pp. 1665-1680
-
-
Rao, S.S.P.1
-
12
-
-
78650758676
-
Histone H3K27ac separates active from poised enhancers and predicts developmental state
-
Creyghton, M.P. et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl. Acad. Sci. USA 107, 21931-21936 (2010).
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 21931-21936
-
-
Creyghton, M.P.1
-
13
-
-
79951516056
-
A unique chromatin signature uncovers early developmental enhancers in humans
-
Rada-Iglesias, A. et al. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279-283 (2011).
-
(2011)
Nature
, vol.470
, pp. 279-283
-
-
Rada-Iglesias, A.1
-
14
-
-
78650802901
-
The unique and cooperative roles of the Grainy head-like transcription factors in epidermal development reflect unexpected target gene specificity
-
Boglev, Y. et al. The unique and cooperative roles of the Grainy head-like transcription factors in epidermal development reflect unexpected target gene specificity. Dev. Biol. 349, 512-522 (2011).
-
(2011)
Dev. Biol.
, vol.349
, pp. 512-522
-
-
Boglev, Y.1
-
15
-
-
0018037762
-
The expression of keratin genes in epidermis and cultured epidermal cells
-
Fuchs, E. & Green, H. The expression of keratin genes in epidermis and cultured epidermal cells. Cell 15, 887-897 (1978).
-
(1978)
Cell
, vol.15
, pp. 887-897
-
-
Fuchs, E.1
Green, H.2
-
16
-
-
81855227640
-
A regulatory archipelago controls Hox genes transcription in digits
-
Montavon, T. et al. A regulatory archipelago controls Hox genes transcription in digits. Cell 147, 1132-1145 (2011).
-
(2011)
Cell
, vol.147
, pp. 1132-1145
-
-
Montavon, T.1
-
17
-
-
84911895715
-
Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci
-
Lonfat, N., Montavon, T., Darbellay, F., Gitto, S. & Duboule, D. Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci. Science 346, 1004-1006 (2014).
-
(2014)
Science
, vol.346
, pp. 1004-1006
-
-
Lonfat, N.1
Montavon, T.2
Darbellay, F.3
Gitto, S.4
Duboule, D.5
-
18
-
-
84929211885
-
Pioneer factors govern super-enhancer dynamics in stem cell plasticity and lineage choice
-
Adam, R.C. et al. Pioneer factors govern super-enhancer dynamics in stem cell plasticity and lineage choice. Nature 521, 366-370 (2015).
-
(2015)
Nature
, vol.521
, pp. 366-370
-
-
Adam, R.C.1
-
19
-
-
84865249952
-
Transcription factors: From enhancer binding to developmental control
-
Spitz, F. & Furlong, E.E.M. Transcription factors: from enhancer binding to developmental control. Nat. Rev. Genet. 13, 613-626 (2012).
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 613-626
-
-
Spitz, F.1
Furlong, E.E.M.2
-
20
-
-
84928206081
-
Widespread rearrangement of 3D chromatin organization underlies Polycomb-mediated stress-induced silencing
-
Li, L. et al. Widespread rearrangement of 3D chromatin organization underlies Polycomb-mediated stress-induced silencing. Mol. Cell 58, 216-231 (2015).
-
(2015)
Mol. Cell
, vol.58
, pp. 216-231
-
-
Li, L.1
-
21
-
-
84861095603
-
Topological domains in mammalian genomes identified by analysis of chromatin interactions
-
Dixon, J.R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376-380 (2012).
-
(2012)
Nature
, vol.485
, pp. 376-380
-
-
Dixon, J.R.1
-
22
-
-
84916880365
-
Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes
-
Dowen, J.M. et al. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell 159, 374-387 (2014).
-
(2014)
Cell
, vol.159
, pp. 374-387
-
-
Dowen, J.M.1
-
23
-
-
0032813661
-
Klf4 is A transcription factor required for establishing the barrier function of the skin
-
Segre, J.A., Bauer, C. & Fuchs, E. Klf4 is A transcription factor required for establishing the barrier function of the skin. Nat. Genet. 22, 356-360 (1999).
-
(1999)
Nat. Genet.
, vol.22
, pp. 356-360
-
-
Segre, J.A.1
Bauer, C.2
Fuchs, E.3
-
24
-
-
84907155418
-
ZNF750 interacts with KLF4 and RCOR1, KDM1A, and CTBP1/2 chromatin regulators to repress epidermal progenitor genes and induce differentiation genes
-
Boxer, L.D., Barajas, B., Tao, S., Zhang, J. & Khavari, P.A. ZNF750 interacts with KLF4 and RCOR1, KDM1A, and CTBP1/2 chromatin regulators to repress epidermal progenitor genes and induce differentiation genes. Genes Dev. 28, 2013-2026 (2014).
-
(2014)
Genes Dev.
, vol.28
, pp. 2013-2026
-
-
Boxer, L.D.1
Barajas, B.2
Tao, S.3
Zhang, J.4
Khavari, P.A.5
-
25
-
-
70349652084
-
C/EBP and β couple interfollicular keratinocyte proliferation arrest to commitment and terminal differentiation
-
Lopez, R.G. et al. C/EBP and β couple interfollicular keratinocyte proliferation arrest to commitment and terminal differentiation. Nat. Cell Biol. 11, 1181-1190 (2009).
-
(2009)
Nat. Cell Biol.
, vol.11
, pp. 1181-1190
-
-
Lopez, R.G.1
-
26
-
-
84858293792
-
ZNF750 is A p63 target gene that induces KLF4 to drive terminal epidermal differentiation
-
Sen, G.L. et al. ZNF750 is A p63 target gene that induces KLF4 to drive terminal epidermal differentiation. Dev. Cell 22, 669-677 (2012).
-
(2012)
Dev. Cell
, vol.22
, pp. 669-677
-
-
Sen, G.L.1
-
27
-
-
84976871478
-
UMI-4C for quantitative and targeted chromosomal contact profiling
-
Schwartzman, O. et al. UMI-4C for quantitative and targeted chromosomal contact profiling. Nat. Methods 13, 685-691 (2016).
-
(2016)
Nat. Methods
, vol.13
, pp. 685-691
-
-
Schwartzman, O.1
-
28
-
-
84866975037
-
Foxp3 exploits A pre-existent enhancer landscape for regulatory T cell lineage specification
-
Samstein, R.M. et al. Foxp3 exploits A pre-existent enhancer landscape for regulatory T cell lineage specification. Cell 151, 153-166 (2012).
-
(2012)
Cell
, vol.151
, pp. 153-166
-
-
Samstein, R.M.1
-
29
-
-
84896691636
-
Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity
-
Kim, T.-H. et al. Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity. Nature 506, 511-515 (2014).
-
(2014)
Nature
, vol.506
, pp. 511-515
-
-
Kim, T.-H.1
-
30
-
-
84927621581
-
Ets homologous factor regulates pathways controlling response to injury in airway epithelial cells
-
Fossum, S.L. et al. Ets homologous factor regulates pathways controlling response to injury in airway epithelial cells. Nucleic Acids Res. 42, 13588-13598 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 13588-13598
-
-
Fossum, S.L.1
-
31
-
-
84923362619
-
Integrative analysis of 111 reference human epigenomes
-
Kundaje, A. et al. Integrative analysis of 111 reference human epigenomes. Nature 518, 317-330 (2015).
-
(2015)
Nature
, vol.518
, pp. 317-330
-
-
Kundaje, A.1
-
32
-
-
33751230475
-
P63 regulates proliferation and differentiation of developmentally mature keratinocytes
-
Truong, A.B., Kretz, M., Ridky, T.W., Kimmel, R. & Khavari, P.A. p63 regulates proliferation and differentiation of developmentally mature keratinocytes. Genes Dev. 20, 3185-3197 (2006).
-
(2006)
Genes Dev.
, vol.20
, pp. 3185-3197
-
-
Truong, A.B.1
Kretz, M.2
Ridky, T.W.3
Kimmel, R.4
Khavari, P.A.5
-
33
-
-
84872135457
-
Control of somatic tissue differentiation by the long non-coding RNA TINCR
-
Kretz, M. et al. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature 493, 231-235 (2013).
-
(2013)
Nature
, vol.493
, pp. 231-235
-
-
Kretz, M.1
-
34
-
-
84979753481
-
Dnmt3a and Dnmt3b associate with enhancers to regulate human epidermal stem cell homeostasis
-
Rinaldi, L. et al. Dnmt3a and Dnmt3b associate with enhancers to regulate human epidermal stem cell homeostasis. Cell Stem Cell 19, 491-501 (2016).
-
(2016)
Cell Stem Cell
, vol.19
, pp. 491-501
-
-
Rinaldi, L.1
-
35
-
-
84952861819
-
HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
-
Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259 (2015).
-
(2015)
Genome Biol.
, vol.16
, pp. 259
-
-
Servant, N.1
-
36
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
Huang, W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57 (2009).
-
(2009)
Nat. Protoc.
, vol.4
, pp. 44-57
-
-
Huang, W.1
Sherman, B.T.2
Lempicki, R.A.3
-
37
-
-
84949978453
-
A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63
-
Bao, X. et al. A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63. Genome Biol. 16, 284 (2015).
-
(2015)
Genome Biol.
, vol.16
, pp. 284
-
-
Bao, X.1
-
38
-
-
84969685671
-
HiCUP: Pipeline for mapping and processing Hi-C data
-
Wingett, S. et al. HiCUP: pipeline for mapping and processing Hi-C data. F1000Res 4, 1310 (2015).
-
(2015)
F1000Res
, vol.4
, pp. 1310
-
-
Wingett, S.1
-
39
-
-
84974539482
-
CHiCAGO: Robust detection of DNA looping interactions in Capture Hi-C data
-
Cairns, J. et al. CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data. Genome Biol. 17, 127 (2016).
-
(2016)
Genome Biol.
, vol.17
, pp. 127
-
-
Cairns, J.1
-
40
-
-
75249087100
-
EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson, M.D., McCarthy, D.J. & Smyth, G.K. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
41
-
-
84943388333
-
FourCSeq: Analysis of 4C sequencing data
-
Klein, F.A. et al. FourCSeq: analysis of 4C sequencing data. Bioinformatics 31, 3085-3091 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. 3085-3091
-
-
Klein, F.A.1
-
42
-
-
85018861658
-
Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells
-
Freire-Pritchett, P. et al. Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells. eLife 6, e21926 (2017).
-
(2017)
ELife
, vol.6
, pp. e21926
-
-
Freire-Pritchett, P.1
-
43
-
-
84865777819
-
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
-
Landt, S.G. et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 22, 1813-1831 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 1813-1831
-
-
Landt, S.G.1
|