69
- Kwasnieski JC, Fiore C, Chaudhari HG, Cohen BA. High-throughput functional testing of
ENCODE segmentation predictions. Genome Res. 2014;24(10):1595–602. - Zhou HY, Katsman Y, Dhaliwal NK, Davidson S, Macpherson NN, Sakthidevi M, et al. A
Sox2 distal enhancer cluster regulates embryonic stem cell differentiation potential. Genes
Dev. 2014;28(24):2699–711. - Li Y, Rivera CM, Ishii H, Jin F, Selvaraj S, Lee AY, et al. CRISPR reveals a distal super-
enhancer required for Sox2 expression in mouse embryonic stem cells. PLoS One.
2014;9(12):e114485. - Lopes R, Korkmaz G, Agami R. Applying CRISPR-Cas9 tools to identify and characterize
transcriptional enhancers. Nat Rev Mol Cell Biol. 2016;17(9):597–604. - Hnisz D, Schuijers J, Lin CY, Weintraub AS, Abraham BJ, Lee TI, et al. Convergence of
developmental and oncogenic signaling pathways at transcriptional super-enhancers. Mol
Cell. 2015;58(2):362–70. - Gröschel S, Sanders MA, Hoogenboezem R, de Wit E, Bouwman BAM, Erpelinck C, et al. A
single oncogenic enhancer rearrangement causes concomitant EVI1and GATA2 deregulation
in leukemia. Cell. 2014;157(2):369–81. - Mansour MR, Abraham BJ, Anders L, Berezovskaya A, Gutierrez A, Durbin AD, et al. An
oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic ele-
ment. Science. 2014;346(6215):1373–7. - Findlay GM, Boyle EA, Hause RJ, Klein JC, Shendure J. Saturation editing of genomic
regions by multiplex homology-directed repair. Nature. 2014;513(7516):120–3. - Canver MC, Smith EC, Sher F, Pinello L, Sanjana NE, Shalem O, et al. BCL11A enhancer
dissection by Cas9-mediated in situ saturating mutagenesis. Nature. 2015;527(7577):192–7. - Korkmaz G, Lopes R, Ugalde AP, Nevedomskaya E, Han R, Myacheva K, et al. Functional
genetic screens for enhancer elements in the human genome using CRISPR-Cas9. Nat
Biotechnol. 2016;34(2):192–8. - Rajagopal N, Srinivasan S, Kooshesh K, Guo Y, Edwards MD, Banerjee B, et al. High-
throughput mapping of regulatory DNA. Nat Biotechnol. 2016;34(2):167–74. - Diao Y, Li B, Meng Z, Jung I, Lee AY, Dixon J, et al. A new class of temporarily phe-
notypic enhancers identified by CRISPR/Cas9-mediated genetic screening. Genome Res.
2016;26(3):397–405. - Fulco CP, Munschauer M, Anyoha R, Munson G, Grossman SR, Perez EM, et al. Systematic
mapping of functional enhancer-promoter connections with CRISPR interference. Science.
2016;354(6313):769–73. - Sanjana NE, Wright J, Zheng K, Shalem O, Fontanillas P, Joung J, et al. High-resolution inter-
rogation of functional elements in the noncoding genome. Science. 2016;353(6307):1545–9. - Feuerborn A, Cook PR. Why the activity of a gene depends on its neighbors. Trends Genet.
2015;31(9):483–90. - Nguyen TA, Jones RD, Snavely AR, Pfenning AR, Kirchner R, Hemberg M, et al. High-
throughput functional comparison of promoter and enhancer activities. Genome Res.
2016;26(8):1023–33. - Goldberg AD, Allis CD, Bernstein E. Epigenetics: a landscape takes shape. Cell.
2007;128(4):635–8. - Waddington CH. The epigenotype. Int J Epidemiol. 2012;41(1):10–3.
- Bonev B, Cavalli G. Organization and function of the 3D genome. Nat Rev Genet.
2016;17(11):661–78. - Berdasco M, Esteller M. Aberrant epigenetic landscape in cancer: how cellular identity goes
awry. Dev Cell. 2010;19(5):698–711. - Reik W. Stability and flexibility of epigenetic gene regulation in mammalian development.
Nature. 2007;447(7143):425–32. - Spivakov M, Fraser P. Defining cell type with chromatin profiling. Nat Biotechnol.
2016;34(11):1126–8.
3 From Reductionism to Holism: Toward a More Complete View of Development...