Precision Medicine, CRISPR, and Genome Engineering Moving from Association to Biology and Therapeutics

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  1. Kwasnieski JC, Fiore C, Chaudhari HG, Cohen BA. High-throughput functional testing of
    ENCODE segmentation predictions. Genome Res. 2014;24(10):1595–602.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Feuerborn A, Cook PR. Why the activity of a gene depends on its neighbors. Trends Genet.
    2015;31(9):483–90.

  16. 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.

  17. Goldberg AD, Allis CD, Bernstein E.  Epigenetics: a landscape takes shape. Cell.
    2007;128(4):635–8.

  18. Waddington CH. The epigenotype. Int J Epidemiol. 2012;41(1):10–3.

  19. Bonev B, Cavalli G.  Organization and function of the 3D genome. Nat Rev Genet.
    2016;17(11):661–78.

  20. Berdasco M, Esteller M. Aberrant epigenetic landscape in cancer: how cellular identity goes
    awry. Dev Cell. 2010;19(5):698–711.

  21. Reik W. Stability and flexibility of epigenetic gene regulation in mammalian development.
    Nature. 2007;447(7143):425–32.

  22. 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...

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