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Epigenomics Volume 14, 2022 - Issue 11
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Editorial

Developments in High-Throughput Functional Epigenomics: Crispr-Single-Cell Assay for Transposase-Accessible Chromatin using Sequencing Screens

Rachel E Yan1 Weill Cornell Medical College, Department of Neurological Surgery, New York, NY 10021, USAORCID Iconhttps://orcid.org/0000-0002-6718-142X
ORCID Icon,
Jeffrey P Greenfield1 Weill Cornell Medical College, Department of Neurological Surgery, New York, NY 10021, USACorrespondence[email protected]
&
Nadia Dahmane1 Weill Cornell Medical College, Department of Neurological Surgery, New York, NY 10021, USACorrespondence[email protected]
Pages 645-649 | Received 18 Mar 2022, Accepted 07 Apr 2022, Published online: 16 May 2022

References

  • Kadoch C , CrabtreeGR. Mammalian SWI/SNF chromatin remodeling complexes and cancer: mechanistic insights gained from human genomics. Sci. Adv.1(5), e1500447 (2015).
  • Mullins MC , AcedoJN , PriyaR , Solnica-KrezelL , WilsonSW. The zebrafish issue: 25 years on. Development148(24), dev200343 (2021).
  • Wieschaus E , Nüsslein-VolhardC. The Heidelberg screen for pattern mutants of Drosophila: a personal account. Ann. Rev. Cell Dev. Biol.32(1), 1–46 (2016).
  • Harland RM , GraingerRM. Xenopus research: metamorphosed by genetics and genomics. Trends Genet.27(12), 507–515 (2011).
  • Mohr SE , SmithJA , ShamuCE , NeumüllerRA , PerrimonN. RNAi screening comes of age: improved techniques and complementary approaches. Nat. Rev. Mol. Cell Biol.15(9), 591–600 (2014).
  • Shalem O , SanjanaNE , HartenianEet al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science343(6166), 84–87 (2014).
  • Wang T , WeiJJ , SabatiniDM , LanderES. Genetic screens in human cells using the CRISPR-Cas9 system. Science343(6166), 80–84 (2014).
  • O’Loughlin TA , GilbertLA. Functional Genomics for Cancer Research: Applications In Vivo and In Vitro. Annual Review of Cancer Biology3(1), 345–363 (2019).
  • Katti A , DiazBJ , CaragineCM , SanjanaNE , DowLE. CRISPR in cancer biology and therapy. Nat. Rev. Cancer doi:10.1038/s41568-022-00441-w (2022).
  • Dixit A , ParnasO , LiBet al. Perturb-seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens. Cell167(7), 1853–1866.e1817 (2016).
  • Datlinger P , RendeiroAF , SchmidlCet al. Pooled CRISPR screening with single-cell transcriptome readout. Nat. Methods14(3), 297–301 (2017).
  • Mimitou EP , ChengA , MontalbanoAet al. Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells. Nat. Methods16(5), 409–412 (2019).
  • Klemm SL , ShiponyZ , GreenleafWJ. Chromatin accessibility and the regulatory epigenome. Nat. Rev. Genet.20(4), 207–220 (2019).
  • Buenrostro JD , GiresiPG , ZabaLC , ChangHY , GreenleafWJ. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods10(12), 1213 (2013).
  • Corces MR , GranjaJM , ShamsSet al. The chromatin accessibility landscape of primary human cancers. Science362(6413), eaav1898 (2018).
  • Corces MR , BuenrostroJD , WuBet al. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat. Genet.48(10), 1193–1203 (2016).
  • Rubin AJ , ParkerKR , SatpathyATet al. Coupled single-cell CRISPR screening and epigenomic profiling reveals causal gene regulatory networks. Cell176(1–2), 361–376.e317 (2019).
  • Pierce SE , GranjaJM , GreenleafWJ. High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer. Nat. Commun.12(1), 2969 (2021).
  • Liscovitch-Brauer N , MontalbanoA , DengJet al. Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens. Nat. Biotechnol. doi:10.1038/s41587-021-00902-x (2021).
  • Cusanovich DA , DazaR , AdeyAet al. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science348(6237), 910–914 (2015).
  • Mimitou EP , LareauCA , ChenKYet al. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells. Nat. Biotechnol.39(10), 1246–1258 (2021).
  • Kiani K , SanfordEM , GoyalY , RajA. Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations. bioRxiv doi:10.1101/2022.02.03.4789812022.2002.2003.478981 (2022).

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