Control of Lineage-Specific Gene Expression by Functionalized gRNA Barcodes

被引：28
作者：
Al'Khafaji, Aziz M. [1 ,2 ]
Deatherage, Daniel [2 ]
Brock, Amy [1 ,2 ]
机构：
[1] Univ Texas Austin, Dept Biomed Engn, Austin, TX 78712 USA
[2] Univ Texas Austin, Inst Cellular & Mol Biol, Austin, TX 78712 USA
来源：
ACS SYNTHETIC BIOLOGY | 2018年 / 7卷 / 10期
基金：
美国国家卫生研究院;
关键词：
lineage tracing; heterogeneity; barcode; clonal dynamics; population variation; CELL HETEROGENEITY; SINGLE CELLS; CANCER; EVOLUTION; DYNAMICS; IDENTIFICATION; TRACKING; MUTATION;
D O I：
10.1021/acssynbio.8b00105
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
Lineage tracking delivers essential quantitative insight into dynamic, probabilistic cellular processes, such as somatic tumor evolution and differentiation. Methods for high diversity lineage quantitation rely on sequencing a population of DNA barcodes. However, manipulation of specific individual lineages is not possible with this approach. To address this challenge, we developed a functionalized lineage tracing tool, Control of Lineages by Barcode Enabled Recombinant Transcription (COLBERT), that enables high diversity lineage tracing and lineage-specific manipulation of gene expression. This modular platform utilizes expressed barcode gRNAs to both track cell lineages and direct lineage-specific gene expression.
引用
收藏
页码：2468 / 2474
页数：13
相关论文
共 30 条
  • [1] Whole-organism clone tracing using single-cell sequencing
    Alemany, Anna
    Florescu, Maria
    Baron, Chloe S.
    Peterson-Maduro, Josi
    van Oudenaarden, Alexander
    [J]. NATURE, 2018, 556 (7699) : 108 - +
  • [2] Heterogeneity for IGF-II production maintained by public goods dynamics in neuroendocrine pancreatic cancer
    Archetti, Marco
    Ferraro, Daniela A.
    Christofori, Gerhard
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2015, 112 (06) : 1833 - 1838
  • [3] Studying clonal dynamics in response to cancer therapy using high-complexity barcoding
    Bhang, Hyo-eun C.
    Ruddy, David A.
    Radhakrishna, Viveksagar Krishnamurthy
    Caushi, Justina X.
    Zhao, Rui
    Hims, Matthew M.
    Singh, Angad P.
    Kao, Iris
    Rakiec, Daniel
    Shaw, Pamela
    Balak, Marissa
    Raza, Alina
    Ackley, Elizabeth
    Keen, Nicholas
    Schlabach, Michael R.
    Palmer, Michael
    Leary, Rebecca J.
    Chiang, Derek Y.
    Sellers, William R.
    Michor, Franziska
    Cooke, Vesselina G.
    Korn, Joshua M.
    Stegmeier, Frank
    [J]. NATURE MEDICINE, 2015, 21 (05) : 440 - U207
  • [4] Beyond genome sequencing: Lineage tracking with barcodes to study the dynamics of evolution, infection, and cancer
    Blundell, Jamie R.
    Levy, Sasha F.
    [J]. GENOMICS, 2014, 104 (06) : 417 - 430
  • [5] OPINION Non-genetic heterogeneity - a mutation-independent driving force for the somatic evolution of tumours
    Brock, Amy
    Chang, Hannah
    Huang, Sui
    [J]. NATURE REVIEWS GENETICS, 2009, 10 (05) : 336 - 342
  • [6] A method for counting PCR template molecules with application to next-generation sequencing
    Casbon, James A.
    Osborne, Robert J.
    Brenner, Sydney
    Lichtenstein, Conrad P.
    [J]. NUCLEIC ACIDS RESEARCH, 2011, 39 (12) : e81
  • [7] Stacks: an analysis tool set for population genomics
    Catchen, Julian
    Hohenlohe, Paul A.
    Bassham, Susan
    Amores, Angel
    Cresko, William A.
    [J]. MOLECULAR ECOLOGY, 2013, 22 (11) : 3124 - 3140
  • [8] Chavez A, 2016, NAT METHODS, V13, P563, DOI [10.1038/nmeth.3871, 10.1038/NMETH.3871]
  • [9] Chavez A, 2015, NAT METHODS, V12, P326, DOI [10.1038/NMETH.3312, 10.1038/nmeth.3312]
  • [10] Tumour cell heterogeneity maintained by cooperating subclones in Wnt-driven mammary cancers
    Cleary, Allison S.
    Leonard, Travis L.
    Gestl, Shelley A.
    Gunther, Edward J.
    [J]. NATURE, 2014, 508 (7494) : 113 - +
123