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从单细胞构建细胞谱系:细胞谱系追踪的遗传技术

Building a lineage from single cells: genetic techniques for cell lineage tracking.

作者信息

Woodworth Mollie B, Girskis Kelly M, Walsh Christopher A

机构信息

Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.

Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.

出版信息

Nat Rev Genet. 2017 Apr;18(4):230-244. doi: 10.1038/nrg.2016.159. Epub 2017 Jan 23.

DOI:10.1038/nrg.2016.159
PMID:28111472
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5459401/
Abstract

Resolving lineage relationships between cells in an organism is a fundamental interest of developmental biology. Furthermore, investigating lineage can drive understanding of pathological states, including cancer, as well as understanding of developmental pathways that are amenable to manipulation by directed differentiation. Although lineage tracking through the injection of retroviral libraries has long been the state of the art, a recent explosion of methodological advances in exogenous labelling and single-cell sequencing have enabled lineage tracking at larger scales, in more detail, and in a wider range of species than was previously considered possible. In this Review, we discuss these techniques for cell lineage tracking, with attention both to those that trace lineage forwards from experimental labelling, and those that trace backwards across the life history of an organism.

摘要

解析生物体中细胞间的谱系关系是发育生物学的一项基本研究内容。此外,研究谱系有助于深入了解包括癌症在内的病理状态,以及有助于理解可通过定向分化进行调控的发育途径。尽管通过注射逆转录病毒文库进行谱系追踪长期以来一直是最先进的技术,但最近在外源标记和单细胞测序方面的一系列方法学进展,使得谱系追踪能够在比以往认为可能的更大规模、更详细以及更广泛的物种范围内进行。在本综述中,我们将讨论这些用于细胞谱系追踪的技术,既关注那些从实验标记向前追踪谱系的技术,也关注那些在生物体的生命历程中向后追溯谱系的技术。

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本文引用的文献

1
Quantitative Analysis of Synthetic Cell Lineage Tracing Using Nuclease Barcoding.使用核酸酶条形码技术对合成细胞谱系追踪进行定量分析。
ACS Synth Biol. 2017 Jun 16;6(6):936-942. doi: 10.1021/acssynbio.6b00309. Epub 2017 Mar 10.
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Rapidly evolving homing CRISPR barcodes.快速进化的归巢CRISPR条形码。
Nat Methods. 2017 Feb;14(2):195-200. doi: 10.1038/nmeth.4108. Epub 2016 Dec 5.
3
Synthetic recording and in situ readout of lineage information in single cells.单细胞谱系信息的合成记录与原位读出
Nature. 2017 Jan 5;541(7635):107-111. doi: 10.1038/nature20777. Epub 2016 Nov 21.
4
Whole-organism lineage tracing by combinatorial and cumulative genome editing.通过组合式和累积式基因组编辑进行全生物体谱系追踪。
Science. 2016 Jul 29;353(6298):aaf7907. doi: 10.1126/science.aaf7907. Epub 2016 May 26.
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Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples.用于有限DNA样本全基因组测序的数字液滴多重置换扩增(ddMDA)
PLoS One. 2016 May 4;11(5):e0153699. doi: 10.1371/journal.pone.0153699. eCollection 2016.
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Ctip1 Controls Acquisition of Sensory Area Identity and Establishment of Sensory Input Fields in the Developing Neocortex.Ctip1控制发育中的新皮层中感觉区域身份的获得和感觉输入场的建立。
Neuron. 2016 Apr 20;90(2):261-77. doi: 10.1016/j.neuron.2016.03.008.
7
Monovar: single-nucleotide variant detection in single cells.Monovar:单细胞中的单核苷酸变异检测
Nat Methods. 2016 Jun;13(6):505-7. doi: 10.1038/nmeth.3835. Epub 2016 Apr 18.
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OncoNEM: inferring tumor evolution from single-cell sequencing data.OncoNEM:从单细胞测序数据推断肿瘤进化
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The Complete Genome Sequences, Unique Mutational Spectra, and Developmental Potency of Adult Neurons Revealed by Cloning.克隆揭示成年神经元的全基因组序列、独特突变谱及发育潜能
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Resolving rates of mutation in the brain using single-neuron genomics.利用单神经元基因组学解析大脑中的突变率
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