单细胞映射斑马鱼胚胎中的基因表达图谱和谱系。
Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo.
机构信息
Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
出版信息
Science. 2018 Jun 1;360(6392):981-987. doi: 10.1126/science.aar4362. Epub 2018 Apr 26.
Abstract
High-throughput mapping of cellular differentiation hierarchies from single-cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single-cell RNA sequencing to >92,000 cells from zebrafish embryos during the first day of development. Using a graph-based approach, we mapped a cell-state landscape that describes axis patterning, germ layer formation, and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon-based barcoding approach (TracerSeq) for reconstructing single-cell lineage histories. Clonally related cells were often restricted by the state landscape, including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in embryos lacking the gene. We provide web-based resources for further analysis of the single-cell data.
摘要
高通量单细胞数据解析细胞分化谱系有望实现对脊椎动物发育和疾病的系统研究。本研究利用单细胞 RNA 测序技术，对斑马鱼胚胎发育第一天的超过 92000 个细胞进行了分析。通过基于图的方法，我们构建了一个描述胚胎轴形成、胚层形成和器官发生的细胞状态图谱。我们通过开发基于转座子的条形码方法（TracerSeq）来重建单细胞谱系历史，测试了克隆相关细胞如何穿越这个状态图谱。克隆相关细胞经常受到状态图谱的限制，包括两个独立谱系趋同于相似命运的情况。在缺乏基因的胚胎中，细胞命运仍然受到这种状态图谱的限制。我们提供了基于网络的单细胞数据分析资源。
相似文献
1
Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo.单细胞映射斑马鱼胚胎中的基因表达图谱和谱系。
Science. 2018 Jun 1;360(6392):981-987. doi: 10.1126/science.aar4362. Epub 2018 Apr 26.
2
Differential regulation of chordin expression domains in mutant zebrafish.突变斑马鱼中脊索蛋白表达域的差异调控。
Dev Biol. 1997 Dec 15;192(2):537-50. doi: 10.1006/dbio.1997.8788.
3
Short- and long-range functions of Goosecoid in zebrafish axis formation are independent of Chordin, Noggin 1 and Follistatin-like 1b.斑马鱼轴形成过程中 Goosecoid 的短程和长程功能独立于脊索蛋白、Noggin 1 和类卵泡抑素 1b。
Development. 2009 May;136(10):1675-85. doi: 10.1242/dev.031161. Epub 2009 Apr 15.
4
Patterning the zebrafish axial skeleton requires early chordin function.斑马鱼轴向骨骼的模式形成需要早期脊索蛋白的功能。
Nat Genet. 1999 Dec;23(4):442-6. doi: 10.1038/70557.
5
Fgf signalling controls the dorsoventral patterning of the zebrafish embryo.成纤维细胞生长因子（Fgf）信号传导控制斑马鱼胚胎的背腹模式形成。
Development. 2004 Jun;131(12):2853-64. doi: 10.1242/dev.01156. Epub 2004 May 19.
6
Downregulation of gene expression with negatively charged peptide nucleic acids (PNAs) in zebrafish embryos.斑马鱼胚胎中带负电荷的肽核酸（PNA）对基因表达的下调作用
Methods Cell Biol. 2004;77:137-58. doi: 10.1016/s0091-679x(04)77008-9.
7
Noggin1 and Follistatin-like2 function redundantly to Chordin to antagonize BMP activity.头蛋白1和类卵泡抑素2与脊索蛋白功能冗余，以拮抗骨形态发生蛋白活性。
Dev Biol. 2006 Oct 15;298(2):514-26. doi: 10.1016/j.ydbio.2006.07.002. Epub 2006 Jul 12.
8
Computational analysis of BMP gradients in dorsal-ventral patterning of the zebrafish embryo.斑马鱼胚胎背腹模式形成中骨形态发生蛋白梯度的计算分析
J Theor Biol. 2007 Oct 21;248(4):579-89. doi: 10.1016/j.jtbi.2007.05.026. Epub 2007 Jun 6.
9
Asymmetric expression of the BMP antagonists chordin and gremlin in the sea anemone Nematostella vectensis: implications for the evolution of axial patterning.骨形态发生蛋白拮抗剂脊索蛋白（chordin）和Gremlin在海葵星状海葵（Nematostella vectensis）中的不对称表达：对轴向模式形成进化的影响
Dev Biol. 2006 Aug 15;296(2):375-87. doi: 10.1016/j.ydbio.2006.06.003. Epub 2006 Jun 7.
10
An ancient chordin-like gene in organizer formation of Hydra.水螅组织者形成过程中的一个古老的类脊索基因。
Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3249-54. doi: 10.1073/pnas.0604501104. Epub 2007 Feb 20.
引用本文的文献
1
Cutting-edge technologies in neural regeneration.神经再生领域的前沿技术。
Cell Regen. 2025 Sep 5;14(1):38. doi: 10.1186/s13619-025-00260-y.
2
Establishing single cell RNA transcriptomics: a brief guide.建立单细胞RNA转录组学：简要指南。
Front Zool. 2025 Sep 2;22(1):25. doi: 10.1186/s12983-025-00579-x.
3
The intrinsic dimension of gene expression during cell differentiation.细胞分化过程中基因表达的内在维度。
Nucleic Acids Res. 2025 Aug 27;53(16). doi: 10.1093/nar/gkaf805.
4
Integrated analysis of single-cell RNA-seq and ATAC-seq in lens epithelial cells: Unveiling the role of ATF6 as a key transcription factor.晶状体上皮细胞中单细胞RNA测序和ATAC测序的综合分析：揭示ATF6作为关键转录因子的作用
Genes Dis. 2025 Mar 22;12(6):101610. doi: 10.1016/j.gendis.2025.101610. eCollection 2025 Nov.
5
Dual lineage origins contribute to neocortical astrocyte diversity.双谱系起源促成了新皮质星形胶质细胞的多样性。
Nat Commun. 2025 Jul 30;16(1):6992. doi: 10.1038/s41467-025-61829-4.
6
In toto analysis of embryonic organisation reduces tissue diversity to two archetypes requiring specific cadherins.对胚胎组织的整体分析将组织多样性简化为两种需要特定钙黏着蛋白的原型。
Nat Commun. 2025 Jul 25;16(1):6872. doi: 10.1038/s41467-025-62127-9.
7
Immune cell type divergence in a basal chordate.一种基索动物中的免疫细胞类型差异
bioRxiv. 2025 May 23:2025.05.20.655184. doi: 10.1101/2025.05.20.655184.
8
A molecular circuit regulates fate plasticity in emerging and adult AT2 cells.一个分子回路调节新生和成年AT2细胞的命运可塑性。
bioRxiv. 2025 May 7:2025.04.28.650846. doi: 10.1101/2025.04.28.650846.
9
Two parallel lineage-committed progenitors contribute to the developing brain.两个平行的谱系定向祖细胞参与发育中的大脑形成。
bioRxiv. 2025 Jul 5:2025.07.02.662771. doi: 10.1101/2025.07.02.662771.
10
Temporal control of progenitor competence shapes maturation in GABAergic neuron development in mice.祖细胞能力的时间控制塑造了小鼠GABA能神经元发育中的成熟过程。
Nat Neurosci. 2025 Jul 8. doi: 10.1038/s41593-025-01999-y.
本文引用的文献
1
SPRING: a kinetic interface for visualizing high dimensional single-cell expression data.SPRING：一种用于可视化高维单细胞表达数据的动力学界面。
Bioinformatics. 2018 Apr 1;34(7):1246-1248. doi: 10.1093/bioinformatics/btx792.
2
A Gene Regulatory Network Balances Neural and Mesoderm Specification during Vertebrate Trunk Development.一个基因调控网络在脊椎动物躯干发育过程中平衡神经和中胚层特化。
Dev Cell. 2017 May 8;41(3):243-261.e7. doi: 10.1016/j.devcel.2017.04.002. Epub 2017 Apr 27.
3
Single-cell barcoding and sequencing using droplet microfluidics.基于液滴微流控技术的单细胞条码标记与测序
Nat Protoc. 2017 Jan;12(1):44-73. doi: 10.1038/nprot.2016.154. Epub 2016 Dec 8.
4
Diffusion pseudotime robustly reconstructs lineage branching.扩散伪时间能够稳健地重建谱系分支。
Nat Methods. 2016 Oct;13(10):845-8. doi: 10.1038/nmeth.3971. Epub 2016 Aug 29.
5
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.
6
CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq.CEL-Seq2：灵敏的高度多重单细胞RNA测序
Genome Biol. 2016 Apr 28;17:77. doi: 10.1186/s13059-016-0938-8.
7
The zebrafish tailbud contains two independent populations of midline progenitor cells that maintain long-term germ layer plasticity and differentiate in response to local signaling cues.斑马鱼尾芽包含两个独立的中线祖细胞群体，它们保持长期的胚层可塑性，并根据局部信号线索进行分化。
Development. 2016 Jan 15;143(2):244-54. doi: 10.1242/dev.129015. Epub 2015 Dec 16.
8
MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.MAST：一种用于评估单细胞RNA测序数据中转录变化和表征异质性的灵活统计框架。
Genome Biol. 2015 Dec 10;16:278. doi: 10.1186/s13059-015-0844-5.
9
Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis.利用Waterfall进行单细胞RNA测序揭示成体神经发生背后的分子级联反应。
Cell Stem Cell. 2015 Sep 3;17(3):360-72. doi: 10.1016/j.stem.2015.07.013. Epub 2015 Aug 20.
10
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.利用纳升液滴对单个细胞进行高度并行的全基因组表达谱分析。
Cell. 2015 May 21;161(5):1202-1214. doi: 10.1016/j.cell.2015.05.002.
Zotero 插件