Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America.
Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America.
PLoS One. 2022 Jun 24;17(6):e0270471. doi: 10.1371/journal.pone.0270471. eCollection 2022.
Our current understanding of the regulation of gene expression in the early Drosophila melanogaster embryo comes from observations of a few genes at a time, as with in situ hybridizations, or observation of gene expression levels without regards to patterning, as with RNA-sequencing. Single-nucleus RNA-sequencing however, has the potential to provide new insights into the regulation of gene expression for many genes at once while simultaneously retaining information regarding the position of each nucleus prior to dissociation based on patterned gene expression. In order to establish the use of single-nucleus RNA sequencing in Drosophila embryos prior to cellularization, here we look at gene expression in control and insulator protein, dCTCF, maternal null embryos during zygotic genome activation at nuclear cycle 14. We find that early embryonic nuclei can be grouped into distinct clusters according to gene expression. From both virtual and published in situ hybridizations, we also find that these clusters correspond to spatial regions of the embryo. Lastly, we provide a resource of candidate differentially expressed genes that might show local changes in gene expression between control and maternal dCTCF null nuclei with no detectable differential expression in bulk. These results highlight the potential for single-nucleus RNA-sequencing to reveal new insights into the regulation of gene expression in the early Drosophila melanogaster embryo.
我们目前对早期黑腹果蝇胚胎中基因表达调控的理解来自于对少数几个基因的观察，例如原位杂交，或者在不考虑模式的情况下观察基因表达水平，例如 RNA 测序。然而，单细胞 RNA 测序有可能同时提供对许多基因表达调控的新见解，同时保留基于模式基因表达的每个核在分离前的位置信息。为了在细胞化之前在果蝇胚胎中建立单细胞 RNA 测序的使用，我们在这里研究了在核循环 14 时合子基因组激活过程中对照和绝缘子蛋白 dCTCF 母性缺失胚胎中的基因表达。我们发现，早期胚胎核可以根据基因表达分为不同的簇。通过虚拟和已发表的原位杂交，我们还发现这些簇与胚胎的空间区域相对应。最后，我们提供了一组候选差异表达基因，这些基因可能在对照和母性 dCTCF 缺失核之间显示局部基因表达变化，而在整体上没有可检测到的差异表达。这些结果强调了单细胞 RNA 测序有可能揭示早期黑腹果蝇胚胎中基因表达调控的新见解。
