4.6 Article

Single-nucleus RNA-sequencing in pre-cellularization Drosophila melanogaster embryos

Journal

PLOS ONE
Volume 17, Issue 6, Pages -

Publisher

PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pone.0270471

Keywords

-

Funding

  1. NIH Training Grant [T21 GM 007127]
  2. National Science Foundation Graduate Research Fellowship Program
  3. American Cancer Society postdoctoral fellowship [126730PF-14-256-01-DDC]
  4. Howard Hughes Medical Institute Investigator award

Ask authors/readers for more resources

Our current understanding of gene expression regulation in the early Drosophila melanogaster embryo is limited to a few genes at a time or gene expression levels without considering spatial patterning. Single-nucleus RNA-sequencing has the potential to provide new insights by simultaneously studying multiple genes and retaining positional information. This study investigates gene expression in control and maternal dCTCF null embryos during zygotic genome activation and identifies distinct clusters of early embryonic nuclei based on gene expression, which correspond to spatial regions of the embryo. Candidate differentially expressed genes are also identified, highlighting the potential of single-nucleus RNA-sequencing to reveal new insights into gene expression regulation in the early Drosophila melanogaster embryo.
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 melanogasterembryo.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.6
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

No Data Available
No Data Available