Characterization of differential transcript abundance through time during Nematostella vectensis development

Abstract

Background: Nematostella vectensis, a burrowing sea anemone, has become a popular species for the study of cnidarian development. In previous studies, the expression of a variety of genes has been characterized during N. vectensis development with in situ mRNA hybridization. This has provided detailed spatial resolution and a qualitative perspective on changes in expression. However, little is known about broad transcriptome-level patterns of gene expression through time. Here we examine the expression of N. vectensis genes through the course of development with quantitative RNA-seq. We provide an overview of changes in the transcriptome through development, and examine the maternal to zygotic transition, which has been difficult to investigate with other tools.

Results: We measured transcript abundance in N. vectensis with RNA-seq at six time points in development: zygote (2 hours post fertilization (HPF)), early blastula (7 HPF), mid-blastula (12 HPF), gastrula (24 HPF), planula (5 days post fertilization (DPF)) and young polyp (10 DPF). The major wave of zygotic expression appears between 7-12 HPF, though some changes occur between 2-7 HPF. The most dynamic changes in transcript abundance occur between the late blastula and early gastrula stages. More transcripts are upregulated between the gastrula and planula than downregulated, and a comparatively lower number of transcripts significantly change between planula and polyp. Within the maternal to zygotic transition, we identified a subset of maternal factors that decrease early in development, and likely play a role in suppressing zygotic gene expression. Among the first genes to be expressed zygotically are genes whose proteins may be involved in the degradation of maternal RNA.

Conclusions: The approach presented here is highly complementary to prior studies on spatial patterns of gene expression, as it provides a quantitative perspective on a broad set of genes through time but lacks spatial resolution. In addition to addressing the problems identified above, our work provides an annotated matrix that other investigators can use to examine genes and developmental events that we do not examine in detail here.

Figure 1

Selected STEM profiles. The five most abundant patterns of changes in transcript abundance through time, ranked by decreasing number of transcripts. Stem pattern 31, which is discussed in the text, is also shown below the dashed line. The full set of STEM profiles are shown in Additional file 4. The vertical axis is relative transcript abundance. The horizontal axis is developmental time, with the 6 time points arranged consecutively on the horizontal axis of each plot, from the first time point (2 HPF) on the left and the last (10 DPF) on the right.

Figure 2

Differential gene expression during early development of N. vectensis. A) Number of transcripts that are significantly (p < 0.05) increasing (red), or decreasing (blue) through time within intervals. (B-F) Pairwise comparison Log₂-fold-change vs log₂CPM (counts per million) for the five pairwise comparisons between adjacent sampling times. The comparisons are between (B) 2 HPF and 7 HPF, (C) 7 HPF and 12 HPF, (D) 12 HPF and 24 HPF, (E) 24 HPF and 5 DPF and (F) 5 DPF and 10 DPF. Each point represents an individual transcript, red points indicate transcripts with significant (adjusted p-value < 0.05) differential expression. Positive log₂-fold-change values indicate increased transcript abundance from the first to the second time point, negative log₂-fold-change values indicate decreased transcript abundance from the first to second time point. Horizontal grey lines indicate 2-fold differences in expression.