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Open Access Research article

Characterization of differential transcript abundance through time during Nematostella vectensis development

Rebecca Rae Helm1*, Stefan Siebert1, Sarah Tulin2, Joel Smith23 and Casey William Dunn1

Author Affiliations

1 Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Box G-W, Providence, RI 02912, USA

2 Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, 7 MBL St., Woods Hole, MA 02543, USA

3 Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02906, USA

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BMC Genomics 2013, 14:266  doi:10.1186/1471-2164-14-266

Published: 19 April 2013

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.

Keywords:
Nematostella vectensis; Transcriptome; Gene expression; Maternal to zygotic transition; Development