Characterization of differential transcript abundance through time during Nematostella vectensis development
Helm, Rebecca R.
Dunn, Casey W.
MetadataShow full item record
KeywordNematostella vectensis; Transcriptome; Gene expression; Maternal to zygotic transition; Development
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. 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. 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.
© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 14 (2013): 266, doi:10.1186/1471-2164-14-266.
The following license files are associated with this item:
Showing items related by title, author, creator and subject.
A quantitative reference transcriptome for Nematostella vectensis early embryonic development : a pipeline for de novo assembly in emerging model systems Tulin, Sarah; Aguiar, Derek; Istrail, Sorin; Smith, Joel (BioMed Central, 2013-06-03)The de novo assembly of transcriptomes from short shotgun sequences raises challenges due to random and non-random sequencing biases and inherent transcript complexity. We sought to define a pipeline for de novo transcriptome ...
Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis Sullivan, James C.; Reitzel, Adam M.; Finnerty, John R. (Oxford University Press, 2007-11-03)The starlet sea anemone, Nematostella vectensis, is a basal metazoan organism that has recently emerged as an important model system in developmental biology and evolutionary genomics. StellaBase, the Nematostella Genomics ...
Fischer, Antje H. L.; Tulin, Sarah; Fredman, David; Smith, Joel (2013-07-11)A key tool for investigating the regulation of genes is represented by Bacterial Artificial Chromosomes-reporter constructs (BAC). BACs are large insert libraries, often >>100 kb, which thus capture the genomic sequences ...