Developmentally regulated long non-coding RNAs in Xenopus tropicalis

Advances in RNA sequencing technologies have led to the surprising discovery that a vast number of transcripts emanate from regions of the genome that are not part of coding genes. Although some of the smaller ncRNAs such as microRNAs have well-characterized functions, the majority of long ncRNA (lncRNA) functions remain poorly understood. Understanding the significance of lncRNAs is an important challenge facing biology today. A powerful approach to uncovering the function of lncRNAs is to explore temporal and spatial expression profiling. This may be particularly useful for classes of lncRNAs that have developmentally important roles as the expression of such lncRNAs will be expected to be both spatially and temporally regulated during development.

Here, researchers from the University of California, Irvine take advantage of their ultra-high frequency (temporal) sampling of Xenopus embryos to analyze gene expression trajectories of lncRNA transcripts over the first 3 days of development. They computationally identify 5689 potential single- and multi-exon lncRNAs. These lncRNAs demonstrate clear dynamic expression patterns. A subset of them displays highly correlative temporal expression profiles with respect to those of the neighboring genes. The researchers also identified spatially localized lncRNAs in the gastrula stage embryo. These results suggest that lncRNAs have regulatory roles during early embryonic development.

Temporal expression dynamics of lncRNAs

The expression values of individual candidate lncRNAs are normalized by their maxima. These expression profiles are assigned (k-means clustering) to 8 different expression clusters. A) The heatmaps show individual normalized expression patterns for all 5689 lncRNAs. B) The plots demonstrate the average expression of all genes within individual clusters. Each blue bar in panel B corresponds to egg (E), late blastula (B), gastrula (G), neurula (N), tailbud (T).