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Dev Biol January 1, 2017; 426 (2): 401-408.

Developmentally regulated long non-coding RNAs in Xenopus tropicalis.

Forouzmand E , Owens NDL , Blitz IL , Paraiso KD , Khokha MK , Gilchrist MJ , Xie X , Cho KWY .

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, we take advantage of our ultra-high frequency (temporal) sampling of Xenopus embryos to analyze gene expression trajectories of lncRNA transcripts over the first 3 days of development. We 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. We also identified spatially localized lncRNAs in the gastrula stage embryo. These results suggest that lncRNAs have regulatory roles during early embryonic development.

PubMed ID: 27418388
PMC ID: PMC5233649
Article link: Dev Biol
Grant support: [+]

Species referenced: Xenopus laevis
Genes referenced: clic3 cops5 foxa2 foxi2 frmd8 gpr155 igf2bp3 pou3f4 rps7 sox2 st6galnac3 tmc5 txnl4a vegt XB17329847 [provisional]

Article Images: [+] show captions
References [+] :
Anders, Differential expression analysis for sequence count data. 2011, Pubmed