title: Developmentally regulated long non-coding RNAs in Xenopus tropicalis.
abstract: 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.
authors.affiliation: Department of Computer Science, University of California, Irvine, CA 92697, USA.
authors.forename: Elmira
authors.initials: E
authors.lastname: Forouzmand
authors.affiliation: The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway Mill Hill, London NW7 1AA, UK.
authors.forename: Nick D L
authors.initials: NDL
authors.lastname: Owens
authors.affiliation: Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA.
authors.forename: Ira L
authors.initials: IL
authors.lastname: Blitz
authors.affiliation: Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA.
authors.forename: Kitt D
authors.initials: KD
authors.lastname: Paraiso
authors.affiliation: Program in Vertebrate Developmental Biology, Department of Pediatrics and Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
authors.forename: Mustafa K
authors.initials: MK
authors.lastname: Khokha
authors.affiliation: The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway Mill Hill, London NW7 1AA, UK.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Gilchrist
authors.affiliation: Department of Computer Science, University of California, Irvine, CA 92697, USA.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Xie
authors.affiliation: Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA. Electronic address: kwcho@uci.edu.
authors.forename: Ken W Y
authors.initials: KWY
authors.lastname: Cho
mesh_terms: D000818:Animals; D004625:Embryo, Nonmammalian / Q000378:metabolism; D005091:Exons / Q000235:genetics; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D008957:Models, Genetic; D062085:RNA, Long Noncoding / Q000096:biosynthesis / Q000235:genetics* / Q000302:isolation & purification; D059467:Transcriptome; D014981:Xenopus / Q000196:embryology / Q000235:genetics*
chemical_list: D062085:RNA, Long Noncoding
keywords: Biological timescales; Expression profile; Gaussian processes; Gene expression; Non-coding RNA; RNA-seq; Systems biology; Xenopus tropicalis