In silico prediction of long intergenic non-coding RNAs in sheep

Abstract

Long non-coding RNAs (lncRNAs) are transcribed RNA molecules >200 nucleotides in length that do not encode proteins and serve as key regulators of diverse biological processes. Recently, thousands of long intergenic non-coding RNAs (lincRNAs), a type of lncRNAs, have been identified in mammalians using massive parallel large sequencing technologies. The availability of the genome sequence of sheep (Ovis aries) has allowed us genomic prediction of non-coding RNAs. This is the first study to identify lincRNAs using RNA-seq data of eight different tissues of sheep, including brain, heart, kidney, liver, lung, ovary, skin, and white adipose. A computational pipeline was employed to characterize 325 putative lincRNAs with high confidence from eight important tissues of sheep using different criteria such as GC content, exon number, gene length, co-expression analysis, stability, and tissue-specific scores. Sixty-four putative lincRNAs displayed tissues-specific expression. The highest number of tissues-specific lincRNAs was found in skin and brain. All novel lincRNAs that aligned to the human and mouse lincRNAs had conserved synteny. These closest protein-coding genes were enriched in 11 significant GO terms such as limb development, appendage development, striated muscle tissue development, and multicellular organismal development. The findings reported here have important implications for the study of sheep genome.

CARMIL family proteins as multidomain regulators of actin-based motility

“…First, CARMIL1 is the most widely expressed isoform, detectable within a variety of tissues across multiple species. Analyses of skin revealed CARMIL1 expression in sheep (Bakhtiarizadeh et al , 2016), mice (Huntley et al , 2016), and humans (FANTOM Consortium and the RIKEN PMI and CLST (DGT) et al , 2014; Uhlen et al , 2015; Human Protein Atlas [www.proteinatlas.org]). Second, CARMIL2 and CARMIL3 are the isoforms most commonly expressed in brain tissues across a variety of organisms (Kapushesky et al , 2012; Petryszak et al , 2014).…”

First identification of long non-coding RNAs in fungal parasite Nosema ceranae

“…RNA sequencing (RNA-seq) data are very useful resources to identify lncRNAs (Wang et al 2009). More than 9000 lincRNA genes were discovered in the human genome (Xing et al 2014;Ganegoda et al 2015;Xue et al 2015), and many lncRNAs were also found in mouse (Karlic et al 2017), sheep (Bakhtiarizadeh et al 2016), pig (Zhou et al 2014), chicken (Li et al 2012), Anopheles gambiae (Jenkins et al 2015), and Drosophila melanogaster (Young et al 2012). However, very little is known about ncRNAs in microsporidia including N .…”

Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat

“…Generally, ncRNAs shorter than 200 nucleotides are usually described as small/short ncRNA, such as microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), small interfering RNAs (siRNAs), and classical ncRNAs such as ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), and small nucleolar RNAs (snoRNAs), whereas ncRNAs longer than 200 nucleotides are described as long ncRNAs (lncRNAs). In the past few years, an increasing number of lncRNAs have been discovered in mammal, including Homo sapiens [1, 2], Mus musculus [3–7], Bos taurus [8, 9], Sus scrofa [10–13], and Ovis aries [14]. And accordingly unveiled that lncRNAs play critical roles in biological processes like transcriptional regulation [15–17], epigenetic modification [18–20], development [21–23], cell differentiation [24–26], as well as in some diseases [27–29].…”