Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

Abstract

BackgroundNumerous long non-coding RNAs (lncRNAs) have been identified and their roles in gene regulation in humans, mice, and other model organisms studied; however, far less research has been focused on lncRNAs in farm animal species. While previous studies in chickens, cattle, and pigs identified lncRNAs in specific developmental stages or differentially expressed under specific conditions in a limited number of tissues, more comprehensive identification of lncRNAs in these species is needed. The goal of the FAANG Consortium (Functional Annotation of Animal Genomes) is to functionally annotate animal genomes, including the annotation of lncRNAs. As one of the FAANG pilot projects, lncRNAs were identified across eight tissues in two adult male biological replicates from chickens, cattle, and pigs.ResultsComprehensive lncRNA annotations for the chicken, cattle, and pig genomes were generated by utilizing RNA-seq from eight tissue types from two biological replicates per species at the adult developmental stage. A total of 9393 lncRNAs in chickens, 7235 lncRNAs in cattle, and 14,429 lncRNAs in pigs were identified. Including novel isoforms and lncRNAs from novel loci, 5288 novel lncRNAs were identified in chickens, 3732 in cattle, and 4870 in pigs. These transcripts match previously known patterns of lncRNAs, such as generally lower expression levels than mRNAs and higher tissue specificity. An analysis of lncRNA conservation across species identified a set of conserved lncRNAs with potential functions associated with chromatin structure and gene regulation. Tissue-specific lncRNAs were identified. Genes proximal to tissue-specific lncRNAs were enriched for GO terms associated with the tissue of origin, such as leukocyte activation in spleen.ConclusionsLncRNAs were identified in three important farm animal species using eight tissues from adult individuals. About half of the identified lncRNAs were not previously reported in the NCBI annotations for these species. While lncRNAs are less conserved than protein-coding genes, a set of positionally conserved lncRNAs were identified among chickens, cattle, and pigs with potential functions related to chromatin structure and gene regulation. Tissue-specific lncRNAs have potential regulatory functions on genes enriched for tissue-specific GO terms. Future work will include epigenetic data from ChIP-seq experiments to further refine these annotations.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5037-7) contains supplementary material, which is available to authorized users.

Identification of Novel lncRNAs Differentially Expressed in Placentas of Chinese Ningqiang Pony and Yili Horse Breeds

“…Using the TopHat (http://ccb.jhu.edu/software/tophat/index.shtml) and Cufflinks (http: //cole-trapnell-lab.github.io/cufflinks/releases/v2.1.1) programs, 86.3-89.5% of all the reads were successfully mapped against the current reference horse genome EquCab3.0. After developing the bioinformatics pipeline for processing the large amounts of transcriptome sequences, 1464 multiple-exon lncRNAs were identified in the placentas of YL and NQ breeds, and 361 of them overlapped with a previous study [7], which did not contain the placenta tissue, supporting the tissue-specific expression of lncRNAs [27]. We identified 107 lncRNAs as being differentially expressed between the YL and NQ breeds.…”

“…Other studies showed the strong association of LCORL/NCAPG, HMGA2, PROP1, LASP [39], ZFAT, DIAPH3 [40], ACTN2, ADAMTS17, GH1, ANKRD1 [40], and ACAN [41,42] with miniature size and dwarfism in a variety of pony breeds, including Shetland [41,43], miniature [44], Welsh ponies [45], German warmblood horses [46], American miniature horses, Brazilian ponies [47], and Jeju ponies [48], as well as B4GALT7 [49] and PROP1 [50] in Friesian horses. These genes were not found in this study, which may be due to the expression specificity of lncRNAs in different horse breeds [27] and different omics levels, since TBX3, under strong selection in Chinese ponies, was also identified in this study. This indicated that more breeds and samples are needed to analyze growth regulation during horse development.…”

Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

“…Using the RNA-seq technology, previous studies have identified 4404, 2481, 39,907, 8691, 1376, 6543, 2597 and 2056 lncRNAs in breast muscle, spleen, cerebrum, ovarian follicle, trachea, liver, testis and adipose of chickens, respectively [33,[92][93][94][95][96][97][98]. Moreover, Kern et al [99] found 9393 lncRNAs in eight tissue types (adipose, cerebellum, cortex, hypothalamus, liver, lung, skeletal muscle and spleen) of chickens and Hong et al [100] obtained 6900 lncRNAs genes in 20 different tissues (breast, gizzard, liver, pancreas, uterus, heart, bone marrow, kidney, cerebrum, cerebellum, eye, immature egg, mature egg, gall-bladder, comb, shank, skin, lung, spleen and fascia) of an individual Ogye, with c.75% of lncRNAs as tissue-specific. In the present study, 818 candidate lncRNAs were identified in the mid-segments of chicken small intestines.…”

Transcriptome and chromatin structure annotation of liver, CD4+ and CD8+ T cells from four livestock species

“…org) aims to support and coordinate the community in the endeavor of creating reference functional maps of the genomes of domesticated animals across different species, tissues and developmental stages, with an initial focus on farm and companion animals [12][13][14][15]. To achieve high quality functional annotation of these genomes, FAANG carries out activities to standardize core biochemical assay protocols, coordinate and facilitate data sharing.…”