Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue

Wang, Guoze; Du, Kun; Hu, Shiyan; Chen, Shiyi; Jia, Xianbo; Cai, Mingcheng; Shi, Yu; Wang, Jie; Lai, Songjia

doi:10.1186/s12944-018-0915-1

Cited by 20 publications

(18 citation statements)

References 75 publications

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“…The vast majority of putative lncRNAs were intronic or intergenic in our study, which confirmed that intragenic and intergenic regions were the major sources of non-coding RNAs (Mattick and Makunin 2006;Xu, Bai, et al 2017). lncRNAs are known to be shorter transcript lengths and fewer exon numbers than mRNAs (Wang et al 2018;Sulayman et al 2019). Approximately 80.51% of our 4155 lncRNAs was shorter than 2800 bp and 87.32% of them had 2-4 exons, which was in agreement with previous studies in cattle (Billerey et al 2014;Liu et al 2017;Choi et al 2019;Yue et al 2019).…”

Section: Discussionsupporting

confidence: 92%

Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

Jia

Chen

et al. 2020

Italian Journal of Animal Science

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Long non-coding RNAs (lncRNAs) have been essentially involved in all kinds of important biological processes, such as cell differentiation and development. In this study, we comprehensively profiled genome-wide lncRNAs of bovine skeletal muscle in two Chinese cattle breeds using RNAseq approach. The longissimus dorsi samples were collected from three Charolais (CH) and three Tongjiang (TJ) adult cattle, respectively. Approximately 80 million reads were obtained per library, and by which we assembled 31,009 unique transcripts. We successfully identified a total of 4155 different lncRNAs in six muscle samples, consisting of 3204 intronic lncRNAs, 737 intergenic lncRNAs, 113 sense lncRNAs and 101 antisense lncRNAs. Among them, 32 lncRNAs were differentially expressed (Fold Change >1.0, FDR < 0.05) between CH and TJ. Among these lncRNAs, 1744 identified bovine lncRNAs were located adjacent to 1146 protein-coding genes (<100 kb upstream and downstream) and functionally enriched in organ development, gene regulation and signal transduction. Our results provide a catalogue of bovine skeletal muscle-related lncRNAs, which will complement the list of bovine lncRNAs and contribute to understanding of the molecular mechanism of underpinning muscle development in cattle. HIGHLIGHTS The first study to compare specialised beef cattle breed with Chinese local beef cattle breed on long non-coding RNA (lncRNA). The 4155 different lncRNAs in beef cattle genome were identified to complement the list of bovine lncRNAs. The 1146 protein-coding genes were found maybe in cis-regulatory relationships with lncRNAs to understand the molecular mechanism underpinning muscle development in cattle.

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Section: Discussionsupporting

confidence: 92%

Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

Jia

Chen

et al. 2020

Italian Journal of Animal Science

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“…This biological mechanism is also related to insulin response (Richardson & Herd, 2004), which supports the relationship between insulin genes and FE, as previously stated. Indeed, several lipid‐related genes were identified, such as SDCBP (Santos, 2018), ACLY (Ji, Osorio, Drackley, & Loor, 2012), OLR1 (Vinsky, Islam, Chen, & Li, 2013), CRTC3 (Raza et al., 2019), PRKDC (Horodyska, Hamill, Varley, Reyer, & Wimmers, 2017), HNRNPA3 (Wang et al., 2018), HTATIP2 (Liao et al., 2014) and NFE2L2 (Wu, Cui, & Klaasen, 2011) genes. The OLR1 and CRTC3 genes were reported associated with body weight, rib eye area and fat thickness in Nellore (Fonseca et al., 2015), and fat deposition in Qinchuan cattle (Raza et al., 2019), respectively.…”

Section: Discussionmentioning

confidence: 99%

Weighted single‐step genome‐wide association study and pathway analyses for feed efficiency traits in Nellore cattle

Brunes

Baldi

Lopes³

et al. 2020

J Animal Breeding Genetics

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The aim was to conduct a weighted single‐step genome‐wide association study to detect genomic regions and putative candidate genes related to residual feed intake, dry matter intake, feed efficiency (FE), feed conversion ratio, residual body weight gain, residual intake and weight gain in Nellore cattle. Several protein‐coding genes were identified within the genomic regions that explain more than 0.5% of the additive genetic variance for these traits. These genes were associated with insulin, leptin, glucose, protein and lipid metabolisms; energy balance; heat and oxidative stress; bile secretion; satiety; feed behaviour; salivation; digestion; and nutrient absorption. Enrichment analysis revealed functional pathways (p‐value < .05) such as neuropeptide signalling (GO:0007218), negative regulation of canonical Wingless/Int‐1 (Wnt) signalling (GO:0090090), bitter taste receptor activity (GO:0033038), neuropeptide hormone activity (GO:0005184), bile secretion (bta04976), taste transduction (bta0742) and glucagon signalling pathway (bta04922). The identification of these genes, pathways and their respective functions should contribute to a better understanding of the genetic and physiological mechanisms regulating Nellore FE‐related traits.

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“…Compared to lncRNAs(Wang et al 2018a), miRNAs and the target genes of DE miRNAs were mainly involved in GO functional terms including metabolic process, cell process and single organism process in the classification of biological processes, partial cells and organisms in the classification of cell components, and binding and catalytic activity in the classification of molecular functions. Based on our in-depth analysis of the 1048 significantly enriched GO terms, it was found that amongst the top 10 GO terms of biological process, cell composition and molecular function, some terms that strongly promote growth and volume increases in adipocytes, including protein localization to the plasma membrane, protein ubiquitination involved in ubiquitin-dependent protein catabolic process, regulation of cell growth, cytoplasm, Golgi apparatus, membrane, protein binding, protein tyrosine phosphatase, zinc ion binding, ATP binding, and cadherin binding were identified.…”

Section: Discussionmentioning

confidence: 99%

Screening and identification of MicroRNAs expressed in perirenal adipose tissue during rabbit growth

Wang

Guo

Tian

et al. 2019

Preprint

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45MiRNAs regulate adipose tissue development, which are closely 46 related to subcutaneous and intramuscular fat deposition and adipocyte 47 differentiation. As an important economic and agricultural animal, rabbits 48 have low adipose tissue deposition and are an ideal model to study 49 adipose regulation. However, the miRNAs related to fat deposition during 50 the growth and development of rabbits are poorly defined. In this study, 51 miRNA-sequencing and bioinformatics analyses were used to profile the 52 miRNAs in rabbit perirenal adipose tissue at 35, 85 and 120 days 53 post-birth. Differentially expressed (DE) miRNAs between different 54 stages were identified by DEseq in R. Target genes of DE miRNAs were 55 predicted by TargetScan and miRanda. To explore the functions of 56 identified miRNAs, Gene Ontology (GO) enrichment and Kyoto 57 Encyclopedia of Genes and Genomes (KEGG) pathway analyses were 58 performed. Approximately 1.6 GB of data was obtained by miRNA-seq. 59 A total of 987 miRNAs (780 known and 207 newly predicted) and 174 60 DE miRNAs were identified. The miRNAs ranged from 18nt to 26nt. GO 61 enrichment and KEGG pathway analyses revealed that the target genes of 62 the DE miRNAs were mainly involved in zinc ion binding, regulation of 63 cell growth, MAPK signaling pathway, and other adipose 64 hypertrophy-related pathways. Six DE miRNAs were randomly selected 65 and their expression profiles were validated by q-PCR. In summary, we 66 4 provide the first report of the miRNA profiles of rabbit adipose tissue 67 during different growth stages. Our data provide a theoretical reference 68 for subsequent studies on rabbit genetics, breeding and the regulatory 69 mechanisms of adipose development.70 Introduction 71 MicroRNAs (miRNAs) are endogenous non-coding RNAs, typically 72 18～26 nucleotides in length, that regulate gene expression in eukaryotic 73 cells. Mature miRNAs are produced from long primary transcripts 74 through a series of nucleases that are further assembled into 75 RNA-induced silencing complexes. These complexes recognize target 76 mRNAs by complementary base pairing, leading to mRNA degradation 77 and the inhibition of translation(Fabian et al. 2010). MiRNAs regulate a 78 wide range of physiological processes, including growth and 79 development, virus defense, cell proliferation, apoptosis and fat 80 metabolism. Meanwhile, it has been well documented that MiRNAs 81 regulate adipose tissue development, which are closely related to 82 subcutaneous and intramuscular fat deposition(Guoxi et al. 2011; Guo et 83 al. 2012) and adipocyte differentiation(Son et al. 2014).MiRNAs, 84 including miR-27b(Karbiener et al. 2009), miR-103(Meihang et al. 2015) 85 and miR-148a(Shi et al. 2015) regulate adipogenic processes, promoting 86 or inhibiting adipogenesis in animals. This implicates miRNAs can be a 87 5 new target for studying the molecular mechanisms governing fat 88 development, growth and deposition in animals. 89 To-date, studies on the role of miRNAs during fat development have 90 ...

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Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue

Cited by 20 publications

References 75 publications

Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

Weighted single‐step genome‐wide association study and pathway analyses for feed efficiency traits in Nellore cattle

Screening and identification of MicroRNAs expressed in perirenal adipose tissue during rabbit growth

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