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

Non-coding RNA in the gut of the blood-feeding parasitic worm, Haemonchus contortus

The intestine of Haemonchus contortus is an essential tissue that has been indicated to be a major target for the prevention of haemonchosis caused by this parasitic nematode of small ruminants. Biological peculiarities of the intestine warrant in-depth exploitation, which can be leveraged for future disease control efforts. Here, we determined the intestinal ncRNA (lncRNA, circRNA and miRNA) atlas using whole-transcriptome sequencing and bioinformatics approaches. In total, 4846 novel lncRNA, 982 circRNA, 96 miRNA (65 known and 31 novel) and 8821 mRNA were identified from the H. contortus intestine. The features of lncRNA, circRNA and miRNA were fully characterized. Comparison of miRNA from the intestines and extracellular vesicles supported the speculation that the miRNA from the latter were of intestinal origin in H. contortus. Further function analysis suggests that the cis-lncRNA targeted genes were involved in protein binding, intracellular anatomical structure, organelle and cellular process, whereas the circRNA parental genes were mainly enriched in molecular function categories, such as ribonucleotide binding, nucleotide binding, ATP binding and carbohydrate derivative binding. The miRNA target genes were related to the cellular process, cellular response to stimulus, cellular protein modification process and signal transduction. Moreover, competing endogenous RNA network analysis revealed that the majority of lncRNA, circRNA and mRNA only have one or two binding sites with specific miRNA. Lastly, randomly selected circRNA, lncRNA and miRNA were verified successfully using RT-PCR. Collectively, these data provide the most comprehensive compilation of intestinal transcripts and their functions, and it will be helpful to decipher the biological and molecular complexity of the intestine and lay the foundation for further functional research.

Integrated analysis of genes and long non-coding RNAs in trachea transcriptome to decipher the host response during Newcastle disease challenge in different breeds of chicken

Newcastle disease is a highly infectious economically devastating disease caused by Newcastle disease Virus in Chicken (Gallus gallus). Leghorn and Fayoumi are two breeds which show differential resistance patterns towards NDV. This study aims to identify the differentially expressed genes and lncRNAs during NDV challenge which could play a potential role in this differential resistance pattern. A total of 552 genes and 1580 lncRNAs were found to be differentially expressing. Of them, 52 genes were annotated with both Immune related pathways and Gene ontologies. We found that most of these genes were upregulated in Leghorn between normal and challenged chicken but several were down regulated between different timepoints after NDV challenge, while Fayoumi showed no such downregulation. We also observed that higher number of positively correlating lncRNAs was found to be downregulated along with these genes. This shows that although Leghorn is showing higher number of differentially expressed genes in challenged than in non-challenged, most of them were downregulated during the disease between different timepoints. With this we hypothesize that the downregulation of immune related genes and co-expressing lncRNAs could play a significant role behind the Leghorn being comparatively susceptible breed than Fayoumi. The computational pipeline is available at https://github.com/Venky2804/FHSpipe.

The novel RNA-RNA activation of H19 on MyoD transcripts promoting myogenic differentiation of goat muscle satellite cells

The elaborate interplay of coding and noncoding factors governs muscle growth and development. Here, we reported a mutual activation between long noncoding RNA (lncRNA) H19 and MyoD (myogenic determination gene number 1) in the muscle process. We successfully cloned the two isoforms of goat H19, which were significantly enriched and positively correlated with MyoD transcripts in skeletal muscles or differentiating muscle satellite cells (MuSCs). To systematically screen genes altered by H19, we performed RNA-seq using cDNA libraries of differentiating H19-deficiency MuSCs and consequently anchored MyoD as the critical genes in mediating H19 function. Intriguingly, some transcripts of MyoD and H19 overlapped in the cytoplasm, which was dramatically damaged when the core complementary nucleotides were mutated. Meanwhile, MyoD RNA successfully pulled down H19 in MS2-RIP experiments. Furthermore, HuR could bind both H19 and MyoD transcripts, while H19 or its truncated mutants successfully stabilized MyoD mRNA, with or without HuR deficiency. In turn, novel functional MyoD protein-binding sites were identified in the promoter and exons of the H19 gene. Our results suggest that MyoD activates H19 transcriptionally, and RNA-RNA hybridization is critical for H19-promoted MyoD expression, which extends our knowledge of the hierarchy of regulatory networks in muscle growth.

A newly identified lncRNA lnc000100 regulates proliferation and differentiation of cattle skeletal muscle cells

Cattle skeletal muscle development is a complex and highly coordinated biological process mediated by a series of myogenic regulators, which plays a critical role in beef yield and quality. Long non-coding RNAs (lncRNAs) have been shown to regulate skeletal muscle development. However, the molecular mechanism by which lncRNAs regulate skeletal muscle development is largely unknown. We performed transcriptome analysis of muscle tissues of adult and embryo Angus cattle to investigate the mechanism by which lncRNA regulates skeletal muscle development between adult and embryo cattle. A total of 37,115 candidate lncRNAs were detected, and a total of 1,998 lncRNAs were differentially expressed between the muscle tissue libraries of adult and embryo cattle, including 1,229 up-regulated lncRNAs and 769 down-regulated lncRNAs (adult cattle were the control group). We verified the expression of 7 differentially expressed lncRNAs by quantitative real-time PCR (RT-qPCR), and analysed the tissue expression profile of lnc000100, which is down-regulated in the longest dorsal muscle during foetal life and which is highly specifically expressed in muscle tissue. We found that the interference of lnc000100 significantly inhibited cell proliferation and promoted cell differentiation. Lnc000100 was located in the nucleus by RNA-FISH. Our research provides certain resources for the analysis of lncRNA regulating cattle skeletal muscle development, and may also provide new insights for improving beef production and breed selection.

Construction and Analysis of ceRNA Networks Reveal the Key Genes Associated with Bovine Herpesvirus Type 1 Infection

Background

Virus infection can cause the changes of lncRNA expression levels to regulate the interaction between virus and host, but the relationship between BHV-1 infection and lncRNA has not been reported.

Methods

In this study, in order to reveal the molecular mechanism of RNA in BoHV-1 infection, the Madin-Darby bovine kidney (MDBK) cells were infected with BoHV-1, transcriptome sequencing were performed by next-generation sequencing at 18 h or 24 h or 33 h of viral infection and then based on the competitive endogenous RNA (ceRNA) theory, lncRNA-miRNA-mRNA networks were constructed using these high-throughput sequencing data. The network analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed for functional annotation and exploration of ncRNA ceRNAs in BoHV-1 infection.

Results

The results showed that 48 lncRNAs, 123 mRNAs and 20 miRNAs as differentially expressed genes, and the mitogen activated protein kinase (MAPK) pathway and calcium signaling pathway were significantly enriched in the ceRNA network. Some differentially expressed lncRNA genes were randomly selected for verification by RT-qPCR, and the results showed that their expression trend was consistent with the results of transcriptome sequencing data.

Conclusion

This study revealed that BoHV-1 infection can affect the expression of RNAs in MDBK cells and the regulation of ceRNA network to carry out corresponding biological functions in the host, but further experimental studies are still necessary to prove the hub genes function in ceRNA network and the molecular mechanism in BoHV-1 infection.

Resveratrol inhibits the formation and accumulation of lipid droplets through AdipoQ signal pathway and lipid metabolism lncRNAs

Resveratrol (RES) is one of the best-known bioactive polyphenols that has received much attention in recent years because of its importance to anti-obesity. However, the exact mechanism underlying this effect and whether it can improve lipid metabolism by regulating the long-chain non-coding RNA (lncRNA) remains unclear. In this study, twenty-four healthy crossbred castrated boars were fed a basal diet (control) and a basal diet supplemented with 200 mg, 400 mg or 600 mg RES per Kilogram (kg) of feed for 41 days, respectively. We founded that 400mg/kg and 600mg/kg RES-supplemented diet did not affect growth rate, but reduced significantly subcutaneous adipose thickness, carcass fat rate, greater dramatically the serum concentration of adiponectin and high-density lipoprotein in pigs. Further, we verified that RES could inhibit the formation and accumulation of lipid droplets by AdipoQ-AdipoR1-AMPKα and AdipoQ-AdipoR2-PPARα signal pathway in vivo and vitro (3T3-L1 preadipocytes). Transcriptome analyses founded that 5 differently expressed (DE) lncRNAs and 77 mRNAs in subcutaneous adipose between control group and 400 mg/kg RES group, which mainly involved in "adipocytokine signaling pathway", "Wnt signaling pathway", "PI3K-Akt signaling pathway" and "MAPK signaling pathway". In conclusion, RES can inhibit the formation and accumulation of lipid droplets through AdipoQ signal pathway and lipid metabolism-related lncRNAs. Our results provide a new insight on the molecular mechanism of RES as a nutritional agents to the prevention and treatment for obesity.

Identification of Key Functional Genes and LncRNAs Influencing Muscle Growth and Development in Leizhou Black Goats

Meat yield and quality are important economic traits of livestock. Herein, longissimus dorsi (LD) muscles of Leizhou black goats aged 0, 3, and 6 months were used to identify differentially expressed messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) by high-throughput RNA sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to analyze differentially expressed genes. Expression levels of regulator of calcineurin 1 (RCAN1) and olfactory receptor 2AP1 (OR2AP1) were significantly different in LD muscles of goats aged 0, 3, and 6 months, indicating potentially important roles in postnatal muscle development. Differentially expressed lncRNAs and mRNAs were mainly enriched in biological processes and pathways related to cellular energy metabolism, consistent with previous studies. Three lncRNAs, TCONS_00074191, TCONS_00074190, and TCONS_00078361, may play a cis-acting role with methyltransferase-like 11B (METTL11B) genes and participate in the methylation of goat muscle proteins. Some of the identified genes may provide valuable resources for future studies on postnatal meat development in goat muscles.

Integrated transcriptome analysis reveals roles of long non-coding RNAs (lncRNAs) in caprine skeletal muscle mass and meat quality

Long non-coding RNAs (lncRNAs) play important roles in the growth and development of skeletal muscle. However, there is limited information on goats. In this study, expression profiles of lncRNAs in Longissimus dorsi muscle from Liaoning cashmere (LC) goats and Ziwuling black (ZB) goats with divergent meat yield and meat quality were compared using RNA-sequencing. Based on our previous microRNA (miRNA) and mRNA profiles obtained from the same tissues, the target genes and binding miRNAs of differentially expressed lncRNAs were obtained. Subsequently, lncRNA-mRNA interaction networks and a ceRNA network of lncRNA-miRNA-mRNA were constructed. A total of 136 differentially expressed lncRNAs were identified between the two breeds. Fifteen cis target genes and 143 trans target genes were found for differentially expressed lncRNAs, and they were enriched in muscle contraction, muscle system process, muscle cell differentiation, and p53 signaling pathway. A total of 69 lncRNA-trans target gene pairs were constructed, with close relationship with muscle development, intramuscular fat deposition, and meat tenderness. A total of 16 lncRNA-miRNA-mRNA ceRNA pairs were identified, of which some reportedly associated with skeletal muscle development and fat deposition were found. The study will provide an improved understanding of the roles of lncRNAs in caprine meat yield and meat quality.

Identification and Characterization of lncRNAs Expression Profile Related to Goat Skeletal Muscle at Different Development Stages

LncRNAs are essential for regulating skeletal muscle. However, the expression profile and function of lncRNAs in goat muscle remains unclear. Here, an average of ~14.58 Gb high-quality reads were obtained from longissimus dorsi tissues of 1-month-old (n = 3) and 9-month-old (n = 3) Wu'an black goats using RNA sequencing. Of a total of 3441 lncRNAs, 1281 were lincRNAs, 805 were antisense lncRNAs, and 1355 were sense_overlapping lncRNAs. These lncRNAs shared some properties with goats, such as fewer exons, shorter transcript, and open reading frames (ORFs) length. Among them, 36 differentially expressed lncRNAs (DE lncRNA) were identified, and then 10 random lncRNAs were validated by RT-qPCR. Furthermore, 30 DE lncRNAs were neighboring 71 mRNAs and several genes were functionally enriched in muscle development-related pathways, such as APC, IFRD1, NKX2-5, and others. Additionally, 36 DE lncRNAs and 2684 mRNAs were included in co-expression interactions. A lncRNA-miRNA-mRNA network containing 4 lncRNAs, 3 miRNAs, and 8 mRNAs was finally constructed, of which XR_001296113.2 might regulate PDLIM7 expression by interaction with chi-miR-1296 to affect skeletal muscle development. This study revealed the expression profile of goat lncRNAs for further investigative studies and provides a fuller understanding of skeletal muscle development.

LncR-133a Suppresses Myoblast Differentiation by Sponging miR-133a-3p to Activate the FGFR1/ERK1/2 Signaling Pathway in Goats

Long noncoding RNAs (lncRNAs) are involved in a variety of biological processes and illnesses. While a considerable number of lncRNAs have been discovered in skeletal muscle to far, their role and underlying processes during myogenesis remain mostly unclear. In this study, we described a new functional lncRNA named lncR-133a. Gene overexpression and interference studies in goat skeletal muscle satellite cells (MuSCs) were used to establish its function. The molecular mechanism by which lncR-133a governs muscle differentiation was elucidated primarily using quantitative real-time PCR (qRT-PCR), Western blotting, dual-luciferase activity assays, RNA immunoprecipitation, biotin-labeled probe, and RNA fluorescence in situ hybridization analyses. LncR-133a was found to be substantially expressed in longissimus thoracis et lumborum muscle, and its expression levels changed during MuSC differentiation in goats. We validated that lncR-133a suppresses MuSC differentiation in vitro. Dual-luciferase reporter screening, Argonaute 2 (AGO2) RNA immunoprecipitation assays, biotin-labeled lncR-133a capture, and fluorescence in situ hybridization showed that lncR-133a interacted with miR-133a-3p. Additionally, miR-133a-3p facilitated MuSC differentiation, but lncR-133a reversed this effect. The luciferase reporter assay and functional analyses established that miR-133a-3p directly targets fibroblast growth factor receptor 1 (FGFR1). Moreover, lncR-133a directly reduced miR-133a-3p’s capacity to suppress FGFR1 expression, and positively regulated the phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2). In summary, our results suggested that lncR-133a suppresses goat muscle differentiation by targeting miR-133a-3p and activating FGFR1/ERK1/2 signaling pathway.

Surviving in the Brine: A Multi-Omics Approach for Understanding the Physiology of the Halophile Fungus Aspergillus sydowii at Saturated NaCl Concentration

Although various studies have investigated osmoadaptations of halophilic fungi to saline conditions, only few analyzed the fungal mechanisms occurring at saturated NaCl concentrations. Halophilic Aspergillus sydowii is a model organism for the study of molecular adaptations of filamentous fungi to hyperosmolarity. For the first time a multi-omics approach (i.e., transcriptomics and metabolomics) was used to compare A. sydowii at saturated concentration (5.13 M NaCl) to optimal salinity (1 M NaCl). Analysis revealed 1,842 genes differentially expressed of which 704 were overexpressed. Most differentially expressed genes were involved in metabolism and signal transduction. A gene ontology multi-scale network showed that ATP binding constituted the main network node with direct interactions to phosphorelay signal transduction, polysaccharide metabolism, and transferase activity. Free amino acids significantly decreased and amino acid metabolism was reprogrammed at 5.13 M NaCl. mRNA transcriptional analysis revealed upregulation of genes involved in methionine and cysteine biosynthesis at extreme water deprivation by NaCl. No modifications of membrane fatty acid composition occurred. Upregulated genes were involved in high-osmolarity glycerol signal transduction pathways, biosynthesis of β-1,3-glucans, and cross-membrane ion transporters. Downregulated genes were related to the synthesis of chitin, mannose, cell wall proteins, starvation, pheromone synthesis, and cell cycle. Non-coding RNAs represented the 20% of the total transcripts with 7% classified as long non-coding RNAs (lncRNAs). The 42% and 69% of the total lncRNAs and RNAs encoding transcription factors, respectively, were differentially expressed. A network analysis showed that differentially expressed lncRNAs and RNAs coding transcriptional factors were mainly related to the regulation of metabolic processes, protein phosphorylation, protein kinase activity, and plasma membrane composition. Metabolomic analyses revealed more complex and unknown metabolites at saturated NaCl concentration than at optimal salinity. This study is the first attempt to unravel the molecular ecology of an ascomycetous fungus at extreme water deprivation by NaCl (5.13 M). This work also represents a pioneer study to investigate the importance of lncRNAs and transcriptional factors in the transcriptomic response to high NaCl stress in halophilic fungi.

Advances in the Immune Regulatory Role of Non-Coding RNAs (miRNAs and lncRNAs) in Insect-Pathogen Interactions

Insects are by far the most abundant and diverse living organisms on earth and are frequently prone to microbial attacks. In other to counteract and overcome microbial invasions, insects have in an evolutionary way conserved and developed immune defense mechanisms such as Toll, immune deficiency (Imd), and JAK/STAT signaling pathways leading to the expression of antimicrobial peptides. These pathways have accessory immune effector mechanisms, such as phagocytosis, encapsulation, melanization, nodulation, RNA interference (RNAi), lysis, autophagy, and apoptosis. However, pathogens evolved strategies that circumvent host immune response following infections, which may have helped insects further sophisticate their immune response mechanisms. The involvement of ncRNAs in insect immunity is undeniable, and several excellent studies or reviews have investigated and described their roles in various insects. However, the functional analyses of ncRNAs in insects upon pathogen attacks are not exhaustive as novel ncRNAs are being increasingly discovered in those organisms. This article gives an overview of the main insect signaling pathways and effector mechanisms activated by pathogen invaders and summarizes the latest findings of the immune modulation role of both insect- and pathogen-encoded ncRNAs, especially miRNAs and lncRNAs during insect–pathogen crosstalk.

Systematic identification and characterization of long noncoding RNAs (lncRNAs) during Aedes albopictus development

Background

Aedes albopictus originated in the tropical forests of Southeast Asia and can currently be found on all continents. As one of the main arboviral vectors, the control of Ae. albopictus requires novel strategies, informed by a deep knowledge of its biology. Little is known regarding mosquito long noncoding RNAs (lncRNAs), which are transcripts longer than 200 nucleotides that lack protein-coding potential and have roles in developmental regulation.

Results

Based on RNA-seq data from five developmental time points, eggs, early larvae, late larvae, pupae, and adults (female and male) of Ae. albopictus, 21,414 lncRNAs were characterized in this study. Differential expression analysis revealed that lncRNAs exhibited developmental stage specificity. The expression of most lncRNAs was upregulated at the onset of metamorphosis developmental stages. More differentially expressed lncRNAs were observed between eggs and early larvae. Weighted gene co-expression network analysis (WGCNA) further confirmed that the expression patterns of lncRNAs were obviously correlated with specific developmental time points. Functional annotation using co-expression analysis revealed that lncRNAs may be involved in the regulation of metamorphic developmental transitions of Ae. albopictus. The hub lncRNAs and hub gene clusters were identified for each module that were highly associated with specific developmental time points.

Conclusions

The results of this study will facilitate future researches to elucidate the regulatory mechanisms of lncRNAs in the development of Ae. albopictus and utilize lncRNAs to assist with mosquito control.

Characterization of XR_311113.2 as a MicroRNA Sponge for Pre-ovulatory Ovarian Follicles of Goats via Long Noncoding RNA Profile and Bioinformatics Analysis

Long noncoding RNAs (lncRNAs) were identified recently as a large class of noncoding RNAs (ncRNAs) with a length ≥200 base pairs (bp). The function and mechanism of lncRNAs have been reported in a growing number of species and tissues. In contrast, the regulatory mechanism of lncRNAs in the goat reproductive system has rarely been reported. In the present study, we sequenced and analyzed the lncRNAs using bioinformatics to identify their expression profiles. As a result, 895 lncRNAs were predicted in the pre-ovulatory ovarian follicles of goats. Eighty-eight lncRNAs were differentially expressed in the Macheng black goat when compared with Boer goat. In addition, the lncRNA XR_311113.2 acted as a sponge of chi-miR-424-5p, as assessed via a luciferase activity assay. Taken together, our findings demonstrate that lncRNAs have potential effects in the ovarian follicles of goats and may represent a promising new research field to understand follicular development.

Identification and the potential roles of long non-coding RNAs in regulating acetyl-CoA carboxylase ACC transcription in spirotetramat-resistant Aphis gossypii

Long non-coding RNAs (lncRNAs) represent the largest class of non-coding transcripts. They act a pivotal part in various insect developmental processes and stress responses. However, the investigation of lncRNA functions in insecticide resistant remains at an early phase. Herein, we conducted whole-transcriptome RNA sequencing for two cotton aphid (Aphis gossypii Glover) strains, i.e., insecticide-susceptible (SS) and spirotetramat-resistant (SR). We discovered 6059 lncRNAs in the RNA-Seq data, and 874 lncRNAs showed differential expression. In addition, 5 lncRNAs among 874 lncRNAs were predicted as targets of acetyl-CoA carboxylase (ACC). Reverse transcription real-time quantitative PCR (RT-qPCR) combined with RNA interference (RNAi) confirmed that selected ACC lncRNA was related to the expression of ACC. Moreover, we also identified two transcription factors, i.e., C/EBP and C/EBPzeta, that regulate the transcription level of ACC lncRNA. These results provide a good basis for the study of cotton aphid lncRNA functions in insecticide resistance development.

Identification of lncRNAs involved in maternal-to-zygotic transition of in vitro-produced porcine embryos by single-cell RNA-seq

Long non-coding RNAs (lncRNAs) function through multiple tiers of molecular circuits and are vital to gamete maturation and early embryo development. However, in pig early embryos, identification and expression dynamics of lncRNAs remain less studied. Here, we systematically analysed the expression dynamics of lncRNAs based on our previously published single-cell RNA-seq data from pig mature oocytes (GSE160334), and single blastomeres biopsied from pig in vitro fertilized (IVF) and early parthenogenetically activated (PA) embryos (1- to 8-cell stages; GSE164812). With the progression of embryo development, the total number of expressed lncRNAs gradually decreased and showed great variation at each developmental stage for both IVF and PA groups. Consecutive stage pairwise comparison of MII oocytes, 1-cell zygotes, 2-cell, 4-cell and 8-cell IVF embryos identified 151, 245, 1119 and 188 differentially expressed (DE) lncRNAs, including 119, 80, 867, 77 up-regulated and 32, 165, 252, 111 down-regulated, while 289, 437, 895 and 495 DE lncRNAs (141, 89, 768, 97 up-regulated and 148, 348, 127, 398 down-regulated) were identified in PA embryos at the same stages. The DE lncRNAs identified within IVF embryos were much different from that identified within PA embryos, showing embryo type-specific manner. Further cross-comparison between PA and IVF embryos identified 184, 656, 2502 and 266 DE lncRNAs for the 1- to 8-cell embryo stages, respectively. Further GO and KEGG enrichment analysis of DE mRNAs targeted by DELs indicated that different signalling pathways were involved in maternal-only and bi-parental embryo development. Collectively, comparative profiling of lncRNA expression dynamics between pig IVF and PA embryos provides a valuable resource, to investigate further regulatory mechanisms of lncRNAs associated with ZGA and maternal RNA decay during early embryo development.

Identification of Long Non-Coding RNAs Involved in Porcine Fat Deposition Using Two High-Throughput Sequencing Methods

Adipose is an important body tissue in pigs, and fatty traits are critical in pig production. The function of long non-coding RNA (lncRNA) in fat deposition and metabolism has been found in previous studies. In this study, we collected the adipose tissue of six Landrace pigs with contrast backfat thickness (n_high = 3, n_low = 3), after which we performed strand-specific RNA sequencing (RNA-seq) based on pooling and biological replicate methods. Biological replicate and pooling RNA-seq revealed 1870 and 1618 lncRNAs, respectively. Using edgeR, we determined that 1512 genes and 220 lncRNAs, 2240 genes and 127 lncRNAs were differentially expressed in biological replicate and pooling RNA-seq, respectively. After target gene prediction, we found that ACSL3 was cis-targeted by lncRNA TCONS-00052400 and could activate the conversion of long-chain fatty acids. In addition, lncRNA TCONS_00041740 cis-regulated gene ACACB regulated the rate-limiting enzyme in fatty acid oxidation. Since these genes have necessary functions in fat metabolism, the results imply that the lncRNAs detected in our study may affect backfat deposition in swine through regulation of their target genes. Our study explored the regulation of lncRNA and their target genes in porcine backfat deposition and provided new insights for further investigation of the biological functions of lncRNA.

Expression profile of long non-coding RNAs in porcine lymphnode response to porcine circovirus type 2 infection

Porcine circovirus type 2 (PCV2) can cause various clinical diseases in pigs, resulting in huge losses for the pig farms all over the world. In order to develop a new strategy to control PCV2, it is essential to understand its mechanisms firstly, especially PCV2 interferes with the host's innate immunity. In the present study, lncRNA and mRNA expression profiles in porcine lymphnode response to PCV2 infection were deeply sequenced and analyzed. 3271 novel lncRNAs were identified in all. 1898 mRNAs and 282 lncRNAs showed differential expression between control and PCV2-infected groups. The bioinformatics analysis including lncRNA-mRNA co-expression network construction, as well as GO and KEGG pathway analysis focused on the DEGs was carried out. The results indicated that lncRNAs might participate in PCV2 infection-induced the pathogenesis of immunosuppression through regulating the host's immune responses, biological regulation, response to stimulus, cellular component organization or biogenesis and metabolism. And these differentially expressed lncRNAs might play important roles in response to PCV2 infection in the host's innate immune system. These findings provided a large-scale survey of dysregulated lncRNAs after PCV2 infection, especially the lncRNAs responded to host's innate immune within the lymphnode. This study will provide a novel insight into the lncRNAs' functions and the possible immunosuppressive mechanism induced by PCV2 infection. However, further research will be required to verify the characteristic function of the dysregulated lncRNAs.

Identification and Analysis of Long Non-coding RNAs in Leuciscus waleckii Adapted to Highly Alkaline Conditions

Leuciscus waleckii is a freshwater fish that is known to inhabit the Dali Nor Lake, Inner Mongolia, China. The water in this lake has an HCO3 -/CO3 2- concentration of 54 mM (pH 9.6) and a salinity of 0.6‰. The physiological mechanisms that allow this fish to tolerate these saline/alkaline conditions have yet to be elucidated. Transcriptional component analysis has shown that the expression levels of a large number of genes involved in the pathways responsible for osmo-ionoregulation and arachidonic acid metabolism pathway expression change significantly (p < 0.05) during the regulation of acid-base balance under high alkaline stress. In this study, we investigated the role of long non-coding RNAs (lncRNAs) during adaptation to high alkaline conditions. Fish were challenged to an NaHCO3-adjusted alkalinity of 0 mM, 30 mM (pH 9.44 ± 0.08), and 50 mM (pH 9.55 ± 0.06) for 20 days in the laboratory. Gill and kidney tissues were then collected for high-throughput sequencing assays. A total of 159 million clean reads were obtained by high-throughput sequencing, and 41,248 lncRNA transcripts were identified. Of these, the mean number of exons and the mean length of the lncRNA transcripts were 4.8 and 2,079 bp, respectively. Based on the analysis of differential lncRNA transcript expression, a total of 5,244 and 6,571 lncRNA transcripts were found to be differentially expressed in the gills and kidneys, respectively. Results derived from Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the coding genes were correlated with the lncRNA expression profiles. GO analysis showed that many lncRNAs were enriched in the following processes: "transporter activity," "response to stimulus," and "binding." KEGG analysis further revealed that metabolic pathways were significantly enriched. A random selection of 16 lncRNA transcripts was tested by RT-qPCR; these results were consistent with our sequencing results. We found that a large number of genes, with the same expression profiles as those with differentially expressed lncRNAs, were associated with the regulation of acid-base balance, ion transport, and the excretion of ammonia and nitrogen. Collectively, our data indicate that lncRNA-regulated gene expression plays an important role in the process of adaptation to high alkaline conditions in L. waleckii.

Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori

Background

20-hydroxyecdysone (20E) plays important roles in insect molting and metamorphosis. 20E-induced autophagy has been detected during the larval–pupal transition in different insects. In Bombyx mori, autophagy is induced by 20E in the larval fat body. Long non-coding RNAs (lncRNAs) function in various biological processes in many organisms, including insects. Many lncRNAs have been reported to be potential for autophagy occurrence in mammals, but it has not been investigated in insects.

Results

RNA libraries from the fat body of B. mori dissected at 2 and 6 h post-injection with 20E were constructed and sequenced, and comprehensive analysis of lncRNAs and mRNAs was performed. A total of 1035 lncRNAs were identified, including 905 lincRNAs and 130 antisense lncRNAs. Compared with mRNAs, lncRNAs had longer transcript length and fewer exons. 132 lncRNAs were found differentially expressed at 2 h post injection, compared with 64 lncRNAs at 6 h post injection. Thirty differentially expressed lncRNAs were common at 2 and 6 h post-injection, and were hypothesized to be associated with the 20E response. Target gene analysis predicted 6493 lncRNA-mRNA cis pairs and 42,797 lncRNA-mRNA trans pairs. The expression profiles of LNC_000560 were highly consistent with its potential target genes, Atg4B, and RNAi of LNC_000560 significantly decreased the expression of LNC_000560 and Atg4B. These results indicated that LNC_000560 was potentially involved in the 20E-induced autophagy of the fat body by regulating Atg4B.

Conclusions

This study provides the genome-wide identification and functional characterization of lncRNAs associated with 20E-induced autophagy in the fat body of B. mori. LNC_000560 and its potential target gene were identified to be related to 20-regulated autophagy in B. mori. These results will be helpful for further studying the regulatory mechanisms of lncRNAs in autophagy and other biological processes in this insect model.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07692-1.

Transcriptome Analysis Reveals the Profile of Long Non-coding RNAs During Chicken Muscle Development

The developmental complexity of muscle arises from elaborate gene regulation. Long non-coding RNAs (lncRNAs) play critical roles in muscle development through the regulation of transcription and post-transcriptional gene expression. In chickens, previous studies have focused on the lncRNA profile during the embryonic periods, but there are no studies that explore the profile from the embryonic to post-hatching period. Here, we reconstructed 14,793 lncRNA transcripts and identified 2,858 differentially expressed lncRNA transcripts and 4,282 mRNAs from 12-day embryos (E12), 17-day embryos (E17), 1-day post-hatch chicks (D1), 14-day post-hatch chicks (D14), 56-day post-hatch chicks (D56), and 98-day post-hatch chicks (D98), based on our published RNA-seq datasets. We performed co-expression analysis for the differentially expressed lncRNAs and mRNAs, using STEM, and identified two profiles with opposite expression trends: profile 4 with a downregulated pattern and profile 21 with an upregulated pattern. The cis- and trans-regulatory interactions between the lncRNAs and mRNAs were predicted within each profile. Functional analysis of the lncRNA targets showed that lncRNAs in profile 4 contributed to the cell proliferation process, while lncRNAs in profile 21 were mainly involved in metabolism. Our work highlights the lncRNA profiles involved in the development of chicken breast muscle and provides a foundation for further experiments on the role of lncRNAs in the regulation of muscle development.

Genome-wide identification of long non-coding RNAs (lncRNAs) associated with malathion resistance in Bactrocera dorsalis

BACKGROUND

Long non-coding RNAs (lncRNAs) play important roles in the regulation of biological processes and have been identified in many species including insects. However, the association between lncRNAs and pesticide resistance in insect species such as Bactrocera dorsalis is unknown.

RESULTS

RNA-seq was performed on malathion resistant (MR1) and susceptible (MS) strains of B. dorsalis and a total of 6171 lncRNAs transcripts were identified. These included 3728 lincRNAs, 653 antisense lncRNAs, 1402 intronic lncRNAs, and 388 sense lncRNAs. A total of 40 and 52 upregulated lncRNAs were found in females and males of the MR1 strain compared to 54 and 49 in the same sexes of the MS strain, respectively. Twenty-seven of these lncRNAs showed the same trend of expression in both females and males in the MR1 strain, in which 15 lncRNAs were upregulated and 12 were downregulated. RT-qPCR results indicated that the differentially expressed lncRNAs were associated with malathion resistance. The lnc15010.10 and lnc3774.2 were highly expressed in the cuticle of the MR1 strain, indicating that these two lncRNAs may be related to malathion resistance. RNAi of lnc3774.2 and a bioassay showed that malathion resistance was possibly influenced by changes in the B. dorsalis cuticle.

CONCLUSION

LncRNAs of B. dorsalis potentially related to the malathion resistance were identified. Two lncRNAs appear to influence malathion resistance via modulating the structure, or components, of the cuticle. © 2021 Society of Chemical Industry.

The PacBio Full-Length Transcriptome of the Tea Aphid as a Reference Resource

The tea aphid, Aphis aurantii, has become one of the destructive pests in tea plantations in the tropics and subtropics. Very few functional studies have so far focused on the developmental and reproductive biology at a molecular level, because of the lack of comprehensive genetic information. Full-length transcriptomes represent a very highly efficient approach to obtain reference gene sequences in non-model insects. In the present study, the transcriptome of A. aurantii was comprehensively sequenced using PacBio Iso-Seq technology. A total of 46.8 Gb nucleotides and 15,938 non-redundant full-length transcripts were obtained, 13,498 (84.69%) of which were annotated into seven databases. Of these transcripts, 2,029 alternative splicing events and 15,223 simple sequence repeats were detected. Among these transcripts, 4,571 (28.68%) and 11,367 (71.32%) were long non-coding RNAs (lncRNAs) and protein-coding genes, respectively. Five hundred and ninety transcription factors were detected. The first full-length transcriptome represents a significant increase in the known genetic information of A. aurantii. It will assist the future functional study of genes involved in its development and reproduction.

Analysis and Screening of Reproductive Long Non-coding RNAs Through Genome-Wide Analyses of Goat Endometrium During the Pre-attachment Phase

Reproduction in goat is highly impeded by implantation failure. Of concern, the underlying mechanism leading to embryo implantation remains unclear. In this study, deep sequencing was employed through strand-specific Ribo-Zero RNA-Seq to characterize transcriptome changes in the endometrium during the maternal recognition of pregnancy. A total of 996 differential transcripts (115 lncRNAs and 881 mRNAs) existing between the pregnant and non-pregnant endometrium were revealed through bioinformatics analysis. The screening was performed on lncRNAs (XR_001918173.1, LNC_002760, and LNC_000599) and LNC_009053, to determine their potential role in regulating the synthesis of retinol and endometrium remolding through the proteasome pathway, respectively. The hypothesis of whether certain lncRNAs, namely, LNC_007223, LNC_005256, and LNC_010092 could play important roles in embryo implantation was tested. These novel findings are of paramount relevance to further elucidate the molecular mechanisms of embryo implantation and uncover new targets to improve goat reproduction.

Genome-Wide Identification of Long Non-coding RNAs in the Gravid Ectoparasite Varroa destructor

Long non-coding RNAs (lncRNAs) emerge as critical regulators across a wide variety of biological functions in living organisms. However, to date, no systematic characterization of lncRNAs has been investigated in the ectoparasitic mite Varroa destructor, the most severe biotic threat to honey bees worldwide. Here, we performed an initial genome-wide identification of lncRNAs in V. destructor via high-throughput sequencing technology and reported, for the first time, the transcriptomic landscape of lncRNAs in the devastating parasite. By means of a lncRNA identification pipeline, 6,645 novel lncRNA transcripts, encoded by 3,897 gene loci, were identified, including 2,066 sense lncRNAs, 2,772 lincRNAs, and 1,807 lncNATs. Compared with protein-coding mRNAs, V. destructor lncRNAs are shorter in terms of full length, as well as of the ORF length, contain less exons, and express at lower level. GO term and KEGG pathway enrichment analyses of the lncRNA target genes demonstrated that these predicted lncRNAs may be potentially responsible for the regulatory functions of cellular and biological progresses in the reproductive phase of V. destructor. To our knowledge, this is the first catalog of lncRNA profile in the parasitiformes species, providing a valuable resource for genetic and genomic studies. Understanding the characteristics and features of lncRNAs in V. destructor would promote sustainable parasite control.

Analysis of dynamic and widespread lncRNA and miRNA expression in fetal sheep skeletal muscle

The sheep is an economically important animal, and there is currently a major focus on improving its meat quality through breeding. There are variations in the growth regulation mechanisms of different sheep breeds, making fundamental research on skeletal muscle growth essential in understanding the regulation of (thus far) unknown genes. Skeletal muscle development is a complex biological process regulated by numerous genes and non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). In this study, we used deep sequencing data from sheep longissimus dorsi (LD) muscles sampled at day 60, 90, and 120 of gestation, as well as at day 0 and 360 following birth, to identify and examine the lncRNA and miRNA temporal expression profiles that regulate sheep skeletal myogenesis. We stained LD muscles using histological sections to analyse the area and circumference of muscle fibers from the embryonic to postnatal development stages. Our results showed that embryonic skeletal muscle growth can be characterized by time. We obtained a total of 694 different lncRNAs and compared the differential expression between the E60 vs. E90, E90 vs. E120, E120 vs. D0, and D0 vs. D360 lncRNA and gene samples. Of the total 701 known sheep miRNAs we detected, the following showed a wide range of expression during the embryonic stage: miR-2387, miR-105, miR-767, miR-432, and miR-433. We propose that the detected lncRNA expression was time-specific during the gestational and postnatal stages. GO and KEGG analyses of the genes targeted by different miRNAs and lncRNAs revealed that these significantly enriched processes and pathways were consistent with skeletal muscle development over time across all sampled stages. We found four visual lncRNA–gene regulatory networks that can be used to explore the function of lncRNAs in sheep and may be valuable in helping improve muscle growth. This study also describes the function of several lncRNAs that interact with miRNAs to regulate myogenic differentiation.

Identification and Characterization of lncRNAs Related to the Muscle Growth and Development of Japanese Flounder (Paralichthys olivaceus)

Long noncoding RNAs (lncRNAs) play an important role in many life activities, but the expression pattern and function of lncRNAs in Japanese flounder skeletal muscle are unclear. In this study, 751 lncRNAs were selected from skeletal muscle in different development stages of the Japanese flounder [stage A: larval 7 days post hatching (dph); stage B: juvenile about 90 dph; stage C (female) and stage D (male): adult about 24 months] using coding potential analysis methods. In total, 232, 211, 194, 28, 29, and 14 differentially expressed lncRNAs and 9549, 8673, 9181, 1821, 1080, and 557 differentially expressed mRNAs were identified in comparisons of A versus B, A versus C, A versus D, B versus C, B versus D, and C versus D, respectively. We identified the cis- and trans-regulatory target genes of differentially expressed lncRNAs, and lncRNA-gene interaction networks were constructed using the Cytoscape program. In total, there were 200, 200, 200, 93, 47, and 11 cis-regulation relationships, and 29, 19, 24, 38, 8, and 47 trans-regulation relationships in the comparisons between A versus B, A versus C, A versus D, B versus C, B versus D, and C versus D, respectively. These results indicate that lncRNA may participate in the development of Japanese flounder skeletal muscle through cis- or trans-acting mechanisms, thus providing a scientific basis for further study of the biological function of lncRNA in Japanese flounder skeletal muscle. Based on these relationships, functional annotation of the related lncRNAs was performed by gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Differentially expressed genes associated with muscle development were enriched in multiple pairs of comparisons (e.g., differentially expressed genes LOC109640370, LOC109634180, LOC109643555, rusc1, and LOC109626999 were enriched in the actin-binding term, and differentially expressed genes LOC109640370, was, LOC109644970, LOC109643555, and itga9 were enriched in the regulation of the actin cytoskeleton pathway in the KEGG pathway analysis in the comparison of stages C and D). We predicted lncRNA-mRNA, miRNA-mRNA, and lncRNA-miRNA regulatory relationships and constructed interactive networks using Cytoscape software. Co-expression networks show that most lncRNAs interact with one or two predicted miRNAs involved in muscle growth and development. These results provide a basis for further study of the function of lncRNAs on skeletal muscle in different developmental stages of Japanese flounder.

Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett)

Background

Long non-coding RNAs (lncRNAs) are involved in many fundamental biological processes, such as transcription regulation, protein degradation, and cell differentiation. Information on lncRNA in the melon fly, Zeugodacus cucurbitae (Coquillett) is currently limited.

Results

We constructed 24 RNA-seq libraries from eight tissues (midgut, Malpighian tubules, fat body, ovary, and testis) of Z. cucurbitae adults. A total of 3124 lncRNA transcripts were identified. Among those, 1464 were lincRNAs, 1037 were intronic lncRNAs, 301 were anti-sense lncRNAs, and 322 were sense lncRNAs. The majority of lncRNAs contained two exons and one isoform. Differentially expressed lncRNAs were analyzed between tissues, and Malpighian tubules versus testis had the largest number. Some lncRNAs exhibited strong tissue specificity. Specifically expressed lncRNAs were identified and filtered in tissues of female and male Z. cucurbitae based on their expression levels. Four midgut-specific lncRNAs were validated by quantitative real-time polymerase chain reaction (RT-qPCR), and the data were consistent with RNA-seq data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of targets of midgut-specific lncRNAs indicated an enrichment of the metabolic process.

Conclusions

This was the first systematic identification of lncRNA in the melon fly. Expressions of lncRNAs in multiple adult tissues were evaluated by quantitative transcriptomic analysis. These qualitative and quantitative analyses of lncRNAs, especially the tissue-specific lncRNAs in Z. cucurbitae, provide useful data for further functional studies.

Exploring the Regulatory Potential of Long Non-Coding RNA in Feed Efficiency of Indicine Cattle

Long non-coding RNA (lncRNA) can regulate several aspects of gene expression, being associated with complex phenotypes in humans and livestock species. In taurine beef cattle, recent evidence points to the involvement of lncRNA in feed efficiency (FE), a proxy for increased productivity and sustainability. Here, we hypothesized specific regulatory roles of lncRNA in FE of indicine cattle. Using RNA-Seq data from the liver, muscle, hypothalamus, pituitary gland and adrenal gland from Nellore bulls with divergent FE, we submitted new transcripts to a series of filters to confidently predict lncRNA. Then, we identified lncRNA that were differentially expressed (DE) and/or key regulators of FE. Finally, we explored lncRNA genomic location and interactions with miRNA and mRNA to infer potential function. We were able to identify 126 relevant lncRNA for FE in Bos indicus, some with high homology to previously identified lncRNA in Bos taurus and some possible specific regulators of FE in indicine cattle. Moreover, lncRNA identified here were linked to previously described mechanisms related to FE in hypothalamus-pituitary-adrenal axis and are expected to help elucidate this complex phenotype. This study contributes to expanding the catalogue of lncRNA, particularly in indicine cattle, and identifies candidates for further studies in animal selection and management.

Comprehensive Identification and Characterization of Long Non-coding RNAs Associated With Rice Black-Streaked Dwarf Virus Infection in Laodelphax striatellus (Fallén) Midgut

Long non-coding RNAs (lncRNAs) are involved in a variety of biological functions through transcriptional and post-transcriptional regulation. However, little is known about their functions in the process of insect mediated virus transmission. In the present study, we analyzed using RNA-Seq, the lncRNAs that were differentially expressed in response to Rice black-streaked dwarf virus (RBSDV) infection in Laodelphax striatellus (Fallén) midgut. A total of 13,927 lncRNAs were identified and over 69% were assigned to intergenic regions. Among them, 176 lncRNAs were differentially expressed and predicted to target 168 trans-regulatory genes. Ten differentially expressed lncRNAs were selected and their expression changes were validated by RT-qPCR. KEGG analysis showed that these target genes were enriched in the essential biological process, such as Purine metabolism, Valine, leucine and isoleucine degradation, and Fatty acid elongation. The expression levels of the differentially expressed lncRNAs and the predicted target genes that were significantly enriched in the Human papillomavirus infection pathway were analyzed by RT-qPCR. The results showed that several lncRNAs were co-expressed with their target genes. One of the lncRNAs called MSTRG15394 and its target gene, encoding a secreted protease inhibitor (PI), were up-regulated at the transcriptional level after RBSDV infection. Knockdown of MSTRG15394 could down-regulate the PI expression at mRNA level. Inhibition of either MSTRG15394 or PI expression by RNA interference promoted RBSDV accumulation in L. striatellus midgut. Our finding provides new insights into the function of lncRNAs in regulating virus infection in an important insect vector.

The Clock-Controlled lncRNA-AK028245 Participates in the Immune Response via Immune Response Factors OTUD7B and A20

Emerging evidence has demonstrated that long noncoding RNAs (lncRNAs) play critical roles in the epigenetic and transcriptional regulation of mammalian circadian systems. Circadian rhythmicity regulates many aspects of our immune system, and perturbation of the circadian clock can augment the inflammatory response. However, knowledge of the precise functions of lncRNAs in the regulation of immune functions within the circadian system is relatively limited. In this study, differentially expressed lncRNAs induced by Clock knockdown were screened via mRNA/lncRNA microarray and bioinformatic prediction analysis. We identified a Clock-regulated lncRNA, AK028245, which was correlated with the activation of the immune response. The expression levels of AK028245 were decreased in the spleen of immunosuppressed mice and elevated in immune-activated mice treated with lipopolysaccharide (LPS). Further, Clock knockdown decreased the expression of OTUD7B and A20, 2 early immune response factors acting on the NF-κB signaling pathway. Interestingly, inhibition of AK028245 increased their expression, mitigating the effects of Clock knockdown. In addition, inhibition of AK028245 downregulated the expression of tumor necrosis factor-α and interleukin-6 in the late stages of LPS stimulation and the expression of interferon-γ and Cxcl12 in the peak stages. We conclude that this newly identified lncRNA plays a role in the crosstalk between Clock and immune response regulators, likely resulting in a proinflammatory response targeting OTUD7B and A20. The lncRNA AK028245 has revealed a new mechanism of the immune response and provided new targets for the treatment of immune disorders.

Systematic analyses reveal RNA editing events involved in skeletal muscle development of goat (Capra hircus)

RNA editing is a posttranscriptional molecular process involved with specific nucleic modification, which can enhance the diversity of gene products. Adenosine-to-inosine (A-to-I, I is read as guanosine by both splicing and translation machinery) is the main type of RNA editing in mammals, which manifested as AG (adenosine-to-guanosine) in sequence data. Here, we aimed to explore patterns of RNA editing using RNA sequencing data from skeletal muscle at four developmental stages (three fetal periods and one postnatal period) in goat. We found the occurrences of RNA editing events raised at fetal periods and declined at the postnatal period. Also, we observed distinct editing levels of AG editing across stages, and significant difference was found between postnatal period and fetal periods. AG editing patterns in newborn goats are similar to those of 45-day embryo compared with embryo at 105 days and embryo at 60 days. In this study, we found a total of 1415 significantly differential edited AG sites among four groups. Moreover, 420 sites were obviously clustered into six time-series profiles, and one profile had significant association between editing level and gene expression. Our findings provided some novel insights into understanding the molecular mechanism of muscle development in mammals.

Comprehensive analysis of dysregulated exosomal long non-coding RNA networks associated with arteriovenous malformations

Arteriovenous malformations (AVMs) are congenital vascular lesions with a high tendency for aggravation and recurrence after treatment, and their genesis remains enigmatic. In this study, we investigated exosomal long non-coding RNA (lncRNA) and mRNA expression and constructed a competitive endogenous RNA regulatory network in AVMs. Ethics approval was provided, and informed written consent was given prior to the inclusion of all participants. Blood samples were obtained from patients with AVMs and healthy controls at Shanghai Ninth People's Hospital, China, from May to November 2018, and total exosomes were isolated and validated. Differentially expressed exosomal lncRNAs and mRNAs were detected by RNA-seq, analysed by bioinformatic methods and validated by qRT-PCR. A competitive endogenous RNA regulatory network was constructed. The characteristics of the captured extracellular vesicles conformed to the features of exosomes. A total of 117 dysregulated exosomal lncRNAs and 1159 dysregulated exosomal mRNAs were identified in AVMs. qRT-PCR demonstrated that the exosomal lncRNAs MIR4435-1HG, LINC00657, LOC101927854 and SEPT5-GP1BB were upregulated in AVM exosomes. The Gene Ontology (GO) terms haemopoiesis and negative regulation of neuron projection development were significantly enriched in relation to dysregulated exosomal cis lncRNAs. A total of 199 GO terms and 80 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were enriched for the dysregulated exosomal mRNAs. In the exosomal lncRNA-miRNA-mRNA-related ceRNA regulatory network, the top 3 significant modules involved 31 dysregulated exosomal lncRNAs and 114 dysregulated exosomal mRNAs, which were enriched in the Rap 1, Ras, MAPK signalling pathways and platelet activation KEGG pathway. This study comprehensively identified dysregulated exosomal lncRNAs and mRNAs in AVMs, demonstrated the involvement of dysregulated lncRNA and mRNA patterns in AVMs and constructed an exosomal competitive endogenous RNA regulatory network.

Genome-Wide Analysis Reveals Changes in Polled Yak Long Non-coding RNAs in Skeletal Muscle Development

Long non-coding RNAs (lncRNAs) have been extensively studied in recent years. Numerous lncRNAs have been identified in mice, rats, and humans, some of which play important roles in muscle formation and development. However, little is known about lncRNA regulators that affect muscle development in yak (Bos grunniens). LncRNA expression during skeletal muscle development in yak was analyzed by RNA sequencing at three development stages: 3 years (group A), 6 months (group M), and 90-day-old fetuses (group E). A total of 1180 lncRNAs were identified in the three development stages. Compared with group E, 154 were upregulated and 130 were downregulated in group A. Compared with group A, 31 were upregulated and 29 were downregulated in group M. Compared with group E, 147 were upregulated and 149 were downregulated in group M (padj < 0.001, |log2FC| > 1.2). In addition, functional annotation analysis based on gene ontology (GO) and the Kyoto protocol encyclopedia of genes and genomes (KEGG) database showed that differentially expressed lncRNAs (DElncRNAs) were cis–trans target genes. The results showed that DElncRNAs were mainly involved in PI3K-Akt signaling pathway, focal adhesion, MAPK signaling pathway, apoptosis, and p53 signaling pathway. Furthermore, RTL1, IGF2, MEF2C, Pax7, and other well-known muscle development regulators were included in a co-expression network of differentially expressed target genes and lncRNAs. These data will help to further clarify the function of lncRNAs in the different stages of skeletal muscle developmental in yak.

LncRNA regulates tomato fruit cracking by coordinating gene expression via a hormone-redox-cell wall network

BACKGROUND

Fruit cracking occurs easily under unsuitable environmental conditions and is one of the main types of damage that occurs in fruit production. It is widely accepted that plants have developed defence mechanisms and regulatory networks that respond to abiotic stress, which involves perceiving, integrating and responding to stress signals by modulating the expression of related genes. Fruit cracking is also a physiological disease caused by abiotic stress. It has been reported that a single or several genes may regulate fruit cracking. However, almost none of these reports have involved cracking regulatory networks.

RESULTS

Here, RNA expression in 0 h, 8 h and 30 h saturated irrigation-treated fruits from two contrasting tomato genotypes, 'LA1698' (cracking-resistant, CR) and 'LA2683' (cracking-susceptible, CS), was analysed by mRNA and lncRNA sequencing. The GO pathways of the differentially expressed mRNAs were mainly enriched in the 'hormone metabolic process', 'cell wall organization', 'oxidoreductase activity' and 'catalytic activity' categories. According to the gene expression analysis, significantly differentially expressed genes included Solyc02g080530.3 (Peroxide, POD), Solyc01g008710.3 (Mannan endo-1,4-beta-mannosidase, MAN), Solyc08g077910.3 (Expanded, EXP), Solyc09g075330.3 (Pectinesterase, PE), Solyc07g055990.3 (Xyloglucan endotransglucosylase-hydrolase 7, XTH7), Solyc12g011030.2 (Xyloglucan endotransglucosylase-hydrolase 9, XTH9), Solyc10g080210.2 (Polygalacturonase-2, PG2), Solyc08g081010.2 (Gamma-glutamylcysteine synthetase, gamma-GCS), Solyc09g008720.2 (Ethylene receptor, ER), Solyc11g042560.2 (Ethylene-responsive transcription factor 4, ERF4) etc. In addition, the lncRNAs (XLOC_16662 and XLOC_033910, etc) regulated the expression of their neighbouring genes, and genes related to tomato cracking were selected to construct a lncRNA-mRNA network influencing tomato cracking.

CONCLUSIONS

This study provides insight into the responsive network for water-induced cracking in tomato fruit. Specifically, lncRNAs regulate the hormone-redox-cell wall network, including plant hormone (auxin, ethylene) and ROS (H2O2) signal transduction and many cell wall-related mRNAs (EXP, PG, XTH), as well as some lncRNAs (XLOC_16662 and XLOC_033910, etc.).

Genome-wide identification of lncRNAs during hickory (Carya cathayensis) flowering

Non-coding RNAs with lengths greater than 200 bp are known as long non-coding RNAs (lncRNAs), and these RNAs play important role in gene regulation and plant development. However, to date, little is known regarding the role played by lncRNAs during flowering in hickory (Carya cathayensis). Here, we performed whole transcriptome RNA-sequencing of samples from hickory female and male floral buds, in which three samples (H0311PF, H0318PF, and H0402PF) represent pre-flowering, flowering, and post-flowering, respectively, while eight male samples collected from May 8th to June 13th as this time course are the key stage for male floral bud differentiation. We identified 2163 lncRNAs in hickory during flowering, containing 213 intronic, 1488 intergenic, and 462 antisense lncRNAs. We noticed that 510 and 648 lncRNAs were differentially expressed corresponding to female and male floral buds, respectively. And some of the lncRNAs were in a tightly tissue-specific or stage-specific manner. To further understand the roles of the lncRNAs, we predicted the function of the lncRNAs in cis- and trans-acting modes. The results showed that 924 lncRNAs were cis-correlated with 1536 protein-coding genes, while 1207 lncRNAs co-expressed (trans-acting) with 7432 protein-coding genes (R > 0.95 or R < - 0.95). These lncRNAs were all enriched in flower development-associated biological processes, i.e., circadian rhythm, vernalization response, response to gibberellin, inflorescence development, floral organ development, etc. To further understand the relationships between lncRNAs and floral-core genes, we build a co-expressing lncRNA-mRNA flowering network. We classified these floral genes into different pathway (photoperiod, vernalization, gibberellin, autonomous, and sucrose pathway) according to their particular functions. We found a set of lncRNAs that preferentially expressed in these pathways. The network showed that some lncRNAs (i.e., XLOC_038669, XLOC_017938) functioned in a particular flowering time pathway, while others (i.e., XLOC_011251, XLOC_04110) were involved in multiple pathway. Furthermore, some lncRNAs (i.e., XLOC_038669, XLOC_009597, and XLOC_049539) played roles in single or multiple pathways via interaction with each other. This study provides a genome-wide survey of hickory flower-related lncRNAs and will contribute to further understanding of the molecular mechanism underpinning flowering in hickory.

Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

Background

The mammary gland is a unique organ for milk synthesis, secretion and storage, and it undergoes cyclical processes of development, differentiation, lactation and degeneration. At different developmental periods, the biological processes governing mammary gland physiology and internal environmental homeostasis depend on a complex network of genes and regulatory factors. Emerging evidence indicates that lncRNAs have arbitrarily critical functions in regulating gene expression in many organisms; however, the systematic characteristics, expression, and regulatory roles of lncRNAs in the mammary gland tissues of dairy goats have not been determined.

Result

In the present study, we profiled long noncoding RNA (lncRNA) expression in the mammary gland tissues of Laoshan dairy goats (Capra hircus) from different lactation periods at the whole-genome level, to identify, characterize and explore the regulatory functions of lncRNAs. A total of 37,249 transcripts were obtained, of which 2381 lncRNAs and 37,249 mRNAs were identified, 22,488 transcripts, including 800 noncoding transcripts and 21,688 coding transcripts, differed significantly (p ≤ 0.01) among the different lactation stages. The results of lncRNA-RNA interaction analysis showed that six known lncRNAs belonging to four families were identified as the precursors of 67 known microRNAs; 1478 and 573 mRNAs were predicted as hypothetical cis-regulation elements and antisense mRNAs, respectively. GO annotation and KEGG analysis indicated that the coexpressed mRNAs were largely enriched in biological processes related to such activities as metabolism, immune activation, and stress,., and most genes were involved in pathways related to such phenomena as inflammation, cancer, signal transduction, and metabolism.

Conclusions

Our results clearly indicated that lncRNAs involved in responses to stimuli, multiorganism processes, development, reproductive processes and growth, are closely related to mammary gland development and lactation.

Trend analysis of the role of circular RNA in goat skeletal muscle development

Background

Circular RNA (circRNA) is produced during the splicing of mRNA (in addition to linear splicing) and is part of the gene regulatory network. The temporal expression patterns the different developmental stages were inseparable from these molecules’ function.

Results

Skeletal muscles of Anhui white goat (AWG) across seven fetal to postnatal development stages were sequenced and 21 RNA sequencing libraries were constructed. We thereby identified 9090 circRNAs and analyzed their molecular properties, temporal expression patterns, and potential functions at the different stages. CircRNAs showed complexities and diversity of formation as the same host gene produces multiple isoforms of these nucleic acids with different expression profiles. The differential expression of 2881 circRNAs (DECs, P < 0.05) was identified and four were randomly selected and validated by qPCR. Moreover, 1118 DECs under strict selected (SDECs, |log2^FC| > 2 and P-adj value < 0.01) showed 4 expression trends (Clusters 0, 19, 16 and 18). Cluster 0 molecules had increasing expression at all stages with effects on muscle through metabolism, regulation of enzyme activity, and biosynthesis. Cluster 16 circRNAs had high expression in the early and late stages and are involved in “Wnt signaling pathway”, “AMPK signaling pathway” and others. Cluster 18 molecules were mainly expressed at F120 and participate in “cytoskeletal protein binding”, “Notch signaling pathway” and so on. Cluster 19 circRNAs were down-regulated at all stages and related to muscle structure and development. Lastly, the SDECs divided the period of skeletal muscle development into three transitional stages: stage 1 (F45 to F90), which related to muscle satellite cell proliferation and muscle fiber structure; stage 2 (F90 to B1), in which the attachment of the cytoplasmic surface to the actin cytoskeleton initiates; and stage 3, which involved the “cGMP-PKG signaling pathway”. Moreover, the paraffin sections messages also validated that there are three transitional stages of skeletal muscle development.

Conclusion

Our current study provides a catalog of goat muscle-related circRNAs that can stratify skeletal muscle development fetus 45 days to newborn 90 days into three developmental stages. These findings better our understanding of functional transitions during mammalian muscle development.

Whole Transcriptome Analysis of Mesenchyme Tissue in Sika Deer Antler Revealed the CeRNAs Regulatory Network Associated With Antler Development

Deer antler is the only completely regenerable organ in mammals. During the rapid growth period, the antler proliferates even faster than cancerous tissue growth. However, the proliferation and development of antler have been in a stable and controllable growth cycle. In this study, we analyzed the time series expression data of nine samples from mesenchyme layer in three male sika deer in the early period of the antler with a saddle-like appearance (30 days), the rapid growth period of the antler with two branches (60 days), and the final period of the antler with three branches (90 days). Whole Transcriptome sequencing results show that in the 30 d versus 60 d group, 1,464 genes, 85 long noncoding RNAs (lncRNAs), and 61 miRNAs were identified as differentially expressed; 1,748 genes, 138 lncRNAs, and 78 miRNAs were identified as differentially expressed in 30d versus 90d group; and 816 differentially expressed genes (DEGs), 49 differentially expressed lncRNAs (DE lncRNAs), and 24 differentially expressed miRNA (DE miRNAs) were identified in 60d versus 90d group. A total of 182 miRNA-mRNA interaction pairs and 89 miRNA-lncRNA interaction pairs were screened from DEGs, DE miRNAs, and DE lncRNAs to construct the ceRNA regulatory network (ceRNET). In summary, we identified candidate mRNAs, miRNAs and lncRNAs that regulate the development of antler tip. It may lay the foundation for further investigating the molecular mechanism of antler rapid growth and development.

miRNAs and lncRNAs in Echinococcus and Echinococcosis

Echinococcosis are considered to be potentially lethal zoonotic diseases that cause serious damage to hosts. The metacestode of Echinococcus multilocularis and E. granulosus can result in causing the alveolar and cystic echinococcoses, respectively. Recent studies have shown that non-coding RNAs are widely expressed in Echinococcus spp. and hosts. In this review, the two main types of non-coding RNAs—long non-coding RNAs (lncRNAs) and microRNAs (miRNAs)—and the wide-scale involvement of these molecules in these parasites and their hosts were discussed. The expression pattern of miRNAs in Echinococcus spp. is species- and developmental stage-specific. Furthermore, common miRNAs were detected in three Echinococcus spp. and their intermediate hosts. Here, we primarily focus on recent insights from transcriptome studies, the expression patterns of miRNAs and lncRNAs, and miRNA-related databases and techniques that are used to investigate miRNAs in Echinococcus and echinococcosis. This review provides new avenues for screening therapeutic and diagnostic markers.

A Novel Long Noncoding RNA, lncR-125b, Promotes the Differentiation of Goat Skeletal Muscle Satellite Cells by Sponging miR-125b

Long noncoding RNAs (lncRNAs) have emerged as essential regulators of skeletal myogenesis, but few myogenesis-associated lncRNAs have been identified and our understanding of their regulatory mechanisms remains limited, particularly in goat. Here, we identified a novel lncRNA, TCONS_00006810 (named lncR-125b), from our previous lncRNA sequencing data on fetal (45, 60, and 105 days of gestation, three biological replicates for each point) and postnatal (3 days after birth, n = 3) goat skeletal muscle, and found that it is highly expressed in skeletal muscle and gradually upregulated during skeletal muscle satellite cell (SMSC) differentiation in goat. Notably, overexpression of lncR-125b accelerated the expression of myogenic differentiation 1 (MyoD 1) and myogenin (MyoG), and the formation of myotubes, and knockdown of lncR-125b showed opposite effects in SMSCs. Results of dual-luciferase assay and quantitative real-time polymerase chain reaction revealed that lncR-125b acts as a molecular sponge for miR-125b and that insulin-like growth factor 2 (IGF2), a critical regulator of skeletal myogenesis, is a direct target gene of miR-125b. Further analyses showed that lncR-125b negatively regulates miR-125b expression and positively regulates IGF2 expression in SMSCs. Mechanistically, lncR-125b promotes SMSC differentiation by functioning as a competing endogenous RNA (ceRNA) for miR-125b to control IGF2 expression. These findings identify lncR-125b as a novel noncoding regulator of muscle cell differentiation and skeletal muscle development in goat.

Zearalenone Exposure Induces the Apoptosis of Porcine Granulosa Cells and Changes Long Noncoding RNA Expression To Promote Antiapoptosis by Activating the JAK2-STAT3 Pathway

Zearalenone (ZEA), a pathogenic toxin produced by Fusarium, is widely detected in moldy feed materials. Previous studies have reported that ZEA exerts a harmful influence on animal reproductive systems; however, its effects on the changes of long noncoding RNAs (lncRNAs) remain unclear. Here, tackling this question, we performed RNA sequencing on porcine granulosa cells (GCs) after being exposed to 10 and 30 μM ZEA in vitro. The results showed that ZEA exposure observably changed the expression of lncRNAs in porcine GCs and increased the rate of apoptosis. Furthermore, Gene Ontology analysis showed that ZEA exposure induced variation of the Janus kinase 2 (JAK2)-signal transducer and activator of transcription 3 (STAT3) signaling pathway in porcine GCs. To verify our bioinformatics analysis, western blotting and immunofluorescence analysis were performed and the results demonstrated that porcine GCs after ZEA exposure increased the expression of key proteins in the JAK2-STAT3 signaling pathway. Further bioinformatics analysis found that MSTRG.22680 and MSTRG.23882 played a pivotal role in activating the JAK2-STAT3 signaling pathway. To summarize, our results throw light on the fact that ZEA exposure dramatically increases the apoptosis of porcine GCs and alters the expression of lncRNAs that play an antiapoptotic role in porcine GCs via activating the JAK2-STAT3 signaling pathway.

The long noncoding RNA T5120 regulates nitrate response and assimilation in Arabidopsis

Long noncoding RNAs (lncRNAs) are crucial regulators in many plant biological processes. However, it remains unknown whether lncRNAs can respond to nitrate or function in nitrate regulation. We detected 695 lncRNAs, 480 known and 215 novel, in Arabidopsis seedling roots; six showed altered expression in response to nitrate treatment, among which T5120 showed the highest induction. Overexpression of T5120 in Arabidopsis promoted the response to nitrate, enhanced nitrate assimilation and improved biomass and root development. Biochemical and molecular analyses revealed that NLP7, a master nitrate regulatory transcription factor, directly bound to the nitrate-responsive cis-element (NRE)-like motif of the T5120 promoter and activated T5120 transcription. In addition, T5120 partially restored the nitrate signalling and assimilation phenotypes of nlp7 mutant, suggesting that T5120 is involved in NLP7-mediated nitrate regulation. Interestingly, the expression of T5120 was regulated by the nitrate sensor NRT1.1. Therefore, T5120 is modulated by NLP7 and NRT1.1 to regulate nitrate signalling. Our work reveals a new regulatory mechanism in which lncRNA T5120 functions in nitrate regulation, providing new insights into the nitrate signalling network. Importantly, lncRNA T5120 can promote nitrate assimilation and plant growth to improve nitrogen use efficiency.

Functions and Regulatory Mechanisms of lncRNAs in Skeletal Myogenesis, Muscle Disease and Meat Production

Myogenesis is a complex biological process, and understanding the regulatory network of skeletal myogenesis will contribute to the treatment of human muscle related diseases and improvement of agricultural animal meat production. Long noncoding RNAs (lncRNAs) serve as regulators in gene expression networks, and participate in various biological processes. Recent studies have identified functional lncRNAs involved in skeletal muscle development and disease. These lncRNAs regulate the proliferation, differentiation, and fusion of myoblasts through multiple mechanisms, such as chromatin modification, transcription regulation, and microRNA sponge activity. In this review, we presented the latest advances regarding the functions and regulatory activities of lncRNAs involved in muscle development, muscle disease, and meat production. Moreover, challenges and future perspectives related to the identification of functional lncRNAs were also discussed.

High-Throughput RNA Sequencing Reveals NDUFC2-AS lncRNA Promotes Adipogenic Differentiation in Chinese Buffalo (Bubalus bubalis L)

The buffalo (Bubalus bubalis L.) is prevalent in China and the increasing demand for meat production has changed its role from being a beast of burden to a meat source. The low fat deposition level has become one of the main barriers for its use in meat production. It is urgent to reveal factors involved in fat deposition in buffalo. This study performed RNA sequencing to investigate both long noncoding RNAs (lncRNAs) and mRNAs of adipose tissues in young and adult buffalos. A total of 124 lncRNAs and 2008 mRNAs showed differential expression patterns between young and adult samples. Coexpression analysis and functional enrichment revealed 585 mRNA–lncRNA pairs with potential function in fat deposition. After validation by qRT-PCR, we focused on a lncRNA transcribed from the ubiquinone oxidoreductase subunit C2 (NDUFC2) antisense (AS) strand which showed high correlation with thyroid hormone responsive protein (THRSP). NDUFC2-AS lncRNA is highly expressed in adipose tissue and maturation adipocytes and mainly exists in the nucleus. Functional assays demonstrated that NDUFC2-AS lncRNA promotes adipogenic differentiation by upregulating the expression levels of THRSP and CCAAT enhancer binding protein alpha (C/EBPα) in buffalo. These results indicate that NDUFC2-AS lncRNA promotes fat deposition in buffalo.