The developmental transcriptome landscape of bovine skeletal muscle defined by Ribo-Zero ribonucleic acid sequencing

Full-length transcriptome sequencing of the longissimus dorsi muscle of yak and cattle-yak using nanopore technology

Short-read RNA sequencing has been used to sequence the transcriptome of the skeletal muscle of yak and cattle-yak; however, full-length transcripts cannot be obtained and alternative splicing (AS) events cannot be inferred using this sequencing approach. Here, we used Oxford Nanopore Technologies (ONT) full-length sequencing to sequence the transcriptome of the longissimus dorsi of yak and cattle-yak. A total of 20,323 novel genes and 172,870 novel transcripts were identified, and 159,700 novel transcripts were successfully annotated. A total of 157,812 AS events, 58,073 simple sequence repeats, 57,468 complete open reading frames, 2296 transcription factors, and 20,404 lncRNAs were detected. Differentially expressed transcripts (DETs) in the longissimus dorsi muscle of yak and cattle-yak were involved in the MAPK and JAK-STAT signaling pathways related to muscle development and growth. Protein-protein interaction analysis of DETs suggested that TNNI2 might make a major contribution to differences in muscle growth and meat quality traits between yak and cattle-yak. The results have enriched the transcriptome data of dorsal muscles, providing new ideas for the study of transcriptional regulation processes, and also providing useful information for the production of higher yields of yak meat.

Expression profile and functional prediction of novel LncRNA 5.8S rRNA-OT1 in cattle

Long non-coding RNAs (LncRNAs) are generally longer than 200 bp in length and play an important regulatory role in the growth and development of skeletal muscle. In the previous work, the non-coding RNAs with abundant expression in bovine tissues were screened out. After quantitative real-time PCR (qPCR), 33 lncRNAs with differential expression in various bovine tissues were identified. Differential expression analysis base on tissue expression profiles of 33 lncRNAs, a long non-coding RNA LncRNA13, which may have effects on bovine muscle development, was found. The expression levels in embryo muscle and adult cattle muscle were significantly different (p < 0.01), so it is speculated that it may have a certain impact on the development of cattle muscle. It was named LncRNA 5.8S rRNA-OT1, and its overexpression vector pcDNA3.1-LncRNA 5.8S rRNA-OT1 was cloned and constructed. The purpose of this study is to further explore its impact on the proliferation and differentiation of bovine muscle cells and accumulate data to lay a foundation for further exploration of the function of LncRNA 5.8S rRNA-OT1 and add basic data for the study of the regulatory mechanism of lncRNA.

A web-based database server using 43,710 public RNA-seq samples for the analysis of gene expression and alternative splicing in livestock animals

BACKGROUND

Livestock animals is of great significance in agricultural production. However, the role of specific gene expression, especially alternative splicing in determining phenotype, is not well understood. The livestock research community needs a gene expression and alternative splicing database contributing to livestock genetic improvement.

DESCRIPTION

We report the construction of LivestockExp ( https://bioinfo.njau.edu.cn/livestockExp ), a web-based database server for the exploration of gene expression and alternative splicing using 43,710 uniformly processed RNA-seq samples from livestock animals and several relative species across six orders. The database is equipped with basic querying functions and multiple online analysis modules including differential/specific expression analysis, co-expression network analysis, and cross-species gene expression conservation analysis. In addition to the re-analysis of public datasets, users can upload personal datasets to perform co-analysis with public datasets. The database also offers a wide range of visualization tools and diverse links to external databases enabling users to efficiently explore the results and to gain additional insights.

CONCLUSION

LivestockExp covers by far the largest number of livestock animal species and RNA-seq samples and provides a valuable data resource and analysis platform for the convenient utilization of public RNA-seq datasets.

Broiler responses to copper levels and sources: growth, tissue mineral content, antioxidant status and mRNA expression of genes involved in lipid and protein metabolism

BACKGROUND

Five hundred 8-d old male broilers Cobb500 were randomly allotted into 10 treatments in factorial arrangement with 5 Cu levels (0, 4, 8, 12, and 16 mg/kg), and 2 sources (Cu proteinate, CuPro and Cu sulphate, CuSO4.5H2O) for a 10-d-experiment.

RESULTS

Feed conversion ratio (FCR) was better (P < 0.05) in CuPro fed chicks compared with CuSO4.5H2O group. Average daily feed intake (ADFI) decreased linearly (P < 0.05) as dietary Cu increased. A quadratic response (P < 0.05) to Cu levels was found for FCR, being optimized at 9.87 and 8.84 mg Cu/kg in CuPro and CuSO4.5H2O diets, respectively. Copper supplementation linearly increased liver Cu content (P < 0.05) and tended to linearly increase (P = 0.07) phosphorus (P) and copper in tibia. Manganese and zinc were higher (P < 0.05) in tibia of CuPro fed birds. Broilers fed CuPro exhibited lower liver iron (P < 0.05) content, lower activities of Cu, Zn superoxide dismutase (CuZnSOD) in breast muscle and liver, and glutathione peroxidase in liver. Glutathione peroxidase reduced linearly (P < 0.05) with CuPro levels and increased linearly (P < 0.05) with CuSO4.5H2O levels and were lower (P < 0.05) in all CuPro levels in breast muscle. Breast muscle malondialdehyde concentration tended to be higher (P = 0.08) in broilers fed CuSO4.5H2O. Copper levels linearly increased (P < 0.05) metallothionein (MT) and malate dehydrogenase (MDH) expression in liver, and six-transmembrane epithelial antigen of the prostate-1 (STEAP-1) in the intestine. Copper elicited a quadratic response (P < 0.050) in AKT-1 and mammalian target of rapamycin (mTOR) in breast muscle, CuZnSOD in liver and antioxidant 1 copper chaperone (ATOX 1) in intestine. Broilers fed CuPro exhibited higher mRNA expression of mTOR in muscle breast and lower CuZnSOD in liver and ATOX 1 in intestine. Interaction (P < 0.05) between levels and sources was found in mRNA expression for GSK-3β, MT, and CuZnSOD in breast muscle, FAS and LPL in liver and MT and CTR1 in intestine.

CONCLUSIONS

CuPro showed beneficial effects on feed conversion and bone mineralization. Organic and inorganic Cu requirements are 9.87 and 8.84 mg Cu/kg, respectively.

Identification of differentially expressed genes at different post-natal development stages of longissimus dorsi muscle in Tianzhu white yak

The regulatory mechanisms controlling post-natal muscle development in the yak (Bos grunniens) are still largely unknown, yet the growth and development of muscle is a complex process that plays a crucial role in determining the yield and quality of an animal's meat. In this study, we performed a transcriptome analysis based on the RNA sequencing (RNA-Seq) of yak longissimus dorsi muscle tissue obtained from calves (6 months of age; 6 M), young adults (30 months of age; 30 M) and adult (54 months of age; 54 M) to identify which genes are differentially expressed and to investigate their temporal expression profiles. In total, 1788 differentially expressed genes (DEGs) (|log2FC| ≥ 1, P-adjusted < 0.05) were detected by pairwise comparisons between the different age groups. The expression levels of 10 of the DEGs were confirmed using reverse transcription-quantitative PCR (RT-qPCR), and the results were consistent with the transcriptome profile. A time-series expression profile analysis clustered the DEGs into four groups that could be divided into two classes (P < 0.05): class 1 profiles, which had up-regulated patterns of gene expression and class 2 profiles, which featured down-regulated patterns. Based on that cluster analysis, GO enrichment analysis revealed 1073, 127, and 184 terms as significantly enriched in biological process (BP), cellular component (CC), and molecular function (MF) categories in the class 1 profiles, while 714, 66, and 206 terms were significantly enriched in BP, CC, and MF in the class 2 profiles. A KEGG pathway analysis revealed that DEGs from the class 1 profiles were enriched in 62 pathways, with the most enriched being the phosphoinositide 3-kinase (PI3K) - protein kinase B (Akt)-signaling pathway. The DEGs from the class 2 profiles were enriched in 16 pathways, of which forkhead box protein O (FoxO) - signaling was the most enriched. Taken together, these results provide insight into the mechanisms of skeletal muscle development, as well suggesting some potential genes of importance for yak meat production.

Profiling and Functional Analysis of mRNAs during Skeletal Muscle Differentiation in Goats

Skeletal myogenesis is a complicated biological event that involves a succession of tightly controlled gene expressions. In order to identify novel regulators of this process, we performed mRNA-Seq studies of goat skeletal muscle satellite cells (MuSCs) cultured under proliferation (GM) and differentiation (DM1/DM5) conditions. A total of 19,871 goat genes were expressed during these stages, 198 of which represented novel transcripts. Notably, in pairwise comparisons at the different stages, 2551 differentially expressed genes (DEGs) were identified (p < 0.05), including 1560 in GM vs. DM1, 1597 in GM vs. DM5, and 959 in DM1 vs. DM5 DEGs. The time-series expression profile analysis clustered the DEGs into eight gene groups, three of which had significantly upregulated and downregulated patterns (p < 0.05). Functional enrichment analysis showed that DEGs were enriched for essential biological processes such as muscle structure development, muscle contraction, muscle cell development, striated muscle cell differentiation, and myofibril assembly, and were involved in pathways such as the MAPK, Wnt and PPAR signaling pathways. Moreover, the expression of eight DEGs (MYL2, DES, MYOG, FAP, PLK2, ADAM, WWC1, and PRDX1) was validated. These findings offer novel insights into the transcriptional regulation of skeletal myogenesis in goats.

Transcriptome-Wide Analyses Identify Dominant as the Predominantly Non-Conservative Alternative Splicing Inheritance Patterns in F1 Chickens

Transcriptome analysis has been used to investigate many economically traits in chickens; however, alternative splicing still lacks a systematic method of study that is able to promote proteome diversity, and fine-tune expression dynamics. Hybridization has been widely utilized in chicken breeding due to the resulting heterosis, but the dynamic changes in alternative splicing during this process are significant yet unclear. In this study, we performed a reciprocal crossing experiment involving the White Leghorn and Cornish Game chicken breeds which exhibit major differences in body size and reproductive traits, and conducted RNA sequencing of the brain, muscle, and liver tissues to identify the inheritance patterns. A total of 40 515 and 42 612 events were respectively detected in the brain and muscle tissues, with 39 843 observed in the liver; 2807, 4242, and 4538 events significantly different between two breeds were identified in the brain, muscle, and liver tissues, respectively. The hierarchical cluster of tissues from different tissues from all crosses, based on the alternative splicing profiles, suggests high tissue and strain specificity. Furthermore, a comparison between parental strains and hybrid crosses indicated that over one third of alternative splicing genes showed conserved patterns in all three tissues, while the second prevalent pattern was non-additive, which included both dominant and transgressive patterns; this meant that the dominant pattern plays a more important role than suppression. Our study provides an overview of the inheritance patterns of alternative splicing in layer and broiler chickens, to better understand post-transcriptional regulation during hybridization.

Gene co-expression and alternative splicing analysis of key metabolic tissues to unravel the regulatory signatures of fatty acid composition in cattle

Increasing the healthy/unhealthy fatty acid (FA) ratio in meat is one of the urgent tasks required to address consumer concerns. However, the regulatory mechanisms ultimately resulting in FA profiles vary among animals and remain largely unknown. In this study, using ~1.2 Tb high-quality RNA-Seq-based transcriptomic data of 188 samples from four key metabolic tissues (rumen, liver, muscle, and backfat) together with the contents of 49 FAs in backfat, the molecular regulatory mechanisms of these tissues contributing to FA formation in cattle were explored. Using this large dataset, the alternative splicing (AS) events, one of the transcriptional regulatory mechanisms in four tissues were identified. The highly conserved and absent AS events were detected in rumen tissue, which may contribute to its functional differences compared with the other three tissues. In addition, the healthy/unhealthy FA ratio related AS events, differential expressed (DE) genes, co-expressed genes, and their functions in four tissues were analysed. Eight key genes were identified from the integrated analysis of DE, co-expressed, and AS genes between animals with high and low healthy/unhealthy FA ratios. This study provides an applicable pipeline for AS events based on comprehensive RNA-Seq analysis and improves our understanding of the regulatory mechanism of FAs in beef cattle.

Transcriptome analysis of differential gene expression in the longissimus dorsi muscle from Debao and landrace pigs based on RNA-sequencing

RNA-seq analysis was used to identify differentially expressed genes (DEGs) at the genetic level in the longissimus dorsi muscle from two pigs to investigate the genetic mechanisms underlying the difference in meat quality between Debao pigs and Landrace pigs. Then, these DEGs underwent functional annotation, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein–protein interaction (PPI) analyses. Finally, the expression levels of specific DEGs were assessed using qRT-PCR. The reference genome showed gene dosage detection of all samples which showed that the total reference genome comprised 22342 coding genes, including 14743 known and 190 unknown genes. For detection of the Debao pig genome, we obtained 14168 genes, including 13994 known and 174 unknown genes. For detection of the Landrace pig genome, we obtained 14404 genes, including 14223 known and 181 unknown genes. GO analysis and KEGG signaling pathway analysis show that DEGs are significantly related to metabolic regulation, amino acid metabolism, muscular tissue, muscle structure development etc. We identified key genes in these processes, such as FOS, EGR2, and IL6, by PPI network analysis. qRT-PCR confirmed the differential expression of six selected DEGs in both pig breeds. In conclusion, the present study revealed key genes and related signaling pathways that influence the difference in pork quality between these breeds and could provide a theoretical basis for improving pork quality in future genetic thremmatology.

Satellite cells and their regulation in livestock

Satellite cells are the myogenic stem and progenitor population found in skeletal muscle. These cells typically reside in a quiescent state until called upon to support repair, regeneration, or muscle growth. The activities of satellite cells are orchestrated by systemic hormones, autocrine and paracrine growth factors, and the composition of the basal lamina of the muscle fiber. Several key intracellular signaling events are initiated in response to changes in the local environment causing exit from quiescence, proliferation, and differentiation. Signals emanating from Notch, wingless-type mouse mammary tumor virus integration site family members, and transforming growth factor-β proteins mediate the reversible exit from growth 0 phase while those initiated by members of the fibroblast growth factor and insulin-like growth factor families direct proliferation and differentiation. Many of these pathways impinge upon the myogenic regulatory factors (MRF), myogenic factor 5, myogenic differentiation factor D, myogenin and MRF4, and the lineage determinate, Paired box 7, to alter transcription and subsequent satellite cell decisions. In the recent past, insight into mouse transgenic models has led to a firm understanding of regulatory events that control satellite cell metabolism and myogenesis. Many of these niche-regulated functions offer subtle differences from their counterparts in livestock pointing to the existence of species-specific controls. The purpose of this review is to examine the mechanisms that mediate large animal satellite cell activity and their relationship to those present in rodents.

Transcriptional regulation of the bovine FGFR1 gene facilitates myoblast proliferation under hypomethylation of the promoter

DNA methylation, which can affect the expression level of genes, is one of the most vital epigenetic modifications in mammals. Fibroblast growth factor receptor 1 (FGFR1) plays an important role in muscle development; however, DNA methylation of the FGFR1 promoter has not been studied to date in cattle. Our study focused on methylation of the FGFR1 promoter and its effect on bovine myoblast proliferation and differentiation. We identified the FGFR1 core promoter by using luciferase reporter assays; we then studied FGFR1 expression by reverse transcription quantitative polymerase chain reaction, and the methylation pattern in the FGFR1 core promoter by bisulfite sequencing polymerase chain reaction in bovine muscle tissue at three different developmental stages. We used RNAi strategy to investigate the function of FGFR1 in myoblast proliferation and differentiation. Results showed that the FGFR1 core promoters were located at the R2 (-509 to ~-202 bp) and R4 (-1295 to ~-794 bp) regions upstream of the FGFR1 gene. FGFR1 expression level was negatively associated with the degree of methylation of the FGFR1 core promoter during the developmental process. In addition, we found that FGFR1 can promote myoblast proliferation, but had no effect on myoblast differentiation. In conclusion, our results suggest that FGFR1 can promote myoblast proliferation and its transcription can be regulated by the methylation level of the core promoter. Our findings provide a mechanistic basis for the improvement of animal breeding.

A comparative analysis of gene expression induced by the embryo in the caprine endometrium

Transcriptomics is an established powerful tool to identify potential mRNAs and ncRNAs (non‐coding RNAs) for endometrial receptivity. In this study, the goat endometrium at estrus day 5 (ED5) and estrus day 15 (ED15) were selected to systematically analyse the differential expressed genes (DEGs) what were induced by the embryo. There were 1,847 genes which were significantly differential expressed in endometrium induced by the embryo at ED5, and 1,346 at ED15 (p‐value < .05). Secreted phosphoprotein 1 (SPP) was the responsive genes for embryo in the goat endometrium during estrus cycle, neurotensis (NTS) and pleiotrophin (PTN) were the responsive genes for embryo in the goat endometrium at ED5, Testin (TES) and Phosphate and Tension Homology Deleted on Chromsome ten (PTEN) at ED15. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes (KEGG) analysis revealed cytoplasm and Endocytosis were indispensable for the endometrium development in dairy goat. In a word, this resulting view of the transcriptome greatly uncovered the global trends in mRNAs expression induced by the embryo in the endometrium of dairy goats.

Transcriptome and DNA Methylation Analyses of the Molecular Mechanisms Underlying with Longissimus dorsi Muscles at Different Stages of Development in the Polled Yak

DNA methylation modifications are implicated in many biological processes. As the most common epigenetic mechanism DNA methylation also affects muscle growth and development. The majority of previous studies have focused on different varieties of yak, but little is known about the epigenetic regulation mechanisms in different age groups of animals. The development of muscles in the different stages of yak growth remains unclear. In this study, we selected the longissimus dorsi muscle tissue at three different growth stages of the yak, namely, 90-day-old fetuses (group E), six months old (group M), and three years old (group A). Using RNA-Seq transcriptome sequencing and methyl-RAD whole-genome methylation sequencing technology, changes in gene expression levels and DNA methylation status throughout the genome were investigated during the stages of yak development. Each group was represented by three biological replicates. The intersections of expression patterns of 7694 differentially expressed genes (DEGs) were identified (padj < 0.01, |log2FC| > 1.2) at each of the three developmental periods. Time-series expression profile clustering analysis indicated that the DEGs were significantly arranged into eight clusters which could be divided into two classes (padj < 0.05), class I profiles that were downregulated and class II profiles that were upregulated. Based on this cluster analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that DEGs from class I profiles were significantly (padj < 0.05) enriched in 21 pathways, the most enriched pathway being the Axon guidance signaling pathway. DEGs from the class II profile were significantly enriched in 58 pathways, the pathway most strongly enriched being Metabolic pathway. After establishing the methylation profiles of the whole genomes, and using two groups of comparisons, the three combinations of groups (M-vs.-E, M-vs.-A, A-vs.-E) were found to have 1344, 822, and 420 genes, respectively, that were differentially methylated at CCGG sites and 2282, 3056, and 537 genes, respectively, at CCWGG sites. The two sets of data were integrated and the negative correlations between DEGs and differentially methylated promoters (DMPs) analyzed, which confirmed that TMEM8C, IGF2, CACNA1S and MUSTN1 were methylated in the promoter region and that expression of the modified genes was negatively correlated. Interestingly, these four genes, from what was mentioned above, perform vital roles in yak muscle growth and represent a reference for future genomic and epigenomic studies in muscle development, in addition to enabling marker-assisted selection of growth traits.

Identification of differentially expressed genes and pathways between intramuscular and abdominal fat-derived preadipocyte differentiation of chickens in vitro

BACKGROUND

The distribution and deposition of fat tissue in different parts of the body are the key factors affecting the carcass quality and meat flavour of chickens. Intramuscular fat (IMF) content is an important factor associated with meat quality, while abdominal fat (AbF) is regarded as one of the main factors affecting poultry slaughter efficiency. To investigate the differentially expressed genes (DEGs) and molecular regulatory mechanisms related to adipogenic differentiation between IMF- and AbF-derived preadipocytes, we analysed the mRNA expression profiles in preadipocytes (0d, Pre-) and adipocytes (10d, Ad-) from IMF and AbF of Gushi chickens.

RESULTS

AbF-derived preadipocytes exhibited a higher adipogenic differentiation ability (96.4% + 0.6) than IMF-derived preadipocytes (86.0% + 0.4) (p < 0.01). By Ribo-Zero RNA sequencing, we obtained 4403 (2055 upregulated and 2348 downregulated) and 4693 (2797 upregulated and 1896 downregulated) DEGs between preadipocytes and adipocytes in the IMF and Ad groups, respectively. For IMF-derived preadipocyte differentiation, pathways related to the PPAR signalling pathway, ECM-receptor interaction and focal adhesion pathway were significantly enriched. For AbF-derived preadipocyte differentiation, the steroid biosynthesis pathways, calcium signaling pathway and ECM-receptor interaction pathway were significantly enriched. A large number of DEGs related to lipid metabolism, fatty acid metabolism and preadipocyte differentiation, such as PPARG, ACSBG2, FABP4, FASN, APOA1 and INSIG1, were identified in our study.

CONCLUSION

This study revealed large transcriptomic differences between IMF- and AbF-derived preadipocyte differentiation. A large number of DEGs and transcription factors that were closely related to fatty acid metabolism, lipid metabolism and preadipocyte differentiation were identified in the present study. Additionally, the microenvironment of IMF- and AbF-derived preadipocyte may play a significant role in adipogenic differentiation. This study provides valuable evidence to understand the molecular mechanisms underlying adipogenesis and fat deposition in chickens.

Comparative transcriptomics to reveal muscle-specific molecular differences in the early postmortem of Chinese Jinjiang yellow cattle

Differences in the expression of functional genes between beef Longissimus Lumborum (LL) and Psoas Major (PM) are not well understood. The aim of present study is to reveal transcriptome changes of beef LL and PM during early postmortem by high-throughput Illumina Hiseq4000 Sequencing. Hierarchical clustering analysis indicated significant differences in transcriptome profiles between LL and PM as well as 1 h and 12 h postmortem. A total of 65 genes differentially expressed between LL and PM (fold change ≥3, and p < 0.05; 34 were up-regulated in LL and 31 in PM), and the majority of them (53 genes) occurred at 12 h postmortem. These differentially expressed genes mainly involved in energy production and conversion, nucleotide metabolic, posttranslational modification, and transcription. KEGG analysis revealed that oxidative phosphorylation was one of the important pathways. This study gave new perspectives to understand the underlying mechanisms associated with muscle-specific beef quality.

Activation of Nrf2 by Phloretin Attenuates Palmitic Acid-Induced Endothelial Cell Oxidative Stress via AMPK-Dependent Signaling

Phloretin, a dihydrochalcone structural flavonoid compound, possesses antioxidant activity. In this study, we conducted studies to explore the function of phloretin on high palmitic acid-induced oxidative stress in human umbilical vein endothelial cells and investigated the potential mechanism using ribonucleic acid sequencing (RNA-Seq). Our findings reveal that phloretin significantly decreased the levels of intracellular reactive oxygen species (ROS) and malondialdehyde (MDA), increased superoxide dismutase (SOD) and glutathione peroxidase-1 (Gpx-1) activity, and restored the loss of mitochondrial membrane potential (MMP). Next, whole transcriptome analysis was performed using RNA-Seq The results indicated more than 3000 differentially expressed genes (DEGs). Gene Ontology analysis revealed that the DEGs were categorized functionally, mainly by the biological processes, cell metabolism, and cellular response to chemical stimulus. The Kyoto Encyclopedia of Genes and Genomes indicated that they were mainly enriched in cAMP, apoptosis, and cytoskeletal regulation signaling pathways. Furthermore, on the basis of the results of RNA-Seq and Western blotting, our study verified that phloretin upregulated the expression of p-Nrf2 and HO-1 by promoting the phosphorylation of AMPK at Thr¹⁷² through activation of liver kinase B1. In conclusion, phloretin attenuates PA-induced oxidative stress in HUVECs via the AMPK/Nrf2 antioxidative pathway.

In-depth characterization of the pituitary transcriptome in Simmental and Chinese native cattle

The pituitary gland is a key endocrine organ responsible for growth and development. To get closer to understanding important molecular mechanisms at work in the bovine pituitary and identifying the core genes controlling growth, in the present study we have analyzed the transcriptome profiling of the pituitary glands of two cattle breeds (Wenshan and Simmental cattle) with extreme growth differences using high-throughput RNA sequencing. Our study revealed that the overall gene expression levels are quite similar between the two breeds. A total of 18,065 annotated genes were identified, which accounted for 85% of the annotated genes in cattle. The five most abundant hormone genes (GH, PRL, POMC, CGA, and LHB) were relatively stable in both breeds, indicating their pivotal roles in maintaining the basic functions of the pituitary. In addition, 105 genes were identified as differentially expressed between Wenshan and Simmental pituitary glands, including 83 known and 22 novel genes. Functional association analyses of the differentially expressed genes between the breeds revealed 60 enriched gene ontology terms and 3 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Interestingly, the most enriched KEGG pathway, cell adhesion molecules, can modulate pituitary hormone secretion by cell-cell contact. Our findings demonstrated that SYTL2, SLC38A4, and NCAM2 are new candidates for crucial functions in the secretory pathways of the pituitary gland. These results will further understanding of the important molecular mechanisms at work in the bovine pituitary.

The mRNA and lncRNA landscape of the non-pregnant endometrium during the oestrus cycle in dairy goat

Cyclic changes in the endometrium are essential for embryo implantation in mammals; many studies report that such changes constitute a complex process involving numerous molecular mediators. In the present study, goat endometria at oestrus Day 5 and oestrus Day 15 were selected to systematically analyse the transcriptome using strand-specific Ribo-Zero RNA sequencing. Over 120 million high-quality paired-end reads were generated and 440400 transcripts were identified in the endometrial tissue of dairy goats. In total, 489 differentially expressed mRNAs and 854 differentially expressed long non-coding RNAs were identified when comparing the endometrium at goat endometria at oestrus Day 5 and oestrus Day 15. Neurotensin was found to play a potentially important role in the non-pregnant goat endometrium during the oestrus cycle. Furthermore, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses of the cis-target genes of the differentially expressed long non-coding RNAs showed that GO:0005198 (structural molecule activity) and ko04510 (focal adhesion) might be involved in cyclic endometrial changes. Taken together, the resulting transcriptomic profiles elucidate global trends in mRNA and lncRNA expression in non-pregnant endometria during the oestrus cycle in dairy goats.

Global Transcriptome Analysis During Adipogenic Differentiation and Involvement of Transthyretin Gene in Adipogenesis in Cattle

Adipose tissue plays central role in determining the gustatory quality of beef, but traditional Chinese beef cattle have low levels of fat content. We applied RNA-seq to study the molecular mechanisms underlying adipocyte differentiation in Qinchuan cattle. A total of 18,283 genes were found to be expressed in preadipocytes and mature adipocytes, respectively. 470 of which were significantly differentially expressed genes (DEGs) [false discovery rate (FDR) values < 0.05 and fold change ≥ 2]. In addition, 4534 alternative splicing (AS) events and 5153 AS events were detected in preadipocytes and adipocytes, respectively. We constructed a protein interaction network, which suggested that collagen plays an important role during bovine adipogenic differentiation. We characterized the function of the most down-regulated DEG (P < 0.001) among genes we have detected by qPCR, namely, the transthyretin (TTR) gene. Overexpression of TTR appears to promote the expression of the peroxisome proliferator activated receptor γ (PPARγ) (P < 0.05) and fatty acid binding Protein 4 (FABP4) (P < 0.05). Hence, TTR appears to be involved in the regulation of bovine adipogenic differentiation. Our study represents the comprehensive approach to explore bovine adipocyte differentiation using transcriptomic data and reports an involvement of TTR during bovine adipogenic differentiation. Our results provide novel insights into the molecular mechanisms underlying bovine adipogenic differentiation.

Long Non-coding RNA Profiling Reveals an Abundant MDNCR that Promotes Differentiation of Myoblasts by Sponging miR-133a

Muscle development is regulated by a series of complicate processes, and non-coding RNAs (ncRNAs) such as lncRNA have been reported to play important roles in regulating skeletal myogenesis and diseases. Here we profile the expression of lncRNA in cattle skeletal muscle tissue from fetus and adult developmental stages and detect 13,580 lncRNA candidates. Many of these lncRNAs are differentially expressed between two developmental stages. We further characterize one abundant lncRNA with the highest expression level of all downregulated lncRNAs, which we named muscle differentiation-associated lncRNA (MDNCR). Via luciferase screening, RNA binding protein immunoprecipitation (RIP), and RNA pull-down assays, MDNCR was observed to directly bind to miR-133a with 32 potential binding sites. GosB was identified as a target of miR-133a by luciferase activity, quantitative real-time qPCR, and western blotting assays. Overexpression of MDNCR increased the expression of GosB, whereas this effect was abolished by miR-133a. We found that MDNCR promotes myoblast differentiation and inhibits cell proliferation by sponging miR-133a. These results demonstrate that MDNCR binding miR-133a promotes cell differentiation by targeting GosB in cattle primary myoblasts.

Identification and characterization of long noncoding RNAs and mRNAs expression profiles related to postnatal liver maturation of breeder roosters using Ribo-zero RNA sequencing

BACKGROUND

The liver is mainly hematopoietic in the embryo, and converts into a major metabolic organ in the adult. Therefore, it is intensively remodeled after birth to adapt and perform adult functions. Long non-coding RNAs (lncRNAs) are involved in organ development and cell differentiation, likely they have potential roles in regulating postnatal liver development. Herein, in order to understand the roles of lncRNAs in postnatal liver maturation, we analyzed the lncRNAs and mRNAs expression profiles in immature and mature livers from one-day-old and adult (40 weeks of age) breeder roosters by Ribo-Zero RNA-Sequencing.

RESULTS

Around 21,939 protein-coding genes and 2220 predicted lncRNAs were expressed in livers of breeder roosters. Compared to protein-coding genes, the identified chicken lncRNAs shared fewer exons, shorter transcript length, and significantly lower expression levels. Notably, in comparison between the livers of newborn and adult breeder roosters, a total of 1570 mRNAs and 214 lncRNAs were differentially expressed with the criteria of log2fold change > 1 or < - 1 and P values < 0.05, which were validated by qPCR using randomly selected five mRNAs and five lncRNAs. Further GO and KEGG analyses have revealed that the differentially expressed mRNAs were involved in the hepatic metabolic and immune functional changes, as well as some biological processes and pathways including cell proliferation, apoptotic and cell cycle that are implicated in the development of liver. We also investigated the cis- and trans- regulatory effects of differentially expressed lncRNAs on its target genes. GO and KEGG analyses indicated that these lncRNAs had their neighbor protein coding genes and trans-regulated genes associated with adapting of adult hepatic functions, as well as some pathways involved in liver development, such as cell cycle pathway, Notch signaling pathway, Hedgehog signaling pathway, and Wnt signaling pathway.

CONCLUSIONS

This study provides a catalog of mRNAs and lncRNAs related to postnatal liver maturation of chicken, and will contribute to a fuller understanding of biological processes or signaling pathways involved in significant functional transition during postnatal liver development that differentially expressed genes and lncRNAs could take part in.

Developmental transcriptome profiling of bovine muscle tissue reveals an abundant GosB that regulates myoblast proliferation and apoptosis

The formation of bovine skeletal muscle involves complex developmental and physiological processes that play a vital role in determining the quality of beef; however, the regulatory mechanisms underlying differences in meat quality are largely unknown. We conducted transcriptome analysis of bovine muscle tissues to compare gene expression profiles between embryonic and adult stages. Total RNAs from skeletal muscle of Qinchuan cattle at fetal and adult stages were used to construct libraries for Illumina next-generation sequencing using the Ribo-Zero RNA sequencing (RNA-Seq) method. We found a total of 19,695 genes to be expressed in fetal and adult stages, whereby 3,299 were expressed only in fetal, and 433 only in adult tissues. We characterized the role of a candidate gene (GosB), which was highly (but differentially) expressed in embryonic and adult skeletal muscle tissue. GosB increased the number of myoblasts in the S-phase of the cell cycle, and decreased the proportion of cells in the G0/G1 phase. GosB promoted the proliferation of myoblasts and protected them from apoptosis via regulating Bcl-2 expression and controlling the intracellular calcium concentration. Modulation of GosB expression in muscle tissue may emerge as a potential target in breeding strategies attempting to alter myoblast numbers in cattle.

The muscle development transcriptome landscape of ovariectomized goat

In practical production, almost all rams and about 50% of ewes are used to fatten. Researchers have proved that ewe ovariectomy could improve the productivity significantly, but the specific molecular mechanism is still unknown. In this study, five independent cDNA libraries (three and two from ovariectomized and normal ewe longissimus dorsi samples, respectively) were constructed to thoroughly explore the global transcriptome, further to reveal how the ovariectomized ewes influence muscle development by Illumina2000 sequencing technology. As a result, 205 358 transcripts and 118 264 unigenes were generated. 15 490 simple sequence repeats (SSRs) were revealed and divided into six types, and the short repeat sequence SSR (monomers, dimers, trimers) was the domain type. Single nucleotide polymorphism analysis found that the number of transition was greater than the number of transversion among the five libraries. Furthermore, 1612 differently expressed genes (DEGs) (Log2fold_change > 1 and p < 0.05) were revealed between ovariectomized and normal ewe groups, in which 903 genes were expressed commonly in the two groups, and 288 and 421 genes were uniquely expressed in normal and ovariectomized ewe groups, respectively. Gene Ontology (GO) analysis categorized all unigenes into 555 GO terms and 56 DEGs were significantly categorized into 43 GO terms (p < 0.05). KEGG enrichment analysis annotated 12 976 genes (containing 137 DEGs) to 86 pathways, among them 24 and 11 DEGs involved in development and reproduction associated pathways, respectively. To validate the reliability of the RNA-seq analysis, 22 candidate DEGs were randomly selected to perform quantitative real-time polymerase chain reaction. The result showed that 9 and 1 genes were significantly and approximately significantly expressed in control and treatment group, respectively, and the results of RNA-seq are believable in this study. Overall, these results were helpful for elucidating the molecular mechanism of muscle development of ovariectomized animals and the application of female ovariectomy in fattening.

Circular RNA profiling reveals an abundant circLMO7 that regulates myoblasts differentiation and survival by sponging miR-378a-3p

Circular RNAs (circRNAs) have been identified from various tissues and species, but their regulatory functions during developmental processes are not well understood. We examined circRNA expression profiles of two developmental stages of bovine skeletal muscle (embryonic and adult musculus longissimus) to provide first insights into their potential involvement in bovine myogenesis. We identified 12 981 circRNAs and annotated them to the Bos taurus reference genome, including 530 circular intronic RNAs (ciRNAs). One parental gene could generate multiple circRNA isoforms, with only one or two isoforms being expressed at higher expression levels. Also, several host genes produced different isoforms when comparing development stages. Most circRNA candidates contained two to seven exons, and genomic distances to back-splicing sites were usually less than 50 kb. The length of upstream or downstream flanking introns was usually less than 105 nt (mean≈11 000 nt). Several circRNAs differed in abundance between developmental stages, and real-time quantitative PCR (qPCR) analysis largely confirmed differential expression of the 17 circRNAs included in this analysis. The second part of our study characterized the role of circLMO7—one of the most down-regulated circRNAs when comparing adult to embryonic muscle tissue—in bovine muscle development. Overexpression of circLMO7 inhibited the differentiation of primary bovine myoblasts, and it appears to function as a competing endogenous RNA for miR-378a-3p, whose involvement in bovine muscle development has been characterized beforehand. Congruent with our interpretation, circLMO7 increased the number of myoblasts in the S-phase of the cell cycle and decreased the proportion of cells in the G0/G1 phase. Moreover, it promoted the proliferation of myoblasts and protected them from apoptosis. Our study provides novel insights into the regulatory mechanisms underlying skeletal muscle development and identifies a number of circRNAs whose regulatory potential will need to be explored in the future.

Dynamic transcriptomic analysis in hircine longissimus dorsi muscle from fetal to neonatal development stages

Muscle growth and development from fetal to neonatal stages consist of a series of delicately regulated and orchestrated changes in expression of genes. In this study, we performed whole transcriptome profiling based on RNA-Seq of caprine longissimus dorsi muscle tissue obtained from prenatal stages (days 45, 60, and 105 of gestation) and neonatal stage (the 3-day-old newborn) to identify genes that are differentially expressed and investigate their temporal expression profiles. A total of 3276 differentially expressed genes (DEGs) were identified (Q value < 0.01). Time-series expression profile clustering analysis indicated that DEGs were significantly clustered into eight clusters which can be divided into two classes (Q value < 0.05), class I profiles with downregulated patterns and class II profiles with upregulated patterns. Based on cluster analysis, GO enrichment analysis found that 75, 25, and 8 terms to be significantly enriched in biological process (BP), cellular component (CC), and molecular function (MF) categories in class I profiles, while 35, 21, and 8 terms to be significantly enriched in BP, CC, and MF in class II profiles. KEGG pathway analysis revealed that DEGs from class I profiles were significantly enriched in 22 pathways and the most enriched pathway was Rap1 signaling pathway. DEGs from class II profiles were significantly enriched in 17 pathways and the mainly enriched pathway was AMPK signaling pathway. Finally, six selected DEGs from our sequencing results were confirmed by qPCR. Our study provides a comprehensive understanding of the molecular mechanisms during goat skeletal muscle development from fetal to neonatal stages and valuable information for future studies of muscle development in goats.

The developmental transcriptome landscape of receptive endometrium during embryo implantation in dairy goats

Under natural conditions, some embryos cannot implant successfully because of the dysfunction of receptive endometrium (RE). Thus, it is imperative for us to study the molecular mechanisms involved in the formation of the RE from pre-receptive endometrium (PE). In this study, the endometrium from gestational day 5 (D5, PE) and gestational day 15 (D15, RE) dairy goats were selected to systematically analyze the transcriptome using strand-specific Ribo-Zero RNA-Seq, >120 million high-quality paired-end reads were generated and 47,616 transcripts were identified in the endometrium of dairy goats. A total of 810 mRNAs were differentially expressed genes (DEGs) between the RE and PE meeting the criteria of P-values<0.05. Bioinformatics analysis of the DEGs revealed that a number of biological processes and pathways were potentially involved in the establishment of the RE, notably energy metabolism and amino acid metabolism. Furthermore, we speculated that CXCL14, IGFBP3, and LGALS15 potentially participated in the development of endometrium. What's more, putative SNPs, InDels and AS events were identified and analyzed in the endometrium. In a word, this resulting view of the transcriptome greatly enhances the comprehensive transcript catalog and uncovers the global trends in gene expression during the formation of receptive endometrium in dairy goats.

Transcriptome analysis of the pectoral muscles of local chickens and commercial broilers using Ribo-Zero ribonucleic acid sequencing

BACKGROUND

The molecular mechanisms underlying meat quality and muscle growth are not clear. The meat quality and growth rates of local chickens and commercial broilers are very different. The Ribo-Zero RNA-Seq technology is an effective means of analyzing transcript groups to clarify molecular mechanisms. The aim of this study was to provide a reference for studies of the differences in the meat quality and growth of different breeds of chickens.

RESULTS

Ribo-Zero RNA-Seq technology was used to analyze the pectoral muscle transcriptomes of Gushi chickens and AA broilers. Compared with AA broilers, 1649 genes with annotated information were significantly differentially expressed (736 upregulated and 913 downregulated) in Gushi chickens with Q≤0.05 (Q is the P-value corrected by multiple assumptions test) at a fold change ≥2 or ≤0.5. In addition, 2540 novel significantly differentially expressed (SDE) genes (1405 upregulated and 1135 downregulated) were discovered. The results showed that the main signal transduction pathways that differed between Gushi chickens and AA broilers were related to amino acid metabolism. Amino acids are important for protein synthesis, and they regulate key metabolic pathways to improve the growth, development and reproduction of organisms.

CONCLUSION

This study showed that differentially expressed genes in the pectoral tissues of Gushi chickens and AA broilers were related to fat metabolism, which affects meat. Additionally, a large number of novel genes were found that may be involved in fat metabolism and thus may affect the formation of meat, which requires further study. The results of this study provide a reference for further studies of the molecular mechanisms of meat formation.

Long non-coding RNA ADNCR suppresses adipogenic differentiation by targeting miR-204

Adipogenesis is a complex and precisely orchestrated process mediated by a network of adipogenic regulatory factors. Several studies have highlighted the relevance of lncRNAs in adipocyte differentiation, but the precise molecular mechanism has largely remained elusive. In the present study, we performed Ribo-Zero RNA-Seq to investigate both the poly(A)+and poly(A)-lncRNAs of in vitro cultured bovine preadipocytes and differentiated adipocytes. A stringent set of 2882 lncRNAs was finally identified. A comparison of the lncRNAs expression profiles revealed that 16 lncRNAs are differentially expressed during adipocyte differentiation. We focused on the most downregulated lncRNA, which we named adipocyte differentiation-associated long noncoding RNA (ADNCR). Mechanistically, ADNCR inhibited adipocyte differentiation by functioning as a competing endogenous RNA (ceRNA) for miR-204, thereby augmenting the expression of the miR-204 target gene, SIRT1, which is known to inhibit adipocyte differentiation and adipogenic gene expression by docking with NCoR and SMART to repress PPARγ activity. Our data not only provide a valuable genomic resource for the identification of lncRNAs with functional roles in adipocyte differentiation but also reveal new insights into understanding the mechanisms of adipogenic differentiation.