CircRNA-006258 Sponge-Adsorbs miR-574-5p to Regulate Cell Growth and Milk Synthesis via EVI5L in Goat Mammary Epithelial Cells

Mining key circRNA-associated-ceRNA networks for milk fat metabolism in cows with varying milk fat percentages

BACKGROUND

Cow milk fat is an essential indicator for evaluating and measuring milk quality and cow performance. Growing research has identified the molecular functions of circular RNAs (circRNAs) necessary for mammary gland development and lactation in mammals.

METHOD

The present study analyzed circRNA expression profiling data in mammary epithelial cells (MECs) from cows with highly variable milk fat percentage (MFP) using differential expression analysis and weighted gene co-expression network analysis (WGCNA).

RESULTS

A total of 309 differentially expressed circRNAs (DE-circRNAs) were identified in the high and low MFP groups. WGCNA analysis revealed that the pink module was significantly associated with MFP (r = - 0.85, P = 0.007). Parental genes of circRNAs in this module were enriched mainly in lipid metabolism-related signaling pathways, such as focal adhesion, ECM-receptor interaction, adherens junction and AMPK. Finally, six DE-circRNAs were screened from the pink module: circ_0010571, circ_0007797, circ_0002746, circ_0003052, circ_0004319, and circ_0012840. Among them, circ_0002746, circ_0003052, circ_0004319, and circ_0012840 had circular structures and were highly expressed in mammary tissues. Subcellular localization revealed that these four DE-circRNAs may play a regulatory role in the mammary glands of dairy cows, mainly as competitive endogenous RNAs (ceRNAs). Seven hub target genes (GNB1, GNG2, PLCB1, PLCG1, ATP6V0C, NDUFS4, and PIGH) were obtained by constructing the regulatory network of their ceRNAs and then analyzed by CytoHubba and MCODE plugins in Cytoscape. Functional enrichment analysis revealed that these genes are crucial and most probable ceRNA regulators in milk fat metabolism.

CONCLUSIONS

Our study identified several vital circRNAs and ceRNAs affecting milk fat synthesis, providing new research ideas and a theoretical basis for cow lactation, milk quality, and breed improvement.

Progress in epigenetic regulation of milk synthesis, with particular emphasis on mRNA regulation and DNA methylation

Inadequate milk secretion and a lack of nutrients in humans and mammals are serious problems. It is of great significance to clarify the mechanisms of milk synthesis and treatment methods. Epigenetic modification, represented by RNA methylation, is an important way of gene expression regulation that profoundly affects human gene expression and participates in various physiological and pathological mechanisms. Epigenetic disorders also have an important impact on the production and secretion of milk. This review systematically summarized the research results of epigenetics in the process of lactation in PubMed, Web of Science, NSTL, and other databases and reviewed the effects of epigenetics on human and mammalian lactation, including miRNAs, circRNAs, lncRNAs, DNA methylations, and RNA methylations. The abnormal expression of miRNAs was closely related to the synthesis and secretion of milk fat, milk protein, and other nutrients in the milk of cattle, sheep, and other mammals. MiRNAs are also involved in the synthesis of human milk and the secretion of nutrients. CircRNAs and lncRNAs mainly target miRNAs and regulate the synthesis of nutrients in milk by ceRNA mechanisms. The abnormal expression of DNA and RNA methylation also has an important impact on milk synthesis. Epigenetic modification has the potential to regulate the milk synthesis of breast epithelial cells. Analyzing the mechanisms of human and mammalian milk secretion deficiency and nutrient deficiency from the perspective of epigenetics will provide a new perspective for the treatment of postpartum milk deficiency in pregnant women and mammalian milk secretion deficiency.

Integrating genome-wide methylation and transcriptome-wide analyses to reveal the genetic mechanism of milk traits in Kazakh horses

Horse Milk has important quantitative characteristics and high economic value. However, the DNA methylation regulators involved in horse milk traits have not been clarified. To explore the important role of genome-wide DNA methylation in regulating equine milk yield, this study systematically investigated the genome-wide DNA methylation profiles of Kazakh horse blood by comparing a high-production group (HP, average daily milk yield of 7.5 kg) and low-production group (LP, average daily milk yield of 3.2 kg) using deep whole-genome bisulfite sequencing. First, both groups showed similar proportions of methylation at CpG sites. Subsequently, we identified 26,677 differential methylated regions (DMRs) of CG, 15 DMRs of CHG, 480 DMRs of CHH and 8268 DMR-related genes (DMGs). GO and KEGG analyses revealed that some DMGs were involved in regulating milk and milk component formation. By combining the WGBS-seq and the previous RNA-seq data, a total of 94 overlapping genes were obtained. Finally, we found that 9 DMGs are likely involved in milk production by Kazakh horses.

The emerging roles of circRNAs in traits associated with livestock breeding

Many indicators can be used to evaluate the productivity and quality of livestock, such as meat and milk production as well as fat deposition. Meat and milk production are measures of livestock performance, while fat deposition affects the taste and flavor of the meat. The circRNAs, are non-coding RNAs, that are involved in the regulation of all these three traits. We review the functions and mechanisms of circRNAs in muscle and fat development as well as lactation to provide a theoretical basis for circRNA research in animal husbandry. Various phenotypic changes presented in livestock may be produced by different circRNAs. Our current concern is how to use the roles played by circRNAs to our advantage to produce the best possible livestock. Hence, we describe the advantages and disadvantages of knockout techniques for circRNAs. In addition, we also put forward our thoughts regarding the mechanism and network of circRNAs to provide researchers with novel ideas of how molecular biology can help us advance our goals in animal farming. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.

Comprehensive Profiling of ceRNA (circRNA-miRNA-mRNA) Networks in Hypothalamic-Pituitary-Mammary Gland Axis of Dairy Cows under Heat Stress

Heat stress (HS) is directly correlated with mammary gland dysfunction and the hypothalamic-pituitary-mammary gland (HPM) axis is involved in regulating stress responses and lactation in dairy cows. Circular RNAs (circRNAs) play major roles in regulating transcription and post-transcription but their expression in the HPM axis of dairy cows under HS is still unclear. In the present study, we performed RNA sequencing to identify diferentially expressed (DE) circRNAs, DE microRNAs(miRNAs) and DEmRNAs, and performed bioinformatics analysis on those in HPM axis-related tissues of heat-stressed and normal cows. A total of 1680, 1112 and 521 DEcircRNAs, 120, 493 and 108 DEmiRNAs, 274, 6475 and 3134 DEmRNAs were identified in the hypothalamic, pituitary, and mammary gland tissues, respectively. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses indicated that the MAPK signaling pathway is potentially a key pathway. Competitive endogenous RNA (ceRNA) networks related to HS response and lactation regulation were established in three tissues. In conclusion, our results indicate that HS induces differential circRNA expression profiles in HPM axis-related tissues, and the predicted ceRNA network provides a molecular basis for regulating the stress response and lactation regulation in heat-stressed dairy cows.

Identification of selection signatures in Capra hircus and Capra aegagrus in Iran

Identification of selection signatures may provide a better understanding of domestication process and candidate genes contributing to this process. In this study, two populations of domestic and wild goats from Iran were analyzed to identify selection signatures. RSB, iHS, and XP-EHH statistics were used in order to identify robust selection signatures in the goat genome. Genotype data of domestic and wild goats from the NextGen project was used. The data was related to 18 Capra aegagrus (wild goat) and 20 Capra hircus (domestic goat) from Iran. The iHS method indicated 675 and 441 selection signatures in C. aegagrus and C. hircus, respectively. RSB and XP-EHH methods showed about 370 and 447 selection signatures in C. aegagrus and C. hircus, respectively. These selection signatures were mainly associated with milk production, fleece trait, mammary epithelial cells, reproduction, and immune system.

LncRNA NALT1 promotes colorectal cancer progression via targeting PEG10 by sponging microRNA-574-5p

Colorectal cancer (CRC) is currently one of the commonest tumors and the main reason for cancer-related deaths worldwide. It has been reported that long non-coding RNAs (lncRNAs) act as important indicators and regulators in various cancers. There is an urgent need to explore new lncRNA biomarkers in CRC, as well as their functions and molecular mechanisms. NALT1 has been implicated in the occurrence of gastric cancer (GC). However, the detailed function and mechanism of NALT1 in CRC progress have not been reported. In this study, RT-qPCR was conducted to detect the expression of NALT1 in 76 CRC patients ranging from stages I through IV. To assess the biological function of NALT1, loss- and gain-of-function experiments were conducted both in vivo and in vitro. Moreover, RNA-seq, bioinformatics analysis, RNA pulldown assay, dual-luciferase reporter, Ago2-RIP, quantitative PCR, Western blot assays, and rescue experiments were performed to reveal the molecular mechanisms of competitive endogenous RNAs (ceRNAs). It was observed that high expression of NALT1 was markedly correlated with advanced cancer stage in the clinic. Functionally, NALT1 downregulation inhibited cell proliferation, migration and invasion, whereas NALT1 overexpression exhibited an opposite trend both in vivo and in vitro. Bioinformatics analysis, RNA pulldown, Ago2-RIP, and luciferase reporter assays showed that miRNA-574-5p was a target of NALT1. Additionally, dual-luciferase reporter assays, Ago2-RIP, and rescue experiments indicated that miRNA-574-5p could target the PEG10 gene directly. Our results suggested that NALT1 promoted CRC proliferation and migration by sponging miRNA-574-5p to upregulate PEG10 expression, and implied that NALT1 might act as a promising biomarker and therapeutic target for CRC.

CircRNA screening and ceRNA network construction for milk fat metabolism in dairy cows

BACKGROUND

Milk fat is one of the main reference elements for evaluating milk quality and is a primary objective trait in dairy cattle breeding. In recent years, circular RNAs (circRNAs) have been found to play crucial roles in many biological processes. However, the function and expression profiles of circRNAs in milk fat synthesis in cows are not completely understood. We performed RNA sequencing to analyze the genome-wide expression of circRNA transcripts in bovine mammary epithelial cells (BMECs) from cows with extreme differences in milk fat percentage. We identified candidate differential circRNAs associated with milk fat metabolism using functional enrichment analysis and constructed a lipid metabolism-related competing endogenous RNA (ceRNA) interactive regulatory network.

RESULTS

A total of 290 circRNAs were significantly differentially expressed (DE-circRNAs) in high milk fat percentage (HMF) cows compared to that in low milk fat percentage (LMF) cows. Of the 290 circRNAs, 142 were significantly upregulated and 148 were significantly downregulated. Enrichment analysis (Gene Ontology and Kyoto Encyclopedia of Genes and Genomes) identified four DE-circRNAs (circ_0001122, circ_0007367, circ_0018269, and circ_0015179) that potentially regulate milk fat metabolism. Among them, circ_0001122, circ_0007367, and circ_0015179 had relatively high expression levels in cow mammary gland tissue compared to other tissues (heart, liver, kidney, uterus, ovaries, and small intestine) of cows. The regulatory networks circ_0001122:miR-12043:LIPG, circ_0007367:miR-331-3p:CIDEA/PML, and circ_0018269:miR-11989:RORC/HPX are potential networks to explore the mechanism of milk fat regulation.

CONCLUSIONS

These results reveal the possible role of circRNAs in milk fat metabolism in dairy cows. Several important circRNAs and ceRNAs affecting milk fat synthesis were identified, providing insights into the complex biology of milk fat synthesis as well as a novel theoretical perspective for future research on lactation, milk quality, and breed improvement in dairy cows.

Tissue-Specific Expression of Circ_015343 and Its Inhibitory Effect on Mammary Epithelial Cells in Sheep

Circular RNAs (circRNAs) are a kind of non-coding RNA that have an important molecular function in mammary gland development and lactation of mammals. In our previous study, circ_015343 was found to be highly expressed in the ovine mammary gland tissue at the peak-lactation period by using RNA sequencing (RNA-seq). In the present study, the authenticity of circ_015343 was confirmed by using reverse transcriptase-polymerase chain reaction (RT-PCR) analysis and Sanger sequencing. The circ_015343 was derived from the complete 10 exons of aminoadipic semialdehyde synthase (AASS), ranging from exon 2 to exon 11 and mainly located in cytoplasm of ovine mammary epithelial cells. The circRNA was found to be expressed in eight ovine tissues, with the highest expression level in the mammary gland and the least expression in Longissimus dorsi muscle. The circ_015343 had a lower level of expression in a sheep breed with higher milk yield and milk fat content. The disturbed circ_015343 increased the viability and proliferation of the ovine mammary epithelial cells. The inhibition of circ_015343 also increased the expression levels of three milk fat synthesis marker genes: acetyl-coenzyme A carboxylase alpha (ACACA), fatty acid-binding protein 4 (FABP4), and sterol regulatory element-binding protein 1 (SREBP1), as well as three proliferation-related genes: cyclin dependent kinase 2 (CDK2), cyclin dependent kinase 4 (CDK4) and proliferating cell nuclear antigen (PCNA), but decreased the expression level of its parent gene AASS. A circRNA-miRNA-mRNA interaction network showed that circ_015343 would bind some microRNAs (miRNAs) to regulate the expression of functional genes related to the development of mammary gland and lactation. This study contributes to a better understanding of the roles of circ_015343 in the mammary gland of sheep.

Expression Profiling and Functional Analysis of Circular RNAs in Inner Mongolian Cashmere Goat Hair Follicles

Background

Inner Mongolian cashmere goats have hair of excellent quality and high economic value, and the skin hair follicle traits of cashmere goats have a direct and important effect on cashmere yield and quality. Circular RNA has been studied in a variety of tissues and cells.

Result

In this study, high-throughput sequencing was used to obtain the expression profiles of circular RNA (circRNA) in the hair follicles of Inner Mongolian cashmere goats at different embryonic stages (45, 55, 65, and 75 days). A total of 21,784 circRNAs were identified. At the same time, the differentially expressed circRNA in the six comparison groups formed in the four stages were: d75vsd45, 59 upregulated and 33 downregulated DE circRNAs; d75vsd55, 61 upregulated and 102 downregulated DE circRNAs; d75vsd65, 32 upregulated and 33 downregulated DE circRNAs; d65vsd55, 67 upregulated and 169 downregulated DE circRNAs; d65vsd45, 96 upregulated and 63 downregulated DE circRNAs; and d55vsd45, 76 upregulated and 42 downregulated DE circRNAs. Six DE circRNA were randomly selected to verify the reliability of the sequencing results by quantitative RT-PCR. Subsequently, the circRNA corresponding host genes were analyzed by the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The results showed that the biological processes related to hair follicle growth and development enriched by GO mainly included hair follicle morphogenesis and cell development, and the signaling pathways related to hair follicle development included the Notch signaling pathway and NF-κB signaling pathway. We combined the DE circRNA of d75vsd45 with miRNA and mRNA databases (unpublished) to construct the regulatory network of circRNA–miRNA–mRNA, and formed a total of 102 pairs of circRNA–miRNA and 126 pairs of miRNA–mRNA interactions. The binding relationship of circRNA3236–chi-miR-27b-3p and circRNA3236–chi-miR-16b-3p was further verified by dual-luciferase reporter assays, and the results showed that circRNA3236 and chi-miR-27b-3p, and circRNA3236 and chi-miR-16b-3p have a targeted binding relationship.

Conclusion

To summarize, we established the expression profiling of circRNA in the fetal skin hair follicles of cashmere goats, and found that the host gene of circRNA may be involved in the development of hair follicles of cashmere goats. The regulatory network of circRNA–miRNA–mRNA was constructed and preliminarily verified using DE circRNAs.

miR-204-5p and miR-211 Synergistically Downregulate the αS1-Casein Content and Contribute to the Lower Allergy of Goat Milk

α_S1-Casein (encoded by the CSN1S1 gene) is associated with higher rates of allergy than other milk protein components for humans. microRNAs (miRNAs) as small noncoding RNA molecules regulate gene expression and influence diverse biological processes. However, little is known about the regulation of milk protein synthesis by miRNAs in ruminants. In this study, we aim to investigate the regulatory roles of miR-204 family members (miR-204-5p and miR-211) on α_S1-casein in goat mammary epithelial cells (GMEC). Here, we observed that the CSN1S1 mRNA level is upregulated, while miR-204-5p and miR-211 (miR-204-5p/-211) abundance is downregulated during peak lactation compared with middle lactation of dairy goats. We found that miR-204-5p/-211 synergistically inhibit α_S1-casein expression via directly binding to the 3'-untranslated region (3'UTR) of CSN1S1 in GMEC. miR-204-5p/-211 increase β-casein mRNA (CSN2) and protein abundance, as well as the signal transducer and activator of transcription 5a (STAT5a) activity. Further, miR-204-5p/-211 enhance β-casein expression via the CSN1S1-STAT5a signaling axis and promote β-casein transcription by activating the STAT5 response element located in the CSN2 promoter. In conclusion, miR-204-5p/-211 regulate α_S1-casein and β-casein synthesis via targeting CSN1S1 in GMEC, which provide the strategy for manipulating miR-204 family members to reduce milk allergy potential and improve ruminant milk quality for human consumption.

Circ11103 Interacts with miR-128/PPARGC1A to Regulate Milk Fat Metabolism in Dairy Cows

The quality of milk is inseparable from its milk components, and fatty acid content is a key factor affecting the quality of milk. In this study, the miRNA and mRNA profiles of the bovine mammary gland tissue during the dry period and the peak lactation period were determined through high-throughput sequencing. In total, 72 miRNA-mRNA regulatory pathways were screened, including miR-128/PPARGC1A regulatory pathways. miR-128 can directly target PPARGC1A and inhibit its expression. In addition, the study also observed that there was a miR-128 binding site in the sequence of the circular RNA circ11103, and circ11103 significantly reduced the expression of miR-128. circ11103 upregulated the triglyceride levels in bovine mammary epithelial cells (BMECs) and increased the contents of unsaturated fatty acids. However, miR-128 decreased triglyceride and cholesterol levels in BMECs. This study aims to analyze the mechanism governing the regulatory effect of circ11103 on milk fat metabolism, which provides new insights into improving milk quality.

Effect of the circCDR1as/miR-641/XIAP regulatory axis on the proliferation and invasion of the prostate cancer PC-3 cell line

Prostate cancer is one of the most common malignant tumors in men. Patients with local infiltration and distant metastasis often have a poor prognosis. The present study aimed to investigate the expression and regulatory mechanism of the circular RNA cerebellar degeneration-related protein 1, anti-sense (circCDR1as) in prostate cancer cell lines. MicroRNAs (miRNAs) regulated by circCDR1as and target genes regulated by miRNAs were predicted using bioinformatics software. Prostate cancer cell lines (LNCaP, 22Rv1 and PC-3), a normal prostate epithelial cell line (RWPE-1) and a human embryonic kidney cell line (293T) were cultured. Relative gene expression was detected using reverse transcription PCR. Small interfering RNAs (siRNAs) targeting circCDR1as and X-linked inhibitor of apoptosis protein (XIAP) and miRNA mimics were designed and transfected into the cell lines using Lipofectamine^® 3000. Cell invasion was determined using a Transwell assay, the cell proliferation rate was detected using an MTT assay and cell migration was examined using a scratch assay. Relative protein expression was detected using western blotting. Double fluorescent reporter gene vectors and an anti-Ago2 RNA-binding protein immunoprecipitation assay were used to verify binding. Bioinformatics analyses indicated that there was a binding site between miR-641 and circCDR1as and between miR-641 and XIAP. The expression of circCDR1as and XIAP was higher and the expression of miR-641 was lower in the prostate cancer cell lines compared with the normal prostate epithelial cell line. After effectively reducing the expression of circCDR1as and XIAP and increasing the expression of miR-641 in PC-3 cells, the proliferation, invasion and migration of PC-3 cells were effectively inhibited. circCDR1as could bind to miR-641, which targeted the 3′-untranslated region of XIAP. Reducing the expression of circCDR1 promoted the expression of miR-641 and inhibited the expression of XIAP. Overall, the circCDR1as/miR-641/XIAP regulatory axis plays a role in the invasion and migration of the prostate cancer PC-3 cell line.

Epigenetics: New Insights into Mammary Gland Biology

The mammary gland undergoes important anatomical and physiological changes from embryogenesis through puberty, pregnancy, lactation and involution. These steps are under the control of a complex network of molecular factors, in which epigenetic mechanisms play a role that is increasingly well described. Recently, studies investigating epigenetic modifications and their impacts on gene expression in the mammary gland have been performed at different physiological stages and in different mammary cell types. This has led to the establishment of a role for epigenetic marks in milk component biosynthesis. This review aims to summarize the available knowledge regarding the involvement of the four main molecular mechanisms in epigenetics: DNA methylation, histone modifications, polycomb protein activity and non-coding RNA functions.