Integrated Analysis Of mRNAs Research Articles

Integrated analysis of mRNAs and lncRNAs reveals candidate marker genes and potential hub lncRNAs associated with growth regulation of the Pacific Oyster, Crassostrea gigas

BackgroundThe Pacific oyster, Crassostrea gigas, is an economically important shellfish around the world. Great efforts have been made to improve its growth rate through genetic breeding. However, the candidate marker genes, pathways, and potential lncRNAs involved in oyster growth regulation remain largely unknown. To identify genes, lncRNAs, and pathways involved in growth regulation, C. gigas spat was cultured at a low temperature (15 ℃) to yield a growth-inhibited model, which was used to conduct comparative transcriptome analysis with spat cultured at normal temperature (25 ℃).ResultsIn total, 8627 differentially expressed genes (DEGs) and 1072 differentially expressed lncRNAs (DELs) were identified between the normal-growth oysters (cultured at 25 ℃, hereinafter referred to as NG) and slow-growth oysters (cultured at 15 ℃, hereinafter referred to as SG). Functional enrichment analysis showed that these DEGs were mostly enriched in the AMPK signaling pathway, MAPK signaling pathway, insulin signaling pathway, autophagy, apoptosis, calcium signaling pathway, and endocytosis process. LncRNAs analysis identified 265 cis-acting pairs and 618 trans-acting pairs that might participate in oyster growth regulation. The expression levels of LNC_001270, LNC_003322, LNC_011563, LNC_006260, and LNC_012905 were inducible to the culture temperature and food abundance. These lncRNAs were located at the antisense, upstream, or downstream of the SREBP1/p62, CDC42, CaM, FAS, and PIK3CA genes, respectively. Furthermore, the expression of the trans-acting lncRNAs, including XR_9000022.2, LNC_008019, LNC_015817, LNC_000838, LNC_00839, LNC_011859, LNC_007294, LNC_006429, XR_002198885.1, and XR_902224.2 was also significantly associated with the expression of genes enriched in AMPK signaling pathway, insulin signaling pathway, autophagy, apoptosis, calcium signaling pathway, and endocytosis process.ConclusionsIn this study, we identified the critical growth-related genes and lncRNAs that could be utilized as candidate markers to illustrate the molecular mechanisms underlying the growth regulation of Pacific oysters.

An integrated analysis of mRNAs and lncRNAs in goat's hypothalamus to explore the onset of puberty.

The time of puberty onset is crucial for female animal, as it can affect the generation interval, feeding costs and the utilization of animals. However, little is known about the mechanism of hypothalamic lncRNAs (long noncoding RNAs) in regulatory goat puberty onset. Therefore, genome-wide transcriptome analysis was performed in goats to clarify the roles of hypothalamic lncRNAs and mRNAs in the onset of puberty. In the present study, the co-expression network of differentially expressed (DE) mRNAs in goat hypothalamus identified FN1 as the hub gene, and ECM-receptor interaction, Focal adhesion and PI3K-Akt signalling pathways are involved in puberty. We also observed the crucial hub transcription factors (TCF12, STAT1, STAT2, GATA3 and TEAD4) associated with reproduction and puberty. Then, genetic correlation analysis of DE mRNAs and DE lncRNAs identified the key lncRNAs involved in puberty. This research supplies a resource for transcriptome studies in goat puberty and indicated DE lncRNAs in the ECM-receptor interaction pathway were novel candidate regulators for genetic studies on female reproduction.

Integrated analysis of mRNA and miRNA transcriptomes reveals the mechanism of regulatory interspecific fiber heterosis

Interspecific hybridization contributes to improving cotton fiber quality, thus addressing the parental genetic diversity bottleneck problems. To elucidate the molecular mechanisms underlying fiber heterosis in interspecific hybrid cotton, an integrated analysis of phenotypes, mRNAs, and miRNAs was performed to compare the immature fibers of the parents (Gossypium hirsutum and Gossypium barbadense) with those of their hybrid at various development stages. The results showed that fiber heterosis was most obvious at 10 days post anthesis. Comprehensive analysis of mRNA and miRNA demonstrated that the main expression pattern was transgressive up-regulation (TUR) at mRNA level, while it was transgressive down-regulation (TDR) at miRNA level. The miR160-ARF and miR319-TCP pairs were mainly responsible for the changes in endogenous auxin content and secondary cell wall deposition in the fiber development stage, and they played an important role in the formation of interspecific fiber heterosis. Meanwhile, the results of indole-3-acetic acid (IAA) content determination and in vitro ovule culture indicated that auxin affected fiber heterosis. This study reveals the mechanism by which miRNA-mRNA regulates fiber heterosis, and it will promote the applications of interspecific hybrid cotton between G. hirsutum and G. barbadense.

Integrated analysis of mRNA and microRNA transcriptome related to immunity and autophagy in shrimp hemocytes infected with Spiroplasma eriocheiris

In recent years, the industry in charge of the cultivation of Macrobrachium nipponense (M.nipponense) has suffered significant economic losses due to an infectious pathogen called Spiroplasma eriocheiris (S.eriocheiris). There has therefore been a need to identify the key immune and autophagy genes that respond to M.nipponense's infection with S. eriocheiris to analyze its immune response mechanism and the regulation of related microRNAs (miRNAs). In this study, the mRNA and miRNA transcriptome of M.nipponense's hemocytes were analyzed at different stages of infection. This analysis employed the second and third-generation sequencing technologies. In the mRNA transcriptome, 1656 genes were expressed in healthy and susceptible M.nipponense. 892 of these were significantly up-regulated, while 764 were down-regulated. 118 genes with significant differences in autophagy, endocytosis, lysosome, Toll, IMD, and VEGF pathways were obtained from the transcriptome. In the miRNA transcriptome, 312 miRNAs (Conserved: 112, PN-type: 18, PC-type: 182) were sequenced. 74 were significantly up-regulated, and 57 were down-regulated. There were 25 miRNAs involved in regulating the Toll and IMD pathways, 41 in endocytosis, 30 in lysosome, and 12 in the VEGF pathway. An integrated analysis of immune-related miRNAs and mRNAs showed that miRNAs with significant differences (P < 0.05) such as ame-miR-29b-3p, dpu-miR-1and PC-3p-945_4074, had corresponding regulatory relationships with 118 important immune genes such as Relish, Dorsal, Caspase-3, and NF-κB. This study obtained the key immune and autophagy-related genes and corresponding regulatory miRNAs in M. nipponense's hemocytes in response to an infection by S.eriocheiris. The results can provide vital data that further reveals the defense mechanism of M.nipponense's immune system against S.eriocheiris. It can also help further comprehension and interpretation of M.nipponense's resistance mechanism to the invading S.eriocheiris, and provide molecular research information for the realization of host-directed therapies (HDT) for M.nipponense.

An integrated analysis of mRNAs, lncRNAs, and miRNAs based on weighted gene co-expression network analysis involved in bovine endometritis

In dairy cattle, endometritis is a severe infectious disease that occurs following parturition. It is clear that genetic factors are involved in the etiology of endometritis, however, the molecular pathogenesis of endometritis is not entirely understood. In this study, a system biology approach was used to better understand the molecular mechanisms underlying the development of endometritis. Forty transcriptomic datasets comprising of 20 RNA-Seq (GSE66825) and 20 miRNA-Seq (GSE66826) were obtained from the GEO database. Next, the co-expressed modules were constructed based on RNA-Seq (Rb-modules) and miRNA-Seq (mb-modules) data, separately, using a weighted gene co-expression network analysis (WGCNA) approach. Preservation analysis was used to find the non-preserved Rb-modules in endometritis samples. Afterward, the non-preserved Rb-modules were assigned to the mb-modules to construct the integrated regulatory networks. Just highly connected genes (hubs) in the networks were considered and functional enrichment analysis was used to identify the biological pathways associated with the development of the disease. Furthermore, additional bioinformatic analysis including protein–protein interactions network and miRNA target prediction were applied to enhance the reliability of the results. Thirty-five Rb-modules and 10 mb-modules were identified and 19 and 10 modules were non-preserved, respectively, which were enriched in biological pathways related to endometritis like inflammation and ciliogenesis. Two non-preserved Rb-modules were significantly assigned to three mb-modules and three and two important sub-networks in the Rb-modules were identified, respectively, including important mRNAs, lncRNAs and miRNAs genes like IRAK1, CASP3, CCDC40, CCDC39, ZMYND10, FOXJ1, TLR4, IL10, STAT3, FN1, AKT1, CD68, ENSBTAG00000049936, ENSBTAG00000050527, ENSBTAG00000051242, ENSBTAG00000049287, bta-miR-449, bta-miR-484, bta-miR-149, bta-miR-30b and bta-miR-423. The potential roles of these genes have been previously demonstrated in endometritis or related pathways, which reinforced putative functions of the suggested integrated regulatory networks in the endometritis pathogenesis. These findings may help further elucidate the underlying mechanisms of bovine endometritis.

Identification and integrated analysis of mRNAs, lncRNAs, and microRNAs of developing seeds in high oleic acid sunflower (Helianthus annuus L.)

High unsaturated fatty acid content of sunflower seed is desirable for human-healthy high oleic acid oil production. Knowledge of lipid metabolic regulatory mechanisms is key to improving oil content and quality. This study is expected to explore regulatory mechanisms of lipid metabolism in high oleic acid seeds. First, we analyzed the oil contents and detected the fatty acid compositions in developing sunflower seeds with high oleic acid content. Next, high-throughput sequencing (HTS) of seed RNA samples from three key seed developmental stages relevant to oil content and quality was performed. Pairwise comparisons of differentially expressed mRNAs, long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) yielded respective differentially expressed transcripts as follows: 52293, 120625, 95 (L7d vs L22d); 57398, 123485, 127 (L7 vs L37d); 15417, 9554, 77 (L22d vs L37d). 15652 novel mRNAs, 123888 novel lncRNAs, and 98 novel miRNAs were identified, which enriched the RNA library of sunflower. Furthermore, gene functions were predicted using GO and KEGG analyses. These prediction analysis revealed that differentially expressed ncRNAs and mRNAs were mainly included in fatty acid metabolism and oil accumulation. Moreover, 9072 pairs of competing endogenous RNA (ceRNA) relationships comprised of interacting lncRNAs, miRNAs, and mRNAs. Pathway network analysis of differentially expressed lipid metabolism-associated ceRNAs revealed several important enzymes including glycerol-3-phosphate O-acyltransferase, linoleate 9S-lipoxygenase, acyl-CoA oxidase, and others that were enriched in fatty acid synthesis and oil accumulation, which highlighted competitive interactions in lipid metabolism. This study will elucidate potential regulatory mechanisms of lipid metabolism in sunflower seeds.

Extracellular vesicle-associated miR-135b and -135a regulate stemness in Group 4 medulloblastoma cells by targeting angiomotin-like 2

BackgroundExtracellular vesicles (EVs) secreted by tumours, including exosomes, are important factors that regulate cell–cell interactions in oncogenesis. Although EV studies are ongoing, the biological understanding of EV-miRNAs derived from brain tumour spheroid-forming cells (BTSCs) of medulloblastoma is poor.PurposesWe explored the specific cellular miRNAs and EV-miRNAs in medulloblastoma BTSCs to determine their potential biological function.MethodsBulk tumor cells (BTCs) and BTSCs were cultured under different conditions from medulloblastoma tissues (N = 10).ResultsTwenty-four miRNAs were simultaneously increased in both cells and EVs derived from BTSCs in comparison to BTCs. After inhibition of miR-135b or miR135a which were the most significantly increased in BTSCs, cell viability, self-renewal and stem cell marker expression decreased remarkably. Through integrated analysis of mRNAs and miRNAs data, we found that angiomotin-like 2 (AMOTL2), which was significantly decreased, was targeted by both miR-135b and miR-135a. STAT6 and GPX8 were targeted only by miR-135a. Importantly, low expression of AMOTL2 was significantly associated with overall poor survival in paediatric Group 3 and Group 4 medulloblastoma patients.ConclusionOur results indicated that inhibition of miR-135b or miR-135a leads to suppress stemness of BTSC through modulation of AMOTL2.

The Oviductal Extracellular Vesicles' RNA Cargo Regulates the Bovine Embryonic Transcriptome.

Oviductal extracellular vesicles (oEVs) are emerging as key players in the gamete/embryo–oviduct interactions that contribute to successful pregnancy. Various positive effects of oEVs on gametes and early embryos have been found in vitro. To determine whether these effects are associated with changes of embryonic gene expression, the transcriptomes of embryos supplemented with bovine fresh (FeEVs) or frozen (FoEVs) oEVs during in vitro culture compared to controls without oEVs were analyzed by low-input RNA sequencing. Analysis of RNA-seq data revealed 221 differentially expressed genes (DEGs) between FoEV treatment and control, 67 DEGs for FeEV and FoEV treatments, and minor differences between FeEV treatment and control (28 DEGs). An integrative analysis of mRNAs and miRNAs contained in oEVs obtained in a previous study with embryonic mRNA alterations pointed to direct effects of oEV cargo on embryos (1) by increasing the concentration of delivered transcripts; (2) by translating delivered mRNAs to proteins that regulate embryonic gene expression; and (3) by oEV-derived miRNAs which downregulate embryonic mRNAs or modify gene expression in other ways. Our study provided the first high-throughput analysis of the embryonic transcriptome regulated by oEVs, increasing our knowledge on the impact of oEVs on the embryo and revealing the oEV RNA components that potentially regulate embryonic development.

Integrative analysis of mRNAs, miRNAs and lncRNAs in urban particulate matter SRM 1648a-treated EA.hy926 human endothelial cells

Considering the unique physiochemical properties of concentrated ambient particles (CAPs), it is extremely important to be aware of their toxic effect. A number of studies have investigated the vascular toxicity of CAPs, while potential mechanisms are still not clearly defined. Differentially expressed mRNAs, miRNAs and lncRNAs were analyzed in EA.hy926 endothelial cells after incubation with 2.5 and 10 μg/cm2 urban particulate matter SRM 1648a for 24 h. As a result, the microarray profile showed that 97 mRNA, 18 miRNA, and 356 lncRNA transcripts are dysregulated in 2.5 μg/cm2 group. And the expression of 440 mRNAs, 40 miRNAs, and 1283 lncRNAs significantly changes in 10 μg/cm2 group. Through the miRNA-mRNA-transcription factor (TF) network, hsa-miR-128-3p, miR-18-5p and miR-376a-3p, miR-4306 as well, are key miRNAs in SRM 1648a-induced endothelial damage. Withal, lncRNA-mRNA-TF analysis hinted the importance of lncRNA T018951 and T200627. Subsequently, competing endogenous RNA (CeRNA) network was constructed for the comprehensive analysis of the regulation dogma between mRNAs and non-coding RNAs. It suggested that 35 GO terms and 1 KEGG pathway are significantly enriched in 2.5 μg/cm2 group. Meanwhile, 185 terms and 18 pathways are important in 10 μg/cm2 group. Pathway analysis revealed that Gap junction, Ras and MAPK signaling pathways are most significant in endothelial cell lesion. In conclusion, integrative analysis of mRNA and non-coding RNA in human endothelial cells suggests that a vast majority of non-coding RNAs regulate vascular toxicity in response to SRM 1648a. Moreover, it highlights the need for comprehensive analysis of latent mechanisms through a combination of signaling pathways with epigenetics studies.

The transcriptional and post-transcriptional regulation in perennial creeping bentgrass in response to γ-aminobutyric acid (GABA) and heat stress

Persistent high temperature inhibits plant growth and development. The γ-aminobutyric acid (GABA) plays a key role in heat tolerance in plants. The increase in endogenous GABA level induced by exogenous GABA effectively alleviated heat damage in creeping bentgrass. Global investigation into mRNAs and miRNAs found that the regulation of HSFs pathways and enhanced carbon metabolism, biosynthesis of amino acids, and plant hormone signal transduction were important adaptive response to heat stress. GABA-induced heat tolerance was closely related to phenylpropanoid biosynthesis, further improved HSFs pathways, and the upregulation of CAD3, ACS, AER, and CA1 associated with lignin and lipids biosynthesis, photosynthesis and water use, and antioxidant defense. Dramatic changes of miR398s, cca-miR156b, aly-miR159c-3p, and ata-miR408-3p had a close correlation with heat-survival. The especial vvi-miR845c, ama-miR156, and other novel miRNAs such as novel-24223, novel-2964, and novel-10098 could be involved in GABA-regulated heat tolerance. The integrated analysis of mRNAs and miRNAs facilitates uncovering of adaptative response in perennial plants under high temperature environmental condition and also reveals that GABA acting as a critical plant growth regulator induces heat tolerance in creeping bentgrass involved in physiological, transcriptional, and post-transcriptional regulation. Particularly, current results provide some key candidate genes and miRNAs for further investigating their potential roles in heat tolerance in non-model plants.

Integrated analysis of mRNAs and long noncoding RNAs in the semen from Holstein bulls with high and low sperm motility

Sperm motility is the main index used to assess the quality of bull semen. It may also be used to evaluate the fertility potential of bulls. Protein-coding mRNA and long noncoding RNA (lncRNA) participate in the regulation of spermatogenesis. Here, we employed strand-specific RNA sequencing to profile the semen transcriptome (mRNA and lncRNA) of six paired full-sibling Holstein bulls with divergent sperm motility and to determine the functions of mRNA and lncRNA in sperm motility. Among 20,875 protein-encoding genes detected in semen, 19 were differentially expressed between the high sperm motility group (H: H1, H2, and H3) and low sperm motility group (L: L1, L2, and L3). Of the 11,561 lncRNAs identified in sperm, 2,517 were differentially expressed between the H and L groups. We found that TCONS_00041733 lncRNA targets the node gene EFNA1 (ephrin A1), involved in male reproductive physiology. Our study provides a global mRNA and lncRNA transcriptome of bull semen, as well as novel insights into the regulation of neighboring protein coding by lncRNAs and the influence of mRNAs on sperm motility.

Exploring the molecular mechanisms of osteosarcoma by the integrated analysis of mRNAs and miRNA microarrays.

Osteosarcoma (OS) is the most frequently occurring primary bone malignancy with a rapid progression and poor survival. In the present study, in order to examine the molecular mechanisms of OS, we analyzed the microarray of GSE28425. GSE28425 was downloaded from Gene Expression Omnibus, which also included the miRNA expression profile, GSE28423, and the mRNA expression profile, GSE28424. Each of the expression profiles included 19 OS cell lines and 4 normal bones. The differentially expressed genes (DEGs) and differentially expressed miRNAs (DE-miRNAs) were screened using the limma package in Bioconductor. The DEGs associated with tumors were screened and annotated. Subsequently, the potential functions of the DEGs were analyzed by Gene Ontology (GO) and pathway enrichment analyses. Furthermore, the protein-protein interaction (PPI) network was constructed using the STRING database and Cytoscape software. Furthermore, modules of the PPI network were screened using the ClusterOne plugin in Cytoscape. Additionally, the transcription factor (TF)-DEG regulatory network, DE-miRNA-DEG regulatory network and miRNA-function collaborative network were separately constructed to obtain key DEGs and DE-miRNAs. In total, 1,609 DEGs and 149 DE-miRNAs were screened. Upregulated FOS-like antigen 1 (FOSL1) also had the function of an oncogene. MAD2 mitotic arrest deficient-like 1 (MAD2L1; degree, 65) and aurora kinase A (AURKA; degree, 64) had higher degrees in the PPI network of the DEGs. In the TF-DEG regulatory network, the TF, signal transducer and activator of transcription 3 (STAT3) targeted the most DEGs. Moreover, in the DE-miRNA-DEG regulatory network, downregulated miR-1 targeted many DEGs and estrogen receptor 1 (ESR1) was targeted by several highly expressed miRNAs. Moreover, in the miRNA-function collaborative networks of upregulated miRNAs, miR-128 targeted myeloid dendritic associated functions. On the whole, our data indicate that MAD2L1, AURKA, STAT3, ESR1, FOSL1, miR-1 and miR-128 may play a role in the development and/or progressio of OS.