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Integrated analysis of miRNA/mRNA network in placenta identifies key factors associated with labor onset of Large White and Qingping sows.

Li H, Wu B, Geng J, Zhou J, Zheng R, Chai J, Li F, Peng J, Jiang S - Sci Rep (2015)

Bottom Line: A set of differentially expressed genes, including 2164 mRNAs and 39 miRNAs, were found.Cytoscape Network analysis of the functional genes found node mRNAs and that the regulatory network between the node mRNAs and miRNAs was established.A comparison of the sequencing data from the shorter gestation period (QS) and the normal gestation period (QL) indicated that these genes were responsible for the quicker and more sensitive reaction to the regulation of labour onset.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.

ABSTRACT
Labour onset is a very complex physiological process, and its mechanism is poorly understood. Here, we obtained the mRNA and miRNA expression profiles from the placentas of four groups of sows: Qingping sows 112 days after insemination with signs of labour onset (QS), Qingping sows 114 days after insemination with signs of labour onset (QL), Large White sows 114 days after insemination with signs of labour onset (LL) and Large White sows 112 days after insemination without signs of labour onset (LN). A set of differentially expressed genes, including 2164 mRNAs and 39 miRNAs, were found. A DAVID analysis of these differentially expressed genes revealed their critical roles in response to hormone stimulus, immune response. Cytoscape Network analysis of the functional genes found node mRNAs and that the regulatory network between the node mRNAs and miRNAs was established. A comparison of the sequencing data from the shorter gestation period (QS) and the normal gestation period (QL) indicated that these genes were responsible for the quicker and more sensitive reaction to the regulation of labour onset. This research not only detected the key factors that were involved in labour onset but also provided useful information for the research of gynaecological diseases.

No MeSH data available.


Related in: MedlinePlus

Quantitative RT-PCR validation of the differential expression of miRNAs.The expression levels of ssc-miR-127, ssc-miR-190a, ssc-miR-221-3p, ssc-miR-222, ssc-miR-299 and ssc-miR-424-5p in LN, LL, QS and QL were detected by qRT-PCR. All of the error bars indicate SD. *P < 0.05, **P < 0.01.
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f1: Quantitative RT-PCR validation of the differential expression of miRNAs.The expression levels of ssc-miR-127, ssc-miR-190a, ssc-miR-221-3p, ssc-miR-222, ssc-miR-299 and ssc-miR-424-5p in LN, LL, QS and QL were detected by qRT-PCR. All of the error bars indicate SD. *P < 0.05, **P < 0.01.

Mentions: To examine the genes that are related to the onset of labour, we determined the gene expression profiles in the placentas of LL, QL, QS and LN using Illumina HiSeq 2000. Compared with those in LN, among the 930 differentially expressed genes (DEGs) in LL (P ≤ 0.01, fold change ≤ 0.5 or fold change ≥ 2), 395 genes were up-regulated and 535 were down-regulated (Supplementary Table S1); among the 1591 DEGs in QL (P ≤ 0.01; fold change ≤ 0.5 or fold change ≥ 2), 690 and 901 genes were up- and down-regulated, respectively (Supplementary Table S2); and among the 1074 DEGs in QS (P ≤ 0.01; fold change ≤ 0.5 or fold change ≥ 2), 503 genes were up-regulated and 571 were down-regulated (Supplementary Table S3). Compared with the LN placenta, 9 up- and 10 down-regulated miRNAs were found in the LL placenta (P ≤ 0.01; fold change ≤ 0.5 or fold change ≥ 2), 13 up- and 10 down-regulated miRNAs were found in the QL placenta(P ≤ 0.01; fold change ≤ 0.5 or fold change ≥ 2), and 14 up- and 7 down-regulated miRNAs were found in the QS placenta (P ≤ 0.01; fold change ≤ 0.5 or fold change ≥ 2) (Supplementary Table S4). The unified set of differentially expressed genes containing a total of 2164 mRNAs and 36 miRNAs was found by the comparison of LL, QL and QS with LN. Remarkably, 182 genes were overlapping among the LL, QL and QS, 76 of which were up-regulated and 106 were down-regulated. In addition, 2 (ssc-miR-132, ssc-miR-323) and 3 (ssc-miR-19a, ssc-miR-664-3p and ssc-miR-296-5p) miRNAs were commonly detected in all of the regulated groups across the comparisons of LL, QL, and QS with LN. To validate the reliability of the mRNA and miRNA profiling results, RT-PCR was performed to detect the levels of 13 randomly selected differential mRNAs and 7 miRNAs from the differential expression data using the primer sequences listed in Supplementary Table S5. The RT-PCR results showed that most of the miRNAs were consistent with the miRNAs profiling results, except for miR-22 (Fig. 1). The RT-PCR results also showed that mRNAs agreed most with the mRNA profiling results (Table 1).


Integrated analysis of miRNA/mRNA network in placenta identifies key factors associated with labor onset of Large White and Qingping sows.

Li H, Wu B, Geng J, Zhou J, Zheng R, Chai J, Li F, Peng J, Jiang S - Sci Rep (2015)

Quantitative RT-PCR validation of the differential expression of miRNAs.The expression levels of ssc-miR-127, ssc-miR-190a, ssc-miR-221-3p, ssc-miR-222, ssc-miR-299 and ssc-miR-424-5p in LN, LL, QS and QL were detected by qRT-PCR. All of the error bars indicate SD. *P < 0.05, **P < 0.01.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4536519&req=5

f1: Quantitative RT-PCR validation of the differential expression of miRNAs.The expression levels of ssc-miR-127, ssc-miR-190a, ssc-miR-221-3p, ssc-miR-222, ssc-miR-299 and ssc-miR-424-5p in LN, LL, QS and QL were detected by qRT-PCR. All of the error bars indicate SD. *P < 0.05, **P < 0.01.
Mentions: To examine the genes that are related to the onset of labour, we determined the gene expression profiles in the placentas of LL, QL, QS and LN using Illumina HiSeq 2000. Compared with those in LN, among the 930 differentially expressed genes (DEGs) in LL (P ≤ 0.01, fold change ≤ 0.5 or fold change ≥ 2), 395 genes were up-regulated and 535 were down-regulated (Supplementary Table S1); among the 1591 DEGs in QL (P ≤ 0.01; fold change ≤ 0.5 or fold change ≥ 2), 690 and 901 genes were up- and down-regulated, respectively (Supplementary Table S2); and among the 1074 DEGs in QS (P ≤ 0.01; fold change ≤ 0.5 or fold change ≥ 2), 503 genes were up-regulated and 571 were down-regulated (Supplementary Table S3). Compared with the LN placenta, 9 up- and 10 down-regulated miRNAs were found in the LL placenta (P ≤ 0.01; fold change ≤ 0.5 or fold change ≥ 2), 13 up- and 10 down-regulated miRNAs were found in the QL placenta(P ≤ 0.01; fold change ≤ 0.5 or fold change ≥ 2), and 14 up- and 7 down-regulated miRNAs were found in the QS placenta (P ≤ 0.01; fold change ≤ 0.5 or fold change ≥ 2) (Supplementary Table S4). The unified set of differentially expressed genes containing a total of 2164 mRNAs and 36 miRNAs was found by the comparison of LL, QL and QS with LN. Remarkably, 182 genes were overlapping among the LL, QL and QS, 76 of which were up-regulated and 106 were down-regulated. In addition, 2 (ssc-miR-132, ssc-miR-323) and 3 (ssc-miR-19a, ssc-miR-664-3p and ssc-miR-296-5p) miRNAs were commonly detected in all of the regulated groups across the comparisons of LL, QL, and QS with LN. To validate the reliability of the mRNA and miRNA profiling results, RT-PCR was performed to detect the levels of 13 randomly selected differential mRNAs and 7 miRNAs from the differential expression data using the primer sequences listed in Supplementary Table S5. The RT-PCR results showed that most of the miRNAs were consistent with the miRNAs profiling results, except for miR-22 (Fig. 1). The RT-PCR results also showed that mRNAs agreed most with the mRNA profiling results (Table 1).

Bottom Line: A set of differentially expressed genes, including 2164 mRNAs and 39 miRNAs, were found.Cytoscape Network analysis of the functional genes found node mRNAs and that the regulatory network between the node mRNAs and miRNAs was established.A comparison of the sequencing data from the shorter gestation period (QS) and the normal gestation period (QL) indicated that these genes were responsible for the quicker and more sensitive reaction to the regulation of labour onset.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.

ABSTRACT
Labour onset is a very complex physiological process, and its mechanism is poorly understood. Here, we obtained the mRNA and miRNA expression profiles from the placentas of four groups of sows: Qingping sows 112 days after insemination with signs of labour onset (QS), Qingping sows 114 days after insemination with signs of labour onset (QL), Large White sows 114 days after insemination with signs of labour onset (LL) and Large White sows 112 days after insemination without signs of labour onset (LN). A set of differentially expressed genes, including 2164 mRNAs and 39 miRNAs, were found. A DAVID analysis of these differentially expressed genes revealed their critical roles in response to hormone stimulus, immune response. Cytoscape Network analysis of the functional genes found node mRNAs and that the regulatory network between the node mRNAs and miRNAs was established. A comparison of the sequencing data from the shorter gestation period (QS) and the normal gestation period (QL) indicated that these genes were responsible for the quicker and more sensitive reaction to the regulation of labour onset. This research not only detected the key factors that were involved in labour onset but also provided useful information for the research of gynaecological diseases.

No MeSH data available.


Related in: MedlinePlus