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Identification and profiling of microRNAs in goat endometrium during embryo implantation.

Song Y, An X, Zhang L, Fu M, Peng J, Han P, Hou J, Zhou Z, Cao B - PLoS ONE (2015)

Bottom Line: There were 110 up-expressed miRNAs and 33 down-expressed miRNAs in receptive endometrium compared with the pre-receptive endometrium meeting the criteria of P-values< 0.05.Moreover, GO and KEGG analysis of the target genes of the differentially expressed miRNAs revealed some candidate miRNAs, genes and pathways that may involve in the formation of the receptive endometrium.Based on stem-loop RT-qPCR, 15 miRNAs were detected and the results suggested that the majority of the miRNA expression data measured by Solexa deep sequencing could represent actual miRNA expression levels.

View Article: PubMed Central - PubMed

Affiliation: College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China.

ABSTRACT

Background: MicroRNAs (miRNAs) are short, highly conserved small noncoding RNAs that had fundamental roles in post-transcriptional gene expression, and they are crucial for proper control of biological processes and known to participate in embryo implantation. However, miRNA expression profiles in the pre-receptive and receptive phases of the goat endometrium during embryo implantation are unknown.

Results: A total of 1,069 and 847 miRNAs were expressed in receptive (R) and pre-receptive (P) goat endometrium, and 632 miRNAs were co-expressed in both phases. We identified 545 (50.98%) known miRNAs in the R library and 522 (61.63%) in the P library. There were 110 up-expressed miRNAs and 33 down-expressed miRNAs in receptive endometrium compared with the pre-receptive endometrium meeting the criteria of P-values< 0.05. Moreover, GO and KEGG analysis of the target genes of the differentially expressed miRNAs revealed some candidate miRNAs, genes and pathways that may involve in the formation of the receptive endometrium. Based on stem-loop RT-qPCR, 15 miRNAs were detected and the results suggested that the majority of the miRNA expression data measured by Solexa deep sequencing could represent actual miRNA expression levels.

Conclusions: Our data revealed the first miRNA profile related to the biology of the goat receptive endometrium during embryo implantation, and the results suggested that a subset of miRNAs might play important roles in the formation of endometrial receptivity. Thus, elucidating the physiological roles of endometrial miRNAs will help us better understand the genetic control of embryo implantation in goats.

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The GO enrichment analysis of predicted targets of differentially expressed miRNAs with P< 0.05.Note: A: Biological process, B: Molecular function, C: Cellular component. The GO terms were sorted by the enrichment p-value calculated by the calculating formula:P=1−∑i =0m−1(Mi)(N−Mn−i)NnThe N represented the number of GO annotated genes in genome, n represented the number of differentially expressed genes in N. M represented the number of particular GO annotated genes in genome, m represented the number of particular GO annotated genes expressed differentially in M.
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pone.0122202.g005: The GO enrichment analysis of predicted targets of differentially expressed miRNAs with P< 0.05.Note: A: Biological process, B: Molecular function, C: Cellular component. The GO terms were sorted by the enrichment p-value calculated by the calculating formula:P=1−∑i =0m−1(Mi)(N−Mn−i)NnThe N represented the number of GO annotated genes in genome, n represented the number of differentially expressed genes in N. M represented the number of particular GO annotated genes in genome, m represented the number of particular GO annotated genes expressed differentially in M.

Mentions: GO enrichment analysis using cellular components showed that 490 genes (13.64%) mapped to GO terms for component topology in the database. The analysis of biological processes showed that 2,087 genes (58.10%) were involved in cellular or metabolic processes, and the analysis of molecular function showed that 1,015 genes (28.26%) were assigned different functions based on gene background (Fig 5 and S5 Table). GO biological process analysis based on the predicted targets showed that the differentially expressed miRNAs were involved in remodeling of the receptive endometrium, including induction of apoptosis by extracellular signals (GO: 0008624) (Fig 6). Other miRNA-gene networks of interest included cell cycle checkpoints (GO: 0000075), vesicle-mediated transport (GO: 0016192), intracellular protein transport (GO: 0006886) and maternal processes involved in female pregnancy (GO: 0060135).


Identification and profiling of microRNAs in goat endometrium during embryo implantation.

Song Y, An X, Zhang L, Fu M, Peng J, Han P, Hou J, Zhou Z, Cao B - PLoS ONE (2015)

The GO enrichment analysis of predicted targets of differentially expressed miRNAs with P< 0.05.Note: A: Biological process, B: Molecular function, C: Cellular component. The GO terms were sorted by the enrichment p-value calculated by the calculating formula:P=1−∑i =0m−1(Mi)(N−Mn−i)NnThe N represented the number of GO annotated genes in genome, n represented the number of differentially expressed genes in N. M represented the number of particular GO annotated genes in genome, m represented the number of particular GO annotated genes expressed differentially in M.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4401794&req=5

pone.0122202.g005: The GO enrichment analysis of predicted targets of differentially expressed miRNAs with P< 0.05.Note: A: Biological process, B: Molecular function, C: Cellular component. The GO terms were sorted by the enrichment p-value calculated by the calculating formula:P=1−∑i =0m−1(Mi)(N−Mn−i)NnThe N represented the number of GO annotated genes in genome, n represented the number of differentially expressed genes in N. M represented the number of particular GO annotated genes in genome, m represented the number of particular GO annotated genes expressed differentially in M.
Mentions: GO enrichment analysis using cellular components showed that 490 genes (13.64%) mapped to GO terms for component topology in the database. The analysis of biological processes showed that 2,087 genes (58.10%) were involved in cellular or metabolic processes, and the analysis of molecular function showed that 1,015 genes (28.26%) were assigned different functions based on gene background (Fig 5 and S5 Table). GO biological process analysis based on the predicted targets showed that the differentially expressed miRNAs were involved in remodeling of the receptive endometrium, including induction of apoptosis by extracellular signals (GO: 0008624) (Fig 6). Other miRNA-gene networks of interest included cell cycle checkpoints (GO: 0000075), vesicle-mediated transport (GO: 0016192), intracellular protein transport (GO: 0006886) and maternal processes involved in female pregnancy (GO: 0060135).

Bottom Line: There were 110 up-expressed miRNAs and 33 down-expressed miRNAs in receptive endometrium compared with the pre-receptive endometrium meeting the criteria of P-values< 0.05.Moreover, GO and KEGG analysis of the target genes of the differentially expressed miRNAs revealed some candidate miRNAs, genes and pathways that may involve in the formation of the receptive endometrium.Based on stem-loop RT-qPCR, 15 miRNAs were detected and the results suggested that the majority of the miRNA expression data measured by Solexa deep sequencing could represent actual miRNA expression levels.

View Article: PubMed Central - PubMed

Affiliation: College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China.

ABSTRACT

Background: MicroRNAs (miRNAs) are short, highly conserved small noncoding RNAs that had fundamental roles in post-transcriptional gene expression, and they are crucial for proper control of biological processes and known to participate in embryo implantation. However, miRNA expression profiles in the pre-receptive and receptive phases of the goat endometrium during embryo implantation are unknown.

Results: A total of 1,069 and 847 miRNAs were expressed in receptive (R) and pre-receptive (P) goat endometrium, and 632 miRNAs were co-expressed in both phases. We identified 545 (50.98%) known miRNAs in the R library and 522 (61.63%) in the P library. There were 110 up-expressed miRNAs and 33 down-expressed miRNAs in receptive endometrium compared with the pre-receptive endometrium meeting the criteria of P-values< 0.05. Moreover, GO and KEGG analysis of the target genes of the differentially expressed miRNAs revealed some candidate miRNAs, genes and pathways that may involve in the formation of the receptive endometrium. Based on stem-loop RT-qPCR, 15 miRNAs were detected and the results suggested that the majority of the miRNA expression data measured by Solexa deep sequencing could represent actual miRNA expression levels.

Conclusions: Our data revealed the first miRNA profile related to the biology of the goat receptive endometrium during embryo implantation, and the results suggested that a subset of miRNAs might play important roles in the formation of endometrial receptivity. Thus, elucidating the physiological roles of endometrial miRNAs will help us better understand the genetic control of embryo implantation in goats.

Show MeSH