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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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Stem-loop structures of 7 selected novel miRNAs in goat.Note: The secondary structures were generated from the goat genome and EST sequences. The uppercase letters refer to mature sequences and were indicated in yellow. A: PC-3p-22067_41, B: PC-3p-61234_13, C: PC-5p-21385_42, D: PC-5p-21767_42, E: PC-5p-32617_26, F: PC-5p-63323_12, G: PC-5p-104298_5.
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pone.0122202.g003: Stem-loop structures of 7 selected novel miRNAs in goat.Note: The secondary structures were generated from the goat genome and EST sequences. The uppercase letters refer to mature sequences and were indicated in yellow. A: PC-3p-22067_41, B: PC-3p-61234_13, C: PC-5p-21385_42, D: PC-5p-21767_42, E: PC-5p-32617_26, F: PC-5p-63323_12, G: PC-5p-104298_5.

Mentions: The characteristic hairpin structure of miRNA precursors can be used to predict potential novel miRNA [28]. Therefore, the secondary structure of potential novel miRNAs was explored using RNAfold software, and the structures of 7 potential novel miRNA precursors (PC-3p-22067_41, PC-3p-61234_13, PC-5p-21385_42, PC-5p-21767_42, PC-5p-32617_26, PC-5p-63323_12 and PC-5p-104298_5) were predicted and showed in Fig 3. Similar to the results with the conserved miRNAs, the 7 sequences had significant stem-loop hairpin secondary structures. Moreover, ten novel miRNAs (PC-5p-5933_158, PC-5p-2673_284, PC-5p-6424_145, PC-5p-20799_45, PC-5p-35677_26, PC-3p-25064_36, PC-5p-26648_38, PC-3p-215602_2, PC-3p-82208_8, and PC-5p-108241_6) were selected due to their highly and differentially expressed levels between our two libraries.


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)

Stem-loop structures of 7 selected novel miRNAs in goat.Note: The secondary structures were generated from the goat genome and EST sequences. The uppercase letters refer to mature sequences and were indicated in yellow. A: PC-3p-22067_41, B: PC-3p-61234_13, C: PC-5p-21385_42, D: PC-5p-21767_42, E: PC-5p-32617_26, F: PC-5p-63323_12, G: PC-5p-104298_5.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4401794&req=5

pone.0122202.g003: Stem-loop structures of 7 selected novel miRNAs in goat.Note: The secondary structures were generated from the goat genome and EST sequences. The uppercase letters refer to mature sequences and were indicated in yellow. A: PC-3p-22067_41, B: PC-3p-61234_13, C: PC-5p-21385_42, D: PC-5p-21767_42, E: PC-5p-32617_26, F: PC-5p-63323_12, G: PC-5p-104298_5.
Mentions: The characteristic hairpin structure of miRNA precursors can be used to predict potential novel miRNA [28]. Therefore, the secondary structure of potential novel miRNAs was explored using RNAfold software, and the structures of 7 potential novel miRNA precursors (PC-3p-22067_41, PC-3p-61234_13, PC-5p-21385_42, PC-5p-21767_42, PC-5p-32617_26, PC-5p-63323_12 and PC-5p-104298_5) were predicted and showed in Fig 3. Similar to the results with the conserved miRNAs, the 7 sequences had significant stem-loop hairpin secondary structures. Moreover, ten novel miRNAs (PC-5p-5933_158, PC-5p-2673_284, PC-5p-6424_145, PC-5p-20799_45, PC-5p-35677_26, PC-3p-25064_36, PC-5p-26648_38, PC-3p-215602_2, PC-3p-82208_8, and PC-5p-108241_6) were selected due to their highly and differentially expressed levels between our two libraries.

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