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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 size distribution of the small RNAs in R and P libraries.
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pone.0122202.g001: The size distribution of the small RNAs in R and P libraries.

Mentions: To systematically identify small RNAs and changes in the expression level of miRNAs between the pre-receptive and receptive phases of the endometrium in Xinong Saanen dairy goats, we purified and sequenced small RNAs from the goat endometrium. A total of 7,717,603 and 6,307,668 raw reads were obtained from the R (receptive) and P (pre-receptive) endometrium, respectively. To assess the efficiency of Solexa sequencing and the quality of the sequences, all reads were annotated and classified by aligning against the miRBase 20.0 database (ftp://mirbase.org/pub/mirbase/CURRENT/), the Rfam database (http://rfam.janelia.org), the Repbase database (http://www.girinst.org/repbase), the Genome database (http://goat.kiz.ac.cn/GGD/download.htm) and the mRNA database (http://goat.kiz.ac.cn/GGD/download.htm). Small RNAs were classified into different categories according to their annotations. Next, 3’ ADT and length filter, junk reads, Rfam, mRNA, repeats, rRNA, tRNA, snRNA and snoRNA sequences, as well as other Rfam RNA sequences, were separated out and discarded. As a result, 4,233,874 clean reads representing 284,622 unique sequences from the R library were obtained, and 5,386,427 clean reads representing 139,040 unique sequences from the P library (Table 1). The lengths of the majority of the clean reads ranged between 18 and 26 nt. The most abundant class size in the small RNA sequence distribution was 22 nt, which accounted for 38.54% and 51.43% of reads in the R and P libraries, respectively, followed by 21 nt (17.03% and 18.27%), 23 nt (13.65% and 11.33%) and 20 nt (8.81% and 11.68%), suggesting that they were typical small RNA (Fig 1, Table 2).


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 size distribution of the small RNAs in R and P libraries.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0122202.g001: The size distribution of the small RNAs in R and P libraries.
Mentions: To systematically identify small RNAs and changes in the expression level of miRNAs between the pre-receptive and receptive phases of the endometrium in Xinong Saanen dairy goats, we purified and sequenced small RNAs from the goat endometrium. A total of 7,717,603 and 6,307,668 raw reads were obtained from the R (receptive) and P (pre-receptive) endometrium, respectively. To assess the efficiency of Solexa sequencing and the quality of the sequences, all reads were annotated and classified by aligning against the miRBase 20.0 database (ftp://mirbase.org/pub/mirbase/CURRENT/), the Rfam database (http://rfam.janelia.org), the Repbase database (http://www.girinst.org/repbase), the Genome database (http://goat.kiz.ac.cn/GGD/download.htm) and the mRNA database (http://goat.kiz.ac.cn/GGD/download.htm). Small RNAs were classified into different categories according to their annotations. Next, 3’ ADT and length filter, junk reads, Rfam, mRNA, repeats, rRNA, tRNA, snRNA and snoRNA sequences, as well as other Rfam RNA sequences, were separated out and discarded. As a result, 4,233,874 clean reads representing 284,622 unique sequences from the R library were obtained, and 5,386,427 clean reads representing 139,040 unique sequences from the P library (Table 1). The lengths of the majority of the clean reads ranged between 18 and 26 nt. The most abundant class size in the small RNA sequence distribution was 22 nt, which accounted for 38.54% and 51.43% of reads in the R and P libraries, respectively, followed by 21 nt (17.03% and 18.27%), 23 nt (13.65% and 11.33%) and 20 nt (8.81% and 11.68%), suggesting that they were typical small RNA (Fig 1, Table 2).

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