Identification and Characterization of MicroRNAs in the Goat (Capra hircus) Rumen during Embryonic Development

Abstract

The rumen is an important digestive organ in ruminants. Numerous regulatory factors including microRNAs (miRNAs) are involved in embryonic organ development. In the present study, miRNAs expressed in the rumens of goats (Capra hircus) and their potential roles in the pathways involved in rumen development were identified using high-throughput sequencing. Histological morphology revealed a distinct difference in each layer of rumen during the period from embryonic day 60 (E60) to embryonic day 135 (E135). We determined the expression profiles of miRNAs in the goat rumen, and identified 423 known miRNAs and 559 potentially novel miRNAs in the E60 and E135 embryonic rumen, respectively. Bioinformatics analysis annotated the 42 differentially expressed miRNAs and the top 10 most highly expressed miRNAs of the two libraries to 48 and 38 gene ontology categories, as well as to 168 and 71 Kyoto Encyclopedia of Genes and Genomes pathways, respectively. The expression patterns of eight randomly selected miRNAs were validated by stem-loop quantitative reverse transcription PCR, suggesting that the sequencing data were reliable. We profiled the genome-wide expression of rumen-expressed miRNAs at different prenatal stages of rumen tissues, revealing that a subset of miRNAs might play important roles in the formation of the rumen layers. Taken together, these findings will aid the investigation of dominant rumen-related miRNA sets and help understand the genetic control of rumen development in goats.

Analysis of MicroRNA Transcriptomes Insights into the miR-148a-3p Inducer of Rumen Development in Goats

“…1a). We previously reported that miRNAs expression in embryonic rumens and less number of DEMs (22 up-regulated and 20 down-regulated) was identi ed between E60 and E135 [18].…”

“…In our previous study, the expression pro le of rumen miRNAs was revealed in the two embryonic stages (E60 and E135) [18]. Here, we investigated the DEMs identi ed in the pre-weaning and post-weaning stages (D30 and D150) and rejoined analyzed the RNA sequencing data.…”

Comparison of MicroRNA Transcriptomes Reveals the Association between MiR-148a-3p Expression and Rumen Development in Goats

“…Goat kids were weaned at D60. The pre-natal samples were collected by cesarean section [17], while the post-natal rumens were dissected and frozen in liquid nitrogen immediately after slaughter, and then stored at −80 • C. All experiments involving animals were conducted according to the Regulations for the Administration of Affairs Concerning Experimental Animals (Ministry of Science and Technology, China, revised in June 2004).…”

“…Two datasets including the newly obtained raw data (D30 and D150) and our previous data (E60 and E135) [17] were jointly analyzed in the present study. The procedures of miRNA identification and expression were performed according to the methods [17,23]. Differential miRNA expression was analyzed using the DESeq R package.…”

“…In our previous study, the expression profiles of the rumen tissue miRNAs were explored in two embryonic stages (E60 and E135) [17]. In the current study, we investigated differentially expressed miRNAs (DEMs) identified between pre-weaning (D30) and post-weaning stage (D150), and jointly analyzed the RNA sequencing data from our previous study.…”