Comparative Transcriptome Profiling of Dairy Goat MicroRNAs from Dry Period and Peak Lactation Mammary Gland Tissues

<div><h3>Background</h3><p>MicroRNAs (miRNAs) are small noncoding RNA molecules that serve as important post-transcriptional gene expression regulators by targeting messenger RNAs for post-transcriptional endonucleolytic cleavage or translational inhibition. miRNAs play important roles in many biological processes. Extensive high-throughput sequencing studies of miRNAs have been performed in several animal models. However, little is known about the diversity of these regulatory RNAs in goat (<em>Capra hircus</em>), which is one of the most important agricultural animals and the oldest domesticated species raised worldwide. Goats have long been used for their milk, meat, hair (including cashmere), and skins throughout much of the world.</p> <h3>Results</h3><p>In this study, two small RNA libraries were constructed based on dry period and peak lactation dairy goat mammary gland tissues and sequenced using the Illumina-Solexa high-throughput sequencing technology. A total of 346 conserved and 95 novel miRNAs were identified in the dairy goat. miRNAs expression was confirmed by qRT-PCR in nine tissues and in the mammary gland during different stages of lactation. In addition, several candidate miRNAs that may be involved in mammary gland development and lactation were found by comparing the miRNA expression profiles in different tissues and developmental stages of the mammary gland.</p> <h3>Conclusions</h3><p>This study reveals the first miRNAs profile related to the biology of the mammary gland in the dairy goat. The characterization of these miRNAs could contribute to a better understanding of the molecular mechanisms of lactation physiology and mammary gland development in the dairy goat.</p> </div

Copy number variations of <i>LRRFIP1</i> gene and the relationship with growth traits in four Chinese sheep

CNVs (copy number variations) are the novel and common structural variants that could cover entire genes found in plenty of species. CNV may influence economically important traits or disease susceptibility in livestock species. Based on the whole genome resequencing results, we found that there was a CNV region on the LRRFIP1 gene. Then we used qPCR to detect the copy number type distribution in 553 individuals of four sheep breeds and used them for association analysis. The results showed that: (1) In the CKS, the sheep with gain type had a larger heart girth (p = 0.049). (2) For the HS, the CNV could significantly affect rump breadth (p = 0.037) and circumference of the cannon (p = 0.035). And the sheep with median type showed better performance in rump breadth and circumference of cannon. (3) At the STHS, the CNV was significantly correlated with chest width (p = 0.000) with loss type as the most favorable CNV type. Meanwhile, the best was the loss type, and the lowest was the median. (4) This CNV had no significant effect on the LTHS. So, the CNV of LRRFIP1 was related to the growth traits of these three sheep breeds and it may be used as a molecular marker for sheep.</p

Small RNA sequencing statistics for the dry period (D) and peak lactation (P) libraries.

<p>Small RNA sequencing statistics for the dry period (D) and peak lactation (P) libraries.</p

Summary of conserved miRNAs expressed in the mammary gland during the dry period and peak lactation.

A<p>the miRNA precursors.</p>B<p>the unique sRNAs matched to the miRNA precursors.</p>C<p>the total sRNAs matched to the miRNA precursors.</p>D<p>known bovine miRNAs in miRBase version 18.0 as a reference.</p

Prediction of the fold-back structure of 10 caprine miRNA precursors.

<p>The precursor sequences were obtained by amplifying the corresponding miRNAs gene from goat genomic DNA. The mature miRNA sequences in the precursors are indicated in red.</p

Abundance and differential expression of the highly abundant caprine miRNAs in the mammary gland.

<p>P and P-NE represent the actual sequencing count and normalized expression level of miRNAs in the small RNA library generated from the mammary gland during peak lactation, respectively.</p><p>D and D-NE represent the actual sequencing count and normalized expression level of miRNAs in the small RNA library generated from the mammary gland during the dry period, respectively.</p><p>Fold-change [log₂ (P-NE/D-NE)] indicates the fold change of the miRNAs in a pair of samples.</p><p>The <i>P</i>-value reflects the significance of the miRNA differential between the samples. A smaller <i>P</i>-value indicates a more significant difference in the miRNA level between samples.</p><p>A sig-label of ** indicates a fold-change (log2)>1 or (log2)<-1 and a <i>P</i>-value<0.01.</p

Summary of conserved and putative novel miRNA precursors in the dairy goat.

*<p>In the “Difference” column, “Difference” indicates that the precursor sequence differs between the bovine and caprine sequence (D: different, S: same). The miR-2478 has a G/A mismatch at the 11^th nt between the bovine and caprine sequences; the miR-143 precursor has a G/A mismatch at the 97^th nt between the bovine and caprine sequences.</p

Corporate social responsibility in the digital age

Circular RNA (circRNA) is a new class of non-coding RNA that has recently attracted researchers' interests. Studies have demonstrated that circRNA can function as microRNA (miRNA) sponges or competing endogenous RNAs. Although circRNA has been explored in some species and tissues, the genetic basic of testis development and spermatogenesis in cattle remains unknown. We performed ribo-depleted total RNA-Seq to detect circRNA expression profiles of neonatal (one week old) and adult (4 years old) Qinchuan cattle testes. We obtained 91 112 596 and 80 485 868 clean reads and detected 21 753 circRNAs. A total of 4248 circRNAs were significantly differentially expressed between neonatal and adult cattle testes. Among these circRNAs, 2225 were upregulated, and 2023 were downregulated in adult cattle testis. Genomic feature, length distribution and other characteristics of the circRNAs in cattle testis were studied. Moreover, Gene Ontology and KEGG pathway analyses were performed for source genes of circRNAs. These source genes were mainly involved in tight junction, adherens junction, TGFβ signalling pathway and reproduction, such as <i>PIWIL1, DPY19L2, SLC26A8, IFT81, SMC1B, IQCG</i> and <i>TTLL5</i>. CircRNA expression patterns were validated by RT-qPCR. Our discoveries provide a solid foundation for the identification and characterization of key circRNAs involved in testis development or spermatogenesis

Table S3 List of 8 validated testis derived circRNAs from Identification and characterization of circular RNAs in Qinchuan cattle testis

Circular RNA (circRNA) is a new class of non-coding RNA that has recently attracted researchers' interest. Studies have demonstrated that circRNA can function as microRNA sponges or competing endogenous RNAs. Although circRNA has been explored in some species and tissues, the genetic basis of testis development and spermatogenesis in cattle remains unknown. We performed ribo-depleted total RNA-Seq to detect circRNA expression profiles of neonatal (one week old) and adult (4 years old) Qinchuan cattle testes. We obtained 91 112 596 and 80 485 868 clean reads and detected 21 753 circRNAs. A total of 4248 circRNAs were significantly differentially expressed between neonatal and adult cattle testes. Among these circRNAs, 2225 were upregulated, and 2023 were downregulated in adult cattle testis. Genomic feature, length distribution and other characteristics of the circRNAs in cattle testis were studied. Moreover, Gene Ontology and KEGG pathway analyses were performed for source genes of circRNAs. These source genes were mainly involved in tight junction, adherens junction, TGFβ signalling pathway and reproduction, such as <i>PIWIL1, DPY19L2, SLC26A8, IFT81, SMC1B, IQCG</i> and <i>TTLL5</i>. CircRNA expression patterns were validated by RT-qPCR. Our discoveries provide a solid foundation for the identification and characterization of key circRNAs involved in testis development or spermatogenesis

miR-378a-3p promotes differentiation and inhibits proliferation of myoblasts by targeting HDAC4 in skeletal muscle development

<p>Muscle development, or myogenesis, is a highly regulated, complex process. A subset of microRNAs (miRNAs) have been identified as critical regulators of myogenesis. Recently, miR-378a was found to be involved in myogenesis, but the mechanism of how miR-378a regulates the proliferation and differentiation of myoblasts has not been determined. We found that miR-378a-3p expression in muscle was significantly higher than in other tissues, suggesting an important effect on muscle development. Overexpression of miR-378a-3p increased the expression of MyoD and MHC in C2C12 myoblasts both at the level of mRNA and protein, confirming that miR-378a-3p promoted muscle cell differentiation. The forced expression of miR-378a-3p promoted apoptosis of C2C12 cells as evidenced by CCK-8 assay and Annexin V-FITC/PI staining results. Through TargetScan, histone acetylation enzyme 4 (HDAC4) was identified as a potential target of miR-378a-3p. We confirmed targeting of HDAC4 by miR-378a-3p using a dual luciferase assay and western blotting. Our RNAi analysis results also showed that HDAC4 significantly promoted differentiation of C2C12 cells and inhibited cell survival through Bcl-2. Therefore, we conclude that miR-378a-3p regulates skeletal muscle growth and promotes the differentiation of myoblasts through the post-transcriptional down-regulation of HDAC4.</p