Improvement, identification, and target prediction for miRNAs in the porcine genome by using massive, public high-throughput sequencing data

IAnimal: a cross-species omics knowledgebase for animals

With the exponential growth of multi-omics data, its integration and utilization have brought unprecedented opportunities for the interpretation of gene regulation mechanisms and the comprehensive analyses of biological systems. IAnimal (https://ianimal.pro/), a cross-species, multi-omics knowledgebase, was developed to improve the utilization of massive public data and simplify the integration of multi-omics information to mine the genetic mechanisms of objective traits. Currently, IAnimal provides 61 191 individual omics data of genome (WGS), transcriptome (RNA-Seq), epigenome (ChIP-Seq, ATAC-Seq) and genome annotation information for 21 species, such as mice, pigs, cattle, chickens, and macaques. The scale of its total clean data has reached 846.46 TB. To better understand the biological significance of omics information, a deep learning model for IAnimal was built based on BioBERT and AutoNER to mine 'gene' and 'trait' entities from 2 794 237 abstracts, which has practical significance for comprehending how each omics layer regulates genes to affect traits. By means of user-friendly web interfaces, flexible data application programming interfaces, and abundant functional modules, IAnimal enables users to easily query, mine, and visualize characteristics in various omics, and to infer how genes play biological roles under the influence of various omics layers.

miRNA-Profiling in Ejaculated and Epididymal Pig Spermatozoa and Their Relation to Fertility after Artificial Insemination

Simple Summary

The present study searched for the presence and abundance of porcine spermatozoa small RNA sequences (microRNAs) that have the potential to alter gene expression patterns. Four different sperm sources were compared: spermatozoa from three different sections of the ejaculate and from the caudal epididymis, also classed as spermatozoa from higher (HF) or lower (LF) fertility boars. Sperm miRNAs were compared using high-output small RNA sequencing. We identified five sperm miRNAs not previously reported in pigs. Differences in abundance of four miRNAs known to affect the expression of genes with key roles in fertility were related to boar fertility. These miRNAs could be used as fertility markers in artificial insemination programs.

Abstract

MicroRNAs (miRNAs) are short non-coding RNAs (20–25 nucleotides in length) capable of regulating gene expression by binding -fully or partially- to the 3’-UTR of target messenger RNA (mRNA). To date, several studies have investigated the role of sperm miRNAs in spermatogenesis and their remaining presence toward fertilization and early embryo development. However, little is known about the miRNA cargo in the different sperm sources and their possible implications in boar fertility. Here, we characterized the differential abundance of miRNAs in spermatozoa from the terminal segment of the epididymis and three different fractions of the pig ejaculate (sperm-peak, sperm-rich, and post-sperm rich) comparing breeding boars with higher (HF) and lower (LF) fertility after artificial insemination (AI) using high-output small RNA sequencing. We identified five sperm miRNAs that, to our knowledge, have not been previously reported in pigs (mir-10386, mir-10390, mir-6516, mir-9788-1, and mir-9788-2). Additionally, four miRNAs (mir-1285, mir-92a, mir-34c, mir-30), were differentially expressed among spermatozoa sourced from ejaculate fractions and the cauda epididymis, and also different abundance was found between HF and LF groups in mir-182, mir-1285, mir-191, and mir-96. These miRNAs target genes with key roles in fertility, sperm survival, immune tolerance, or cell cycle regulation, among others. Linking the current findings with the expression of specific sperm proteins would help predict fertility in future AI-sires.