Biology subjects

Clop, A.

Publications and source records attributed to Clop, A..

8 recordsLinked to original sources

bioRxiv2023

Construction of a multi-tissue cell atlas reveals cell-type-specific regulation of molecular and complex phenotypes in pigs

The systematic characterization of cellular heterogeneity among tissues and cell-type-specific regulation underlying complex phenotypes remains elusive in pigs. Within the Pig Genotype-Tissue Expression (PigGTEx) project, we present a single-cell transcriptome atlas of adult pigs encompassing 229,268 high-quality nuclei from 19 tissues, annotated to 67 major cell types. Besides cellular heterogeneity within and across tissues, we further characterize prominent tissue-specific features and functions of muscle, epithelial, and immune cells. Through deconvoluting 3,921 bulk RNA-seq samples from 17 matching tissues, we dissect thousands of genetic variants with cell-type interaction effects on gene expression (ieQTL). By colocalizing these ieQTL with variants associated with 268 complex traits, we provide new insights into the cellular mechanisms behind these traits. Moreover, we highlight that orthologous genes with cell-type-specific regulation in pigs exhibit significant heritability enrichment for some human complex phenotypes. Altogether, our work provides a valuable resource and highlights novel insights in cellular regulation of complex traits for accelerating pig precision breeding and human biomedical research.

genetics↗

bioRxiv2022

A compendium of genetic regulatory effects across pig tissues

The Farm animal Genotype-Tissue Expression (FarmGTEx, https://www.farmgtex.org/) project has been established to develop a comprehensive public resource of genetic regulatory variants in domestic animal species, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biology discovery and exploitation in animal breeding and human biomedicine. Here we present results from the pilot phase of PigGTEx (http://piggtex.farmgtex.org/), where we processed 9,530 RNA-sequencing and 1,602 whole-genome sequencing samples from pigs. We build a pig genotype imputation panel, characterize the transcriptional landscape across over 100 tissues, and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We study interactions between genotype and breed/cell type, evaluate tissue specificity of regulatory effects, and elucidate the molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying about 80% of the genetic associations for 207 pig complex phenotypes, and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, corroborating the importance of pigs as a human biomedical model.

genomics↗

bioRxiv2021

Micrococcal nuclease sequencing of porcine sperm suggests a nucleosomal involvement on semen quality and early embryo development

BackgroundThe mammalian mature spermatozoon has a unique chromatin structure in which the vast majority of histones are replaced by protamines during spermatogenesis and a small fraction of nucleosomes are retained at specific locations of the genome. The chromatin structure of sperm remains unresolved in most livestock species, including the pig. However, its resolution could provide further light into the identification of the genomic regions related to sperm biology and embryo development and it could also help identifying molecular markers for sperm quality and fertility traits. Here, for the first time in swine, we performed Micrococcal Nuclease coupled with high throughput sequencing on pig sperm and characterized the mono-nucleosomal (MN) and sub-nucleosomal (SN) chromatin fractions. ResultsWe identified 25,293 and 4,239 peaks in the mono-nucleosomal and sub-nucleosomal fractions, covering 0.3% and 0.02% of the porcine genome, respectively. A cross-species comparison of nucleosome-associated DNAs in sperm revealed positional conservation of the nucleosome retention between human and pig. Gene ontology analysis of the genes mapping nearby the mono-nucleosomal peaks and identification of putative transcription factor binding motifs within the mono-nucleosomal peaks showed enrichment for sperm function and embryo development related processes. We found motif enrichment for the transcription factor Znf263, which in humans was suggested to be a key regulator of the genes with paternal preferential expression during early embryo development. Moreover, we found enriched co-occupancy between the RNAs present in pig sperm and the RNA related to sperm quality, and the mono-nucleosomal peaks. We also found preferential co-location between GWAS hits for semen quality in swine and the mono-nucleosomal sites identified in this study. ConclusionsThese results suggest a clear relationship between nucleosome positioning in sperm and sperm and embryo development.

genomics↗

bioRxiv2020

Characterisation of sperm piRNAs and their correlation with semen quality traits in swine.

Piwi-interacting RNAs (piRNAs) are a class of non-coding RNAs which main reported function consists on the silencing of transposable elements and genome stability in mammalian germline. In this study we have identified piRNAs in porcine sperm, using male germline and zygote datasets from human, mice, cow and swine, and evaluated the relation between their abundances and sperm quality traits. Our analysis identified 283,382 piRNAs, 1,355 of which correlated to at least one semen quality trait. Indeed, genome analysis of the correlated piRNAs evidenced that 57% of these were less than 50kb apart and were significantly enriched near Long Interspersed Nuclear Elements (LINEs). Moreover, some of the significant piRNAs mapped within or close to genes relevant for fertility or spermatogenesis such as CSNK1G2 and PSMF1.

genomics↗

bioRxiv2020

A RNA-seq characterization of the porcine sperm microbiome.

The microbiome plays a key role in homeostasis and health and it has been also linked to fertility and semen quality in several animal species including swine. Despite the more than likely importance of sperm bacteria on the boars reproductive ability and the dissemination of pathogens and antimicrobial resistance genes, a high throughput characterization of the swine sperm microbiome remains undone. The current study aimed at profiling the boar sperm bacterial population and its relationship with seven semen quality traits. We carried RNA-seq on 40 ejaculates and we found that it contains a broad population of bacteria. The most abundant phyla were Proteobacteria (39.1%), Firmicutes (27.5%), Actinobacteria (14.9%) and Bacteroidetes (5.7%). The predominant species contaminated sperm after ejaculation from soil, faeces and water sources (Bacillus megaterium, Brachybacterium faecium, Bacillus coagulans). Some potential pathogens were also found but at relatively low levels (Escherichia coli, Clostridioides difficile, Clostridium perfringens, Clostridium botulinum and Mycobacterium tuberculosis). We also identified 3 potential antibiotic resistant genes from E. coli against chloramphenicol, Neisseria meningitidis against spectinomycin and Staphylococcus aureus against linezolid. None of these genes were highly abundant. Finally, we classified the ejaculates into categories according to their bacterial features and semen quality parameters and identified two categories that significantly differed for 5 semen quality traits and 13 bacterial features including the genera Acinetobacter, Stenotrophomonas and Rhodobacter. Our results show that boar semen contains a rich microbiome with potential pathogens and antibiotic resistance genes which may affect its reproductive performance.

genomics↗

bioRxiv2019

Identification of circular RNAs in porcine spermatozoa and their relation to sperm motility

Circular RNAs (circRNAs) are emerging as a novel class of noncoding RNAs which potential role as gene regulators is quickly gaining interest. Although circRNAs have been studied in several tissues and cell types across several animal species, the characterization of the circRNAome in ejaculated sperm remains unexplored. In this study, we profiled the sperm circRNA catalogue in 40 boar samples. A complex population of 1,598 circRNAs was shared in at least 30 samples. The predicted circRNAs presented in general low abundances and were highly tissue-specific. Circa 80% of the circRNAs identified in the boar sperm were reported as novel. We also constructed a circRNA-miRNA interaction network based on experimental and predictive microRNA (miRNA) binding sites. Moreover, we found significant correlation between the abundance of some circRNAs and sperm motility parameters and confirmed two of these correlations by RT-qPCR in 36 samples with extreme sperm quality. Our study provides a thorough characterization of a novel cell type for the circRNA encyclopedia collection and suggests that circRNAs are potential noninvasive biomarkers for male sperm quality and thus, might also hold potential to predict male fertility.

genomics↗

bioRxiv2018

A thorough RNA-seq characterization of the porcine sperm transcriptome and its seasonal changes

Understanding the molecular basis of cell function and ultimate phenotypes is crucial for the development of biological markers. With this aim, several RNA-seq studies have been devoted to characterize the transcriptome of ejaculated spermatozoa in relation to sperm quality and fertility. Semen quality follows a seasonal pattern and decays in the summer months in several animal species. The aim of this study was to deeply profile the transcriptome of the boar sperm and to evaluate its seasonal changes. We sequenced the total and the short fractions of the sperm RNA from 10 Pietrain boars, 5 collected in summer and 5 five sampled in winter, and identified a complex and rich transcriptome with 4,436 coding genes of moderate to high abundance. Transcript fragmentation was high but less obvious in genes related to spermatogenesis, chromatin compaction and fertility. Short non-coding RNAs mostly included piwi-interacting RNAs, transfer RNAs and micro-RNAs. We also compared the transcriptome of the summer and the winter ejaculates and identified 34 coding genes and 7 micro-RNAs with a significantly distinct distribution. These genes were mostly related to oxidative stress, DNA damage and autophagy. This is the deepest characterization of the boar sperm transcriptome and the first study linking the transcriptome and the seasonal variability of semen quality in animals. The annotation described here can be used as a reference for the identification of markers of sperm quality in pigs.

genomics↗

bioRxiv2017

Low mitochondrial diversity in native Italian pig breeds is consistent with the occurrence of strong population bottlenecks

In this study, we have analysed the variation of 81 Italian pigs from the Calabrese, Casertana, Cinta Senese, Sarda and Nero Siciliano breeds as well as 54 Italian wild boars by using a dataset of mitochondrial control region sequences generated by us and others. Diversity parameters were rather low in Italian native pigs, with haplotype and nucleotide diversities ranging between 0.35-0.79 and 0.0013-0.0061, respectively. This result is consistent with the strong population bottlenecks that traditional Italian breeds have suffered due to competition with more productive foreign pig varieties. Moreover, median-joining network analysis showed that the majority of Italian pig sequences are distributed in two main clusters and that all of them belong to the E1 haplogroup. Conversely, Italian wild boars were more diverse than their domestic counterparts and they harboured the E1 and E2 haplogroups. The absence of the E2 haplogroup in Italian pigs and its moderate frequency in wild boars might suggest that this haplogroup was rare at the time that wild boars were domesticated in Italy.

genetics↗