Biology subjects

Giuffra, E.

Publications and source records attributed to Giuffra, E..

7 recordsLinked to original sources

bioRxiv2025

Differential chromatin accessibility between pre- and post-natal stages highlights putative causal regulatory variants in pig skeletal muscle

Deciphering how chromatin dynamics shape the effects of regulatory variants on complex traits across development remains largely unexplored in farmed animals. Focusing on porcine skeletal muscle, we integrated chromatin accessibility (ATAC-seq), molecular QTL (molQTL), and GWAS data to identify putative stage-specific regulatory variants influencing agronomically important traits. We aggregated and analyzed 202 ATAC-seq libraries spanning prenatal (fetal) and postnatal (piglet) stages. We intersected consensus and differential peaks with cis-molQTLs from the Porcine Genotype-by-Tissue-by-Expression Atlas (PigGTEx) followed by functional enrichment analysis, promoter-focused functional annotation, integration with gene-trait pairs, and intersection with eGenes (i.e., genes whose expression is regulated by at least one cis-eQTL) to link variants previously associated with QTLs for production traits. We identified 132,275 differentially accessible peaks (DAPs) distinguishing fetal and piglet muscle. Fetal DAPs were enriched in promoter and intergenic regions, whereas piglet DAPs were enriched in intronic regions, indicating a shift from transcriptional priming to postnatal regulatory refinement. Overlaps between accessible regions and molQTLs were highly significant (p < 0.001), with the strongest eQTLs predominating in the fetal stage (14 fetal vs. 4 piglet). Gene Ontology analysis of promoter-accessible eGenes revealed enrichment for RNA metabolism and chromatin organization in fetuses, and for muscle contraction and lipid metabolism in piglets. The intersection with colocalized complex traits loci identified 107 fetal- and 30 piglet-stage regulatory elements, with only three eGenes shared between stages. These findings provide insights into developmental chromatin dynamics in skeletal muscle and an effective framework for prioritising putative regulatory variants affecting pig traits at prenatal stages.

genomics↗

bioRxiv2025

Porcine Intestinal Organoids as Models of Regional Gut and Animal Identities: a Transcriptomic Approach

BackgroundOrganoids offer controlled epithelial systems for functional follow-up of candidate genes and variants in farm animals, but their usefulness for genotype-to-phenotype research depends on whether they retain intestinal regional identity and animal-specific molecular signatures. We profiled 32 RNA-seq libraries from matched tissues and organoids derived from duodenum, jejunum, ileum and colon of four slaughter-age Large White pigs. ResultsOrganoids were transcriptionally distinct from native tissues but remained within the intestinal transcriptional space and retained regional structure, particularly when epithelial cell signature genes were considered. Most expressed genes were shared between tissues and organoids (81.2% of all detected genes and 81.8% of epithelial cell signature genes). Innate immune genes were also largely detected in organoids (79.6% shared), but with a lower regional organisation. Projection of ileal organoids onto an in vivo developmental reference positioned them closer to foetal or newborn samples than to slaughter-age ileum tissue, consistent with a comparatively immature transcriptional state. Differential expression and enrichment analyses showed attenuation of gene-level segment differences in organoids but partial preservation of regional markers and Gene Ontology terms linked to intestinal development and regionalisation, absorption, metabolism, epithelial signalling, mucosal immune responses and transport. Animal-associated differences were retained for selected epithelial signatures, notably the glycosylation-related genes FUT2 and B4GALNT2. FUT2 expression was strongly reduced in one animal and associated with linked intronic variants, whereas B4GALNT2 separated two pairs of animals and segregated with candidate variants affecting protein expression or transcript processing. ConclusionsAdult porcine intestinal organoids retain a substantial epithelial component of regional identity and preserve selected animal-specific regulatory signatures, while showing reduced immune spatial patterning and immature transcriptional features. Standardised organoid biobanks from genotyped and phenotyped pigs may support functional follow-up of candidate genes, variants and pathways when intestinal epithelial mechanisms are implicated.

genomics↗

bioRxiv2025

Guiding eQTL mapping and genomic prediction of gene expression in three pig breeds with tissue-specific epigenetic annotations from early development

Gene expression is a dynamic phenotype influenced by tissue-specific regulatory mechanisms, which can modulate expression directly or indirectly through cis or trans factors. Identifying genetic variants in these regulatory regions can improve both expression quantitative trait locus (eQTL) mapping and gene expression prediction. Whole genome sequences offer the possibility for enhanced eQTL mapping accuracy, but detecting causal variants remains challenging. Here, we evaluate the potential added-value of integrating tissue-specific epigenetic annotations, such as chromatin accessibility and methylation status, into within-breed genomic predictions of expression for three pig breeds. Functional annotations from early developmental stages improved eQTL mapping interpretability as shown by the enrichment of trait-relevant QTLs. However, despite the use of functional annotations, predictions across breeds remain challenging due to differences in genetic architectures. Our work contributes to the understanding of gene expression regulation in livestock and highlights the value of functional annotations, despite continued challenges for predictions across breeds. HighlightsO_LIMatched whole-genome sequences and expressions reveal transcriptional regulatory variants. C_LIO_LIEarly epigenetic marks can guide transcriptome prediction and eQTL mapping. C_LIO_LIAnnotation-guided models can enhance the interpretability of eQTL mapping. C_LIO_LIPorting predictions across pig breeds remains challenging even with annotations. C_LIO_LIA case study linked IGF2 liver eQTLs with annotations and cholesterol QTLs. C_LI

genomics↗

bioRxiv2024

Differences in maternal diet fiber content influence patterns of gene expression and chromatin accessibility in fetuses and piglets

This study investigates the impact of maternal gestation diets with varying fiber contents on gene expression and chromatin accessibility in fetuses and piglets fed a low fiber diet post weaning. High-fiber maternal diets, enriched with sugar beet pulp or pea internal fiber, were compared to a low-fiber maternal diet to evaluate their effects on liver and muscle tissues. The findings demonstrate that maternal high-fiber diets significantly alter the chromatin accessibility, predicted transcription factor activity and transcriptional landscape in both fetuses and piglets. A gene set enrichment analysis revealed over-expression of gene ontology terms related to metabolic processes and under-expression of those linked to immune responses in piglets from sows given the high-fiber diets during gestation. This suggests better metabolic health and immune tolerance of the fetus and offspring, in line with the documented epigenetic effects of short chain fatty acids on immune and metabolic pathways. A deconvolution analysis of the bulk RNA-seq data was performed using cell-type specific markers from a single cell transcriptome atlas of adult pigs. These results confirmed that the transcriptomic and chromatin accessibility data do not reflect different cell type compositions between maternal diet groups but rather phenotypic changes triggered by the critical role of maternal nutrition in shaping the epigenetic and transcriptional environment of fetus and offspring. Our findings have implications for improving animal health and productivity as well as broader implications for human health, suggesting that optimizing maternal diet with high-fiber content could enhance metabolic health and immune function in the formative years after birth and potentially to adulthood.

genomics↗

bioRxiv2023

Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues.

Gene atlases for livestock are steadily improving thanks to new genome assemblies and new expression data improving the gene annotation. However, gene content varies across databases due to differences in RNA sequencing data and bioinformatics pipelines, especially for long non-coding RNAs (lncRNAs) which have higher tissue and developmental specificity and are harder to consistently identify compared to protein coding genes (PCGs). As done previously in 2020 for chicken assemblies galgal5 and GRCg6a, we provide a new gene atlas, lncRNA-enriched, for the latest GRCg7b chicken assembly, integrating "NCBI RefSeq", "EMBL-EBI Ensembl/GENCODE" reference annotations and other resources such as FAANG and NONCODE. As a result, the number of PCGs increases from 18,022 (RefSeq) and 17,007 (Ensembl) to 24,102, and that of lncRNAs from 5,789 (RefSeq) and 11,944 (Ensembl) to 44,428. Using 1,400 public RNA-seq transcriptome representing 47 tissues, we provided expression evidence for 35,257 (79%) lncRNAs and 22,468 (93%) PCGs, supporting the relevance of this atlas. Further characterization including tissue-specificity, sex-differential expression and gene configurations are provided. We also identifiend conserved miRNA-hosting genes with human counterparts, suggesting common function. The annotated atlas is available at www.fragencode.org/lnchickenatlas.html.

genomics↗

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↗

bioRxiv2018

Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig.

BackgroundFunctional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project (http://www.fragencode.org) aimed to profile the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in four livestock species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells).\n\nResultsRNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically Associating Domains (TADs) and epigenetic A/B compartments annotated from Hi-C data were consistent with RNA-seq and ATAC-seq data. Multi-species comparisons showed that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species.\n\nConclusionsWe report the first multi-species and multi-assay genome annotation results obtained by a FAANG project. Beyond the generation of reference annotations and the confirmation of previous findings on model animals, the integrative analysis of data from multiple assays and species sheds a new light on the multi-scale selective pressure shaping genome organization from birds to mammals. Overall, these results emphasize the value of FAANG for research on domesticated animals and reinforces the importance of future meta-analyses of the reference datasets being generated by this community on different species.

genomics↗