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Profiling of chromatin accessibility across multiple tissues and developmental stages of pig [RNA-seq]

ABSTRACT: Landscape of chromatin accessibility across tissues and developmental stages is essential to elucidate the transcriptional regulation in various biological processes and phenotypes. However, the chromatin accessibility profiles of multiple tissues in newborn pigs and across porcine liver development have been seldomly investigated. Here, we profiled open chromatin maps and transcriptional features of the heart, kidney, liver, lung, skeletal muscle, and spleen tissues in newborn pigs and that of porcine liver tissue at suckling and adult stages using ATAC-seq and rRNA-depleted RNA-seq, respectively. Employing a union set of protein coding genes (PCGs) and two kinds of transcripts (lncRNAs and TUCPs), we obtained a comprehensive annotation of consensus ATAC-seq peaks for each tissue or developmental stage. The PCGs with tissue-specific accessible promoters, as expected, had active transcription and were relevant to tissue-specific functions. Other non-coding tissue-specific peaks were involved in both physical activities and morphogenesis in the neonatal tissues. We also characterized stage-specific peaks and observed a close association between dynamic chromatin accessibility and hepatic function transition during liver postnatal development. Overall, this study expands the understanding of epigenetic regulation in mammalian tissue functions and organ development, which can benefit both economic trait improvement and better biomedical use of pigs.

ORGANISM(S): Sus scrofa

PROVIDER: GSE229521 | GEO | 2023/08/15

REPOSITORIES: GEO

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Project description:Breed, gender and diet are factors affecting porcine metabolism. The aim of this study has been to investigate the gene expression patterns of the major sites for lipid metabolism, liver and fat, conditional on gender and on a moderate feeding restriction in Iberian pigs, as a model of obese porcine breed. Our results show that tissue effect account for more differentially expressed genes than gender or feeding restriction. The results obtained from the comparison between tissues support the studies showing adipose tissue is not only a fat-storage depot, we report a high number of upregulated genes in adipose tissue which represent relevant biological functions such as carbohydrate and energy metabolisms and endocrine function. Besides, key genes implicated in lipid metabolism are specifically overrepresented in liver or fat, particularly the differentially expressed genes related to fatty acid synthesis support previous studies showing that in pig, as in cattle or sheep, this process largely occurs in fat. We identified metabolic differences between genders such as oxidation capacity or response to toxins, reflected at gene expression level in liver but no in adipose tissue, contrarily to previous studies. Finally, our results seem to indicate that a moderate feeding restriction does not have large effects on liver or fat gene expression of obese pigs. Although the list of differentially expressed genes due to the effect of feeding restriction is limited, we could identify expression differences in genes related to antiageing mechanisms associated with feeding restriction as enhancement of immune response and anticoagulation and the balance between prosurvival and cell-death. Breed, gender and diet are factors affecting porcine metabolism. The aim of this study has been to investigate the gene expression patterns of the major sites for lipid metabolism, liver and fat, conditional on gender and on a moderate feeding restriction in Iberian pigs, as a model of obese porcine breed. Our results show that tissue effect account for more differentially expressed genes than gender or feeding restriction. The results obtained from the comparison between tissues support the studies showing adipose tissue is not only a fat-storage depot, we report a high number of upregulated genes in adipose tissue which represent relevant biological functions such as carbohydrate and energy metabolisms and endocrine function. Besides, key genes implicated in lipid metabolism are specifically overrepresented in liver or fat, particularly the differentially expressed genes related to fatty acid synthesis support previous studies showing that in pig, as in cattle or sheep, this process largely occurs in fat. We identified metabolic differences between genders such as oxidation capacity or response to toxins, reflected at gene expression level in liver but no in adipose tissue, contrarily to previous studies. Finally, our results seem to indicate that a moderate feeding restriction does not have large effects on liver or fat gene expression of obese pigs. Although the list of differentially expressed genes due to the effect of feeding restriction is limited, we could identify expression differences in genes related to antiageing mechanisms associated with feeding restriction as enhancement of immune response and anticoagulation and the balance between prosurvival and cell-death. 16 liver and subcutaneous backfat samples from eight animals at slaughter, 211 days old, four males and four females, four under high feeding level and four under 20% restriction

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Profiling of chromatin accessibility across multiple tissues and developmental stages of pig [RNA-seq]

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