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Characterization of 3D genomic interactions in fetal pig muscle

Marti Marimon, Maria Eugenia and Acloque, Hervé and Zytnicki, Matthias and Robelin, David and Djebali Quelen, Sarah and Villa-Vialaneix, Nathalie and Madsen, Ole and Lahbib Mansais, Yvette and Esquerré, Diane and Mompart, Florence and Yerle-Bouissou, Martine and Groenen, Martien and Foissac, Sylvain Characterization of 3D genomic interactions in fetal pig muscle. (2017) In: 36th International Society for Animal Genetics Conference, 17 July 2017 - 21 July 2017 (Dublin, Ireland).

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Official URL: https://prodinra.inra.fr/record/403700

Abstract

Genome sequence alone is not sufficient to explain the overall coordination of nuclear activity in a particular tissue. The nuclear organisation and genomic long-range intra- and inter-chromosomal interactions play an important role in the regulation of gene expression and the activation of tissue- specific gene networks. Here we present an overview of the pig genome architecture in muscle at two late developmental stages. The muscle maturation process occurs between the 90th day and the end of gestation (114 days), a key period for survival at birth. To characterise this period we profiled chromatin interactions genome-wide with in situ Hi-C (High Throughput Chromosome Conformation Capture) in muscle samples collected at 90 and 110 days of gestation, specific moments where a drastic change in gene expression has been reported. About 200 million read pairs per library were generated (3 replicates per condition). This allowed: (a) the design of an experimental Hi-C protocol optimized for frozen fetal tissues, (b) the first Hi-C contact heatmaps in fetal porcine muscle cells, and (c) to profile Topologically Associated Domains (TADs) defined as genomic domains with high levels of chromatin interactions. Using the new assembly version Sus scrofa v11, we could map 82% of the Hi-C reads on the reference genome. After filtering, 49% of valid read pairs were used to infer the genomic interactions in both developmental stages. In addition, ChIP-seq experiments were performed to map the binding of the structural protein CTCF, known to regulate genome structure by promoting interactions between genes and distal enhancers. The Hi-C and ChIP-seq data were analysed in combination with the results of a previous transcriptome analysis, focusing on the hun-dreds of genes that were reported as differentially expressed during muscle maturation. We will report the observed general differences between both developmental stages in terms of transcription and structure.

Item Type:Conference or Workshop Item (Paper)
HAL Id:hal-02868765
ProdINRA Id:403700
Audience (conference):International conference proceedings
Uncontrolled Keywords:
Institution:Université de Toulouse > Ecole Nationale Vétérinaire de Toulouse - ENVT (FRANCE)
Université de Toulouse > Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE)
French research institutions > Institut National de la Recherche Agronomique - INRA (FRANCE)
Other partners > Wageningen University & Research - WUR (NETHERLANDS)
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Deposited On:18 Mar 2020 14:10

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