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Poster communications

Selection of cell lines for the functional validation of 3D genomic interactions by genome editing

Abstract : Numerous studies have pointed out the major role of 3D nuclear architecture in the regulation of gene expression. Individual chromosomes occupy discrete territories in the nucleus but chromosomal regions often loop out and neighboring chromosomes can intermingle resulting in potential functional contacts between genomic regions from the same or different chromosomes.These cis- and trans-interactions could contribute to gene expression regulation by facilitating the consolidation of co-regulated genes in specific transcription factories. Thus, their dynamic recruitment could result in activation or abatement of gene transcription. In this context, we investigated by means of DNA fluorescence in situ hybridization (FISH) the 3D genome organization in porcine fetal muscle cells particularly long-range chromatin interactions implicating the imprinted loci IGF2 (SSC2) and other loci located on different chromosomes (Lahbib-Mansais et al. 2017). We showed that IGF2 alleles associate with the reciprocally imprinted DLK1/MEG3 region (SSC7). We furthermore demonstrated that these trans-interactions preferentially occurred between the expressed alleles. To prove their suggested functional character, we tested cell lines in which we plan to delete the genomic region containing IGF2 to determine if this deletion compromises the occurrence of the interactions. The first step has consisted in analyzing different types of porcine cell lines (4 somatic cell hybrid clones, an iPS cell line, a primary muscle and a permanent cell lines) to determine if they could be a good cell model for this purpose. Both 2D and 3D FISH experiments were performed to verify the presence in these cell lines of: i) the target chromosomes/genes, ii) the genomic interactions between IGF2-DLK1 and IGF2-MEG3. The expression of all target genes was also analyzed.We were able to select one cell line for which we plan to delete IGF2 by CRISPR-Cas9 to determine if this implies the modification of the interactions.
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Submitted on : Tuesday, June 2, 2020 - 1:40:51 PM
Last modification on : Friday, May 7, 2021 - 3:01:10 AM




Florence Mompart, Yvette Lahbib Mansais, Anne Calgaro, Hervé Acloque, Martine Bouissou-Matet Yerle. Selection of cell lines for the functional validation of 3D genomic interactions by genome editing. 23. International Colloquium on Animal Cytogenetics and Genomics (23 ICACG), Jun 2018, Saint-Petersburg, Russia. Pensoft Publishers, Comparative Cytogenetics, 12 (3), 360 p., 2018, 23rd International Colloquium on Animal Cytogenetics and Genomics (23 ICACG). ⟨hal-02734307⟩



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