title: Expressed alleles of imprinted IGF2, DLK1 and MEG3 colocalize in 3D-preserved nuclei of porcine fetal cells.
abstract: BACKGROUND
  To explore the relationship between spatial genome organization and gene expression in the interphase nucleus, we used a genomic imprinting model, which offers parental-specific gene expression. Using 3D FISH in porcine fetal liver cells, we compared the nuclear organization of the two parental alleles (expressed or not) of insulin-like growth factor 2 (IGF2), a paternally imprinted gene located on chromosome 2. We investigated whether its nuclear positioning favors specific locus associations. We also tested whether IGF2 is implicated in long-range chromatin trans-associations as previously shown in the mouse model species for its reciprocal imprinted gene H19.
  
  
  RESULTS
  We focused on the 3D position of IGF2 alleles, with respect to their individual chromosome 2 territories. The paternally expressed allele was tagged with nascent RNA. There were no significant differences in the position of the two alleles (p = 0.06). To determine long-range chromatin trans-interactions, we chose 12 genes, some of which are known to be imprinted in mammalian model species and belong to a network of imprinted genes (i.e. SLC38A4, DLK1, MEG3, and ZAC1). We screened them and ABCG2, OSBP2, OSBPL1, RPL32, NF1, ZAR1, SEP15, GPC3 for associations with IGF2 in liver cells. All imprinted genes tested showed an association with IGF2. The DLK1/MEG3 locus showed the highest rate of colocalization. This gene association was confirmed by 3D FISH (in 20 % of the nuclei analyzed), revealing also the close proximity of chromosomes 2 and 7 (in 60 % of nuclei). Furthermore, our observations showed that the expressed paternal IGF2 allele is involved in this association. This IGF2-(DLK1/MEG3) association also occurred in a high percentage of fetal muscle cells (36 % of nuclei). Finally, we showed that nascent IGF2, DLK1 and MEG3 RNAs can associate in pairs or in a three-way combination.
  
  
  CONCLUSIONS
  Our results show that trans-associations occur between three imprinted genes IGF2, DLK1 and MEG3 both in fetal liver and muscle cells. All three expressed alleles associated in muscle cells. Our findings suggest that the 3D nuclear organization is linked to the transcriptional state of these genes.
authors.affiliation: GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France. yvette.lahbib@toulouse.inra.fr.
authors.forename: Yvette
authors.initials: Y
authors.lastname: Lahbib-Mansais
authors.affiliation: GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France.
authors.forename: Harmonie
authors.initials: H
authors.lastname: Barasc
authors.affiliation: GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France.
authors.forename: Maria
authors.initials: M
authors.lastname: Marti-Marimon
authors.affiliation: GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Mompart
authors.affiliation: GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France.
authors.forename: Eddie
authors.initials: E
authors.lastname: Iannuccelli
authors.affiliation: GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France.
authors.forename: David
authors.initials: D
authors.lastname: Robelin
authors.affiliation: GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France.
authors.forename: Juliette
authors.initials: J
authors.lastname: Riquet
authors.affiliation: GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France.
authors.forename: Martine
authors.initials: M
authors.lastname: Yerle-Bouissou
mesh_terms: D000483:Alleles; D000818:Animals; D002452:Cell Count; D002467:Cell Nucleus / Q000378:metabolism*; D033481:Chromosomes, Mammalian / Q000378:metabolism; D004247:DNA / Q000235:genetics; D005333:Fetus / Q000166:cytology*; D056426:Genetic Loci; D018392:Genomic Imprinting; D017404:In Situ Hybridization, Fluorescence; D007335:Insulin-Like Growth Factor II / Q000235:genetics* / Q000378:metabolism; D008099:Liver / Q000166:cytology / Q000378:metabolism; D008565:Membrane Proteins / Q000235:genetics* / Q000378:metabolism; D009132:Muscles / Q000166:cytology / Q000378:metabolism; D034443:RNA Transport; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D034421:Sus scrofa / Q000196:embryology*
chemical_list: C094335:H19 long non-coding RNA; D008565:Membrane Proteins; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D007335:Insulin-Like Growth Factor II; D004247:DNA
keywords: 3D RNA-DNA FISH; Colocalization; DLK1/MEG3; Fetal pig; IGF2; Imprinting; Interchromosomal associations; Liver; Muscle