Genomic matrix attachment region and chromosome conformation capture quantitative real time PCR assays identify novel putative regulatory elements at the imprinted Dlk1/Gtl2 locus.
We previously showed that genomic imprinting regulates matrix attachment region activities at the mouse Igf2 (insulin-like growth factor 2) locus and that these activities are functionally linked to neighboring differentially methylated regions (DMRs). Here, we investigate the similarly structured Dlk1/Gtl2 imprinted domain and show that in the mouse liver, the G/C-rich intergenic germ line-derived DMR, a sequence involved in domain-wide imprinting, is highly retained within the nuclear matrix fraction exclusively on the methylated paternal copy, reflecting its differential function on that chromosome. Therefore, not only "classical" A/T-rich matrix attachment region (MAR) sequences but also other important regulatory DNA elements (such as DMRs) can be recovered from genomic MAR assays following a high salt treatment. Interestingly, the recovery of one A/T-rich sequence (MAR4) from the "nuclear matrix" fraction is strongly correlated with gene expression. We show that this element possesses an intrinsic activity that favors transcription, and using chromosome conformation capture quantitative real time PCR assays, we demonstrate that the MAR4 interacts with the intergenic germ line-derived DMR specifically on the paternal allele but not with the Dlk1/Gtl2 promoters. Altogether, our findings shed a new light on gene regulation at this locus.
Braem
Caroline
C
Institut de Génétique Moléculaire, UMR 5535 CNRS-Université Montpellier II, IFR 122, 1919, Route de Mende, 34293 Montpellier Cedex 5, France.
Recolin
Bénédicte
B
Rancourt
Rebecca C
RC
Angiolini
Christopher
C
Barthès
Pauline
P
Branchu
Priscillia
P
Court
Franck
F
Cathala
Guy
G
Ferguson-Smith
Anne C
AC
Forné
Thierry
T
D000818:Animals; D002135:Calcium-Binding Proteins; D002478:Cells, Cultured; D033481:Chromosomes, Mammalian / Q000235:genetics; D019175:DNA Methylation; D016678:Genome / Q000502:physiology*; D018392:Genomic Imprinting / Q000502:physiology*; D006801:Humans; D007335:Insulin-Like Growth Factor II / Q000235:genetics; D036341:Intercellular Signaling Peptides and Proteins / Q000235:genetics*; D045170:Matrix Attachment Regions / Q000502:physiology*; D051379:Mice; D011401:Promoter Regions, Genetic / Q000235:genetics; D011506:Proteins / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000502:physiology*; D062085:RNA, Long Noncoding
D002135:Calcium-Binding Proteins; C512925:Dlk1 protein, mouse; C513121:IGF2 protein, mouse; D036341:Intercellular Signaling Peptides and Proteins; C422882:MEG3 non-coding RNA, mouse; D011506:Proteins; D062085:RNA, Long Noncoding; D007335:Insulin-Like Growth Factor II