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E-GEOD-55504 - Domains of genomewide gene expression dysregulation in Down syndrome [RNA-seq]

Status
Released on 8 April 2014, last updated on 6 May 2014
Organism
Homo sapiens, Mus musculus
Samples (30)
Protocols (3)
Description
Trisomy 21 (T21) is the most frequent genetic cause of cognitive impairment. To assess the perturbations of gene expression in T21, and to eliminate the noise of the genomic variability, we studied the transcriptome of fetal fibroblasts from a pair of monozygotic twins discordant for T21. Here we show that the differential expression between the twins is organized in domains along all chromosomes that are either up- or downregulated. These gene expression dysregulation domains (GEDDs) can be defined by the expression level of their gene content, and are well conserved in induced pluripotent stem cells derived from the twins’ fibroblasts. Comparison of the transcriptome of the Ts65Dn mouse model of DS and wild-type, also showed GEDDs along the mouse chromosomes that were syntenic in human. The GEDDs correlate with the lamina-associated (LADs) and replication domains of mammalian cells. The overall LADs position was not altered in trisomic cells. However, the H3K4me3 profile of the trisomic fibroblasts was modified and accurately followed the GEDD pattern. These results suggest that the nuclear compartments of trisomic cells undergo modifications of the chromatin environment influencing the overall transcriptome and that GEDDs may therefore contribute to some T21 phenotypes. mRNA-Seq profiling in Down syndrome: fibroblasts derived from a pair of monozygotic twins discordant for trisomy 21 (4 replicates), iPS cells from the same pair of discordant twins, fibroblasts from a pair of normal monozygotic twins, fibroblasts from 16 unrelated individuals (8 trisomic and 8 euploid controls), fibroblasts from the Ts65Dn mouse model of Down syndrome (1 trisomic mouse and 1 control wt).
Experiment type
RNA-seq of coding RNA 
Contacts
Anis Feki, Anne Vannier, Audrey Letourneau, Bas van Steensel, Christelle Borel, Claire Chevalier, Corinne Gehrig, Daniel Robyr, David Gonzalez, Emilie Falconnet, Eugenia Migliavacca, Federico A Santoni, John A Stamatoyannopoulos, Jop Kind, Konstantin Popadin, Laurent Farinelli, M.Reza Sailani, Marco Garieri, Maryline Gagnebin, Michel Guipponi, Richard S Sandstrom, Robert Thurman, Roderic Guigo, Samuel Deutsch, Stylianos E Antonarakis, Ximena Bonilla, Yann Herault, Youssef Hibaoui
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-55504.idf.txt
Sample and data relationshipE-GEOD-55504.sdrf.txt
Additional data (1)E-GEOD-55504.additional.1.zip
Links