Genomics

Dataset Information

76

Domains of genomewide gene expression dysregulation in Down syndrome [ChIP-seq]


ABSTRACT: 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. H3K4me3 ChIP-Seq profiling of monozygotic twins discordant for trisomy 21.

ORGANISM(S): Homo sapiens  

SUBMITTER: Youssef Hibaoui  John A Stamatoyannopoulos   Corinne Gehrig   Ximena Bonilla   Richard S Sandstrom   Michel Guipponi   Bas van Steensel   Federico A Santoni   Laurent Farinelli   Robert Thurman   Emilie Falconnet   M.Reza Sailani   David Gonzalez   Daniel Robyr   Konstantin Popadin   Audrey Letourneau   Samuel Deutsch   Yann Herault   Maryline Gagnebin   Marco Garieri   Stylianos E Antonarakis   Anis Feki   Roderic Guigo   Christelle Borel   Jop Kind   Anne Vannier   Eugenia Migliavacca   Claire Chevalier    

PROVIDER: E-GEOD-55506 | ArrayExpress| 2014-05-06

SECONDARY ACCESSION(S): GSE55506SRP039363PRJNA239812

REPOSITORIES: GEO, ArrayExpress, ENA

altmetric image

Publications

Sorry, this publication's infomation has not been loaded in the Indexer, please go directly to PUBMED or Altmetric.

Similar Datasets

2014-05-06 | E-GEOD-55504 | ArrayExpress
2014-06-01 | E-GEOD-55425 | ArrayExpress
2014-05-30 | E-GEOD-55505 | ArrayExpress
2014-06-03 | E-GEOD-55289 | ArrayExpress
2015-04-03 | E-GEOD-64840 | ArrayExpress
2017-08-25 | E-GEOD-52249 | ArrayExpress
2017-11-01 | PXD004880 | Pride
2014-06-03 | E-GEOD-52250 | ArrayExpress
| GSE72582 | GEO
2007-12-11 | GSE9559 | GEO