Transcriptomics,Genomics

Dataset Information

368

A SNF2 protein targets variable copy number repeats and thereby influences allele-specific expression


ABSTRACT: ATRX is an X-linked gene of the SWI/SNF family whose role in vivo is currently unknown. Mutations in ATRX cause syndromal mental retardation. ATRX binds to tandem repeat (TR) sequences both in heterochromatin (e.g. telomeres) and euchromatin. Genes associated with these TRs can be dysregulated when ATRX is mutated and the degree to which their expression changes is determined by the size of the TR, producing skewed allelic expression. This explains the nature of the affected genes, the variable phenotypes seen with identical ATRX mutations and also illustrates a new mechanism underlying variable penetrance. Many of the TRs in ATRX targets are G-rich and predicted to form non-B DNA structures (including G quadruplex) in vivo. We have shown that ATRX binds G quadruplex structures in vitro suggesting a mechanism by which ATRX may play a role in various nuclear processes and how this is perturbed when ATRX is mutated. 4 Human Erythroblast, 1 HEP3B and 1 Fibroblast ChIP-ChIP Sample For ChIP-Seq: one human erythroblasts, one mouse ES, one human erythroblast reference Sample, and one mouse ES input reference Sample.

ORGANISM(S): Musculus  

SUBMITTER: Joe Cross   Helena Ayyub  Hsiao P Voon  Douglas R Higgs  Daniela Rhodes  Richard J Gibbons  Steven P Wilder  Stephen Taylor  David Garrick  Andrew Morris  Vip Viprakasit  Yongjun Zhao  Matthew Mitson  Martin J Law  Ian Dunham  Guilherme M Santos  Steven Jones  Jiannis Ragoussis  Aaron Abbott  Jim R Hughes  Karen M Lower 

PROVIDER: E-GEOD-22162 | ArrayExpress | 2010-11-02

SECONDARY ACCESSION(S): SRP002608GSE22162PRJNA127699

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications


ATRX is an X-linked gene of the SWI/SNF family, mutations in which cause syndromal mental retardation and downregulation of α-globin expression. Here we show that ATRX binds to tandem repeat (TR) sequences in both telomeres and euchromatin. Genes associated with these TRs can be dysregulated when ATRX is mutated, and the change in expression is determined by the size of the TR, producing skewed allelic expression. This reveals the characteristics of the affected genes, explains the variable phen  ...[more]

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