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| Status |
Public on Nov 02, 2010 |
| Title |
A SNF2 protein targets variable copy number repeats and thereby influences allele-specific expression |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by array
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
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.
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| Contributor(s) |
Law MJ, Lower KM, Voon HP, Garrick D, Viprakasit V, Mitson M, Zhao Y, Hughes JR, Morris A, Abbott A, Wilder SP, Taylor S, Santos GM, Cross J, Ayyub H, Jones S, Ragoussis J, Rhodes D, Dunham I, Higgs DR, Gibbons RJ |
| Citation(s) |
21029860 |
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| Submission date |
Jun 04, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard J Gibbons |
| E-mail(s) |
richard.gibbons@imm.ox.ac.uk
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| Phone |
+441865222632
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| Fax |
+441865222500
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| URL |
http://www.imm.ox.ac.uk/wimm-research/molhaem/richard-gibbons
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| Organization name |
Weatherall Institute of Molecular Medicine
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| Department |
MRC Molecular Haematology Unit
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| Lab |
Gibbons
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| Street address |
John Radcliffe Hospital,
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| City |
Oxford |
| State/province |
Oxon |
| ZIP/Postal code |
OX3 9DU |
| Country |
United Kingdom |
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| Platforms (3) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
| GPL10485 |
Dunham lab Human 16p Array H300A |
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| Samples (10)
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| Relations |
| SRA |
SRP002608 |
| BioProject |
PRJNA127699 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE22162_RAW.tar |
4.7 Gb |
(http)(custom) |
TAR (of BED, SAM, TXT) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Processed data included within Sample table |
| Raw data are available in SRA |
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