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Status |
Public on Mar 21, 2024 |
Title |
The disordered extensions of the Arid5a core ARID domain modulate its DNA- and RNA-binding propensities |
Organism |
synthetic construct |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
ARID (AT-rich interacting domain) proteins are a heterogeneous family of DNA-binding proteins involved in transcriptional regulation. No precise DNA-binding preferences have yet been defined for the aberrant member Arid5a. In addition, the protein binds to mRNA motifs for transcript stabilisation, presumably through the DNA-binding ARID domain. Here we first provide an unbiased definition of RNA motifs and a clear breakdown of nucleic acid binding by the ARID domain. An RNA Bind-n-Seq (RBNS) experiment was performed to find a consensus motif of the Arid5a domain. It reveals a preference for an unexpected CAGGCAG consensus motif, accompanied by a general preference for AU-rich motifs.
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Overall design |
RNA Bind-n-Seq (RBNS) experiment to to test ARID’s capability to interact with specific RNA motifs. An RNA pool (1 µM) of 20 random nucleotides flanked by short constant adapter sequences was incubated with different concentrations of the Strep-tagged Arid49-152 domain (0.25, 1, 5 µM)
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Contributor(s) |
Oberstrass L, Weigand JE, von Ehr J, Korn SM, McNicoll F, Yazgan E, Schnaubelt L, Blümel N, Zarnack K, Müller-McNicoll M, Schlundt A |
Citation(s) |
38866324 |
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Submission date |
Feb 18, 2024 |
Last update date |
Jun 20, 2024 |
Contact name |
Julia E. Weigand |
E-mail(s) |
julia.weigand@uni-marburg.de
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Organization name |
University of Marburg
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Department |
Pharmacy
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Street address |
Marbacher Weg 6
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City |
Marburg |
ZIP/Postal code |
35037 |
Country |
Germany |
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Platforms (1) |
GPL27484 |
Illumina HiSeq 3000 (synthetic construct) |
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Samples (4)
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Relations |
BioProject |
PRJNA1077695 |
Supplementary file |
Size |
Download |
File type/resource |
GSE256029_Arid_enrichment_R.w_all_Zscores.xlsx |
1.9 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
Raw data are available in SRA |
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