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Series GSE256029 Query DataSets for GSE256029
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
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.
 
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)
 
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
Submission date Feb 18, 2024
Last update date Jun 20, 2024
Contact name Julia E. Weigand
E-mail(s) julia.weigand@uni-marburg.de
Organization name University of Marburg
Department Pharmacy
Street address Marbacher Weg 6
City Marburg
ZIP/Postal code 35037
Country Germany
 
Platforms (1)
GPL27484 Illumina HiSeq 3000 (synthetic construct)
Samples (4)
GSM8084404 Arid5a, 20mer Input library
GSM8084405 Arid5a, 0.25 µM
GSM8084406 Arid5a, 1 µM
Relations
BioProject PRJNA1077695

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE256029_Arid_enrichment_R.w_all_Zscores.xlsx 1.9 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA

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