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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
Published on: July 2, 2010
Cloning and characterization of a novel sequence-specific single-stranded-DNA-binding protein
D Bayarsaihan1, R J Soto, L N Lukens
1Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA.
The Biochemical Journal
|June 11, 1998
Summary
Researchers identified a novel protein, SSDP (sequence-specific single-stranded DNA-binding protein), that binds to a conserved pyrimidine-rich element in the alpha2(I) collagen gene promoter. This protein may play a role in gene regulation.
Area of Science:
- Molecular Biology
- Genetics
- Biochemistry
Background:
- The alpha2(I) collagen gene promoter contains a conserved, pyrimidine-rich element.
- This element forms unusual DNA structures and binds nuclear proteins, including Y-box-binding protein 1.
Purpose of the Study:
- To isolate and characterize proteins that bind to the single-stranded pyrimidine-rich sequence in the alpha2(I) collagen gene promoter.
Main Methods:
- Isolation of a partial cDNA clone from a chick embryo fibroblast expression library.
- Affinity purification and characterization of the recombinant protein encoded by the cDNA.
- Sequence analysis and comparison with existing gene databases.
Main Results:
- A novel protein, SSDP (sequence-specific single-stranded DNA-binding protein), was identified.
- The recombinant SSDP protein specifically binds to the target single-stranded DNA sequence.
- The cDNA and corresponding amino acid sequences show high conservation across human and mouse species.
Conclusions:
- SSDP is a highly conserved protein that binds a specific DNA sequence in the alpha2(I) collagen gene promoter.
- Its high affinity suggests a role in the transcriptional regulation of this gene.
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