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Updated: Jun 14, 2026
11:34
Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
Published on: August 9, 2019
Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts
C Lorenz1, T Gesell, B Zimmermann
1Department of Biochemistry, Medical University of Vienna and University of Veterinary Medicine, Vienna, Austria.
Nucleic Acids Research
|March 30, 2010
Summary
Researchers identified novel RNA molecules that bind to the Hfq protein in Escherichia coli. These Hfq aptamers are frequently located on antisense strands, suggesting a role in regulating gene expression via cis-antisense RNAs.
Area of Science:
- Molecular Biology
- Genomics
- RNA Biology
Background:
- Regulatory RNAs fine-tune gene expression at multiple levels.
- The Hfq protein in Escherichia coli interacts with numerous RNAs to modulate their function.
Purpose of the Study:
- To identify novel regulatory RNAs interacting with the Hfq protein using Genomic SELEX.
- To investigate the genomic distribution and potential regulatory roles of Hfq-binding RNAs in Escherichia coli.
Main Methods:
- Genomic SELEX (Systematic Evolution of Ligands by Exponential Enrichment) was employed to isolate Hfq-binding RNAs.
- Deep sequencing of the enriched SELEX pool to identify and map Hfq aptamers to the Escherichia coli genome.
- DMS footprinting was used to confirm the binding of a specific motif to Hfq.
Main Results:
- 8865 sequences representing genomic Hfq aptamers were identified in Escherichia coli.
- A specific motif (5'-AAYAAYAA-3') was enriched, conferring low-nanomolar affinity for Hfq.
- Hfq aptamers were found to be significantly more frequent on the antisense strands of protein-coding genes, particularly near translation start sites and operon intergenic regions.
Conclusions:
- The study expands the known targets of the Hfq protein.
- The findings suggest that Hfq may regulate a substantial number of genes through interactions with cis-antisense RNAs.
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