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A DNA base-specific sequence interposed between CRX and NRL contributes to RHODOPSIN expression
Rosa Maritato1, Alessia Medugno1, Emanuela D'Andretta1
1Department of Translational Medicine, University of Naples Federico II, Naples, Italy.
Scientific Reports
|November 2, 2024
Summary
The DNA sequence between transcription factors (TFs) and binding sites significantly controls gene expression. Specific DNA sequences, not just TF affinity, dictate gene activity levels, revealing a novel layer of genetic regulation.
Area of Science:
- Molecular Biology
- Genetics
- Epigenetics
Background:
- Gene expression relies on transcription factors (TFs) binding to DNA cis-regulatory sequences.
- TF binding affinity varies based on DNA sequence composition, influencing cell-specific gene expression.
- The role of DNA sequence structure beyond TF binding affinity in gene regulation is not fully understood.
Purpose of the Study:
- To investigate the role of the DNA sequence interposed between transcription factors (TFs) and cis-regulatory elements in controlling gene expression.
- To determine if DNA sequence composition and length contribute to TF activity and gene expression levels.
- To explore evolutionary adaptations in cis-regulatory elements affecting gene expression.
Main Methods:
- Mutagenesis of DNA linker sequences between CRX and NRL transcription factors in the RHODOPSIN (RHO) gene promoter.
- Exchange of homologous cis-regulatory elements between human and mouse RHO genes.
- Targeting orthogonal DNA-binding proteins to the DNA linker to assess their impact on RHO expression.
Main Results:
- The composition and length of the DNA sequence between CRX and NRL TFs critically control RHO gene expression levels.
- Mutations in the DNA linker sequence led to unpredictable variations in gene expression.
- Swapping human and mouse RHO cis-regulatory elements resulted in similar, yet species-specific, RHO expression patterns.
- Orientation-dependent activation or repression of RHO expression was observed when DNA-binding proteins were directed to the DNA linker.
Conclusions:
- DNA sequences, beyond TF binding sites, contain regulatory information that dictates gene expression levels.
- A DNA-based code, dependent on specific base sequences and length, influences TF activity and optimizes gene expression.
- This study reveals a novel mechanism of gene regulation where the DNA linker itself actively participates in controlling gene expression.
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