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Some microsatellites may act as novel polymorphic cis-regulatory elements through transcription factor binding
Alvaro Rada Iglesias1, Ellen Kindlund, Martti Tammi
1Department of Genetics and Pathology, Unit of Clinical Genetic, Rudbeck Laboratory, Uppsala University, Uppsala SE-75185, Sweden.
Gene
|October 12, 2004
Summary
Certain microsatellites, often dismissed as "junk" DNA, may function as cis-regulatory elements. These DNA repeats can bind transcription factors and form secondary structures, influencing gene expression and genetic variation.
Area of Science:
- Genomics
- Molecular Biology
- Epigenetics
Background:
- Microsatellites, repetitive DNA sequences, are typically considered non-functional.
- Their potential role in gene regulation has been largely overlooked.
Purpose of the Study:
- To investigate if specific microsatellites function as cis-regulatory elements.
- To explore their potential role in controlling gene expression.
Main Methods:
- Created a database of short tandem repeats (2-10 bp) in the 5' promoter regions of human genes.
- Selected 114 microsatellites for size and location, identifying 51 polymorphic ones.
- Utilized electrophoretic mobility shift assay (EMSA) to study protein binding and DNA structure formation.
Main Results:
- Three out of five studied microsatellite motifs showed specific protein binding.
- The CTC/GAG repeat bound specificity protein 1 (SP1) and formed DNA triplexes.
- Distinct protein binding was observed for different repeat numbers of CTC/GAG, AAACA, and AAAAT sequences.
- Polypyrimidine strand of CTC/GAG bound PTBP1 as single-stranded DNA.
Conclusions:
- Certain microsatellites can act as cis-regulatory elements.
- They influence gene expression via transcription factor binding and secondary DNA structure formation.
- Their polymorphism and abundance suggest a role in quantitative genetic variation.