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In Cellulo DNA Analysis: LMPCR Footprinting
Régen Drouin1,2, Nathalie Bastien3, Jean-François Millau4
1Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada. Regen.Drouin@USherbrooke.ca.
Methods in Molecular Biology (Clifton, N.J.)
|September 26, 2015
Summary
Ligation-mediated polymerase chain reaction (LMPCR) precisely analyzes DNA-protein interactions and chromatin structure in living cells. This genomic sequencing technique is crucial for understanding gene expression regulation in complex genomes.
Area of Science:
- Molecular Biology
- Genomics
- Epigenetics
Background:
- Understanding gene expression regulation requires analyzing protein-DNA interactions and chromatin structure within intact cells.
- Nuclease-hypersensitive sites and transcription factor binding sites are key genetic regulatory elements.
Purpose of the Study:
- To present ligation-mediated polymerase chain reaction (LMPCR) as a method for in cellulo footprinting and DNA structure studies.
- To demonstrate the capability of LMPCR in analyzing DNA-protein interactions and unusual DNA structures in living cells.
Main Methods:
- Ligation-mediated polymerase chain reaction (LMPCR) technology.
- Genomic sequencing technique to map DNA single-strand breaks at single-nucleotide resolution.
- Application to complex animal genomes, including human.
Main Results:
- LMPCR enables precise analysis of DNA sequences within intact cells.
- The method can identify DNA-protein interactions and unusual DNA structures in vivo.
- Detailed conventional and automated LMPCR protocols are provided.
Conclusions:
- LMPCR is the method of choice for in cellulo footprinting and DNA structure studies.
- This technique is vital for investigating gene regulation mechanisms in complex genomes.
- The presented protocols facilitate the application of LMPCR in research settings.
