Visualizing individual sequence-specific protein-DNA interactions in situ
(English)Manuscript (preprint) (Other academic)
Gene expression – a key feature for modulating cell fate – is regulated in part by histone modifications, which modulate accessibility of the chromatin to transcription factors. Until now, protein-DNA interactions have mostly been studied in bulk without retrieving spatial information from the sample or with poor sequence resolution. New tools are needed to reveal proteins interacting with specific DNA sequences in situ for further understanding of the orchestration of transcription control within the nucleus.
We present herein an approach to visualize individual protein-DNA interactions within cells, based on the in situ proximity ligation assay (PLA). This assay, previously used for detection of protein-protein interactions in situ, was adapted for analysis of target protein-DNA interactions, using padlock probes to identify unique DNA sequences in complex genomes. As a proof-of-principle we detected histone H3 interacting with a 26 bp consensus sequence of the Alu-repeat abundantly expressed in the human genome, but absent in mice. However, the mouse genome contains a highly similar sequence, providing a model system to analyze the selectivity of the developed methods. Although efficiency of detection currently is limiting, we conclude that in situ PLA can be used to achieve a highly selective analysis of protein-DNA interactions in single cells.
protein-DNA interaction, in situ, fluorescence microscopy, proximity ligation assay, padlock probe
Research subject Molecular Medicine
IdentifiersURN: urn:nbn:se:uu:diva-151578OAI: oai:DiVA.org:uu-151578DiVA: diva2:410503