Formaldehyde crosslinking: a tool for the study of chromatin complexes.
Formaldehyde has been used for decades to probe macromolecular structure and function and to trap complexes, cells, and tissues for further analysis. Formaldehyde crosslinking is routinely employed for detection and quantification of protein-DNA interactions, interactions between chromatin proteins, and interactions between distal segments of the chromatin fiber. Despite widespread use and a rich biochemical literature, important aspects of formaldehyde behavior in cells have not been well described. Here, we highlight features of formaldehyde chemistry relevant to its use in analyses of chromatin complexes, focusing on how its properties may influence studies of chromatin structure and function.
From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908 and.
Elizabeth A
EA
Hoffman
the Department of Chemistry and Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706.
Brian L
BL
Frey
the Department of Chemistry and Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706.
Lloyd M
LM
Smith
From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908 and auble@virginia.edu.
David T
DT
Auble
D000818:Animals; D002843:Chromatin / Q000737:chemistry* / Q000378:metabolism; D003432:Cross-Linking Reagents / Q000737:chemistry*; D005557:Formaldehyde / Q000737:chemistry*; D006801:Humans; D013329:Structure-Activity Relationship
D002843:Chromatin; D003432:Cross-Linking Reagents; D005557:Formaldehyde
chromatin immunoprecipitation (ChIP); chromatin structure; formaldehyde chemistry; nucleic acid chemistry; protein cross-linking; transcription factor