Emerging toolkits for decoding the co-occurrence of modified histones and chromatin proteins.
Anne-Sophie PepinRobert SchneiderPublished in: EMBO reports (2024)
In eukaryotes, DNA is packaged into chromatin with the help of highly conserved histone proteins. Together with DNA-binding proteins, posttranslational modifications (PTMs) on these histones play crucial roles in regulating genome function, cell fate determination, inheritance of acquired traits, cellular states, and diseases. While most studies have focused on individual DNA-binding proteins, chromatin proteins, or histone PTMs in bulk cell populations, such chromatin features co-occur and potentially act cooperatively to accomplish specific functions in a given cell. This review discusses state-of-the-art techniques for the simultaneous profiling of multiple chromatin features in low-input samples and single cells, focusing on histone PTMs, DNA-binding, and chromatin proteins. We cover the origins of the currently available toolkits, compare and contrast their characteristic features, and discuss challenges and perspectives for future applications. Studying the co-occurrence of histone PTMs, DNA-binding proteins, and chromatin proteins in single cells will be central for a better understanding of the biological relevance of combinatorial chromatin features, their impact on genomic output, and cellular heterogeneity.
Keyphrases
- transcription factor
- genome wide
- dna damage
- gene expression
- dna methylation
- dna binding
- circulating tumor
- single cell
- single molecule
- cell free
- magnetic resonance imaging
- cell therapy
- computed tomography
- magnetic resonance
- cell fate
- oxidative stress
- cell cycle arrest
- nucleic acid
- cell death
- contrast enhanced
- cell proliferation
- current status
- simultaneous determination