Chromatin conformation

About

Abstract: Stanford researchers have found a new way to analyze the three-dimensional folding of DNA into compact structures. This method could have wide-ranging uses in both research and clinical applications. Chromatin is the means by which DNA is packaged and condensed into a form suitable for storage in the nucleus. Chromatin fiber compaction plays a crucial role in determining the accessibility of DNA to transcription factors and transcription machinery. However, much is still unknown about the means by which this takes place. To gain a better understanding of chromatin architecture the inventors have developed RICC-seq (ionizing Radiation-Induced spatially Correlated Cleavage of DNA with SEQuencing), an assay for analyzing chromatin structure. It uses ionizing radiation to break up DNA, in situ, in such a way that small DNA fragments are created, which can then be analyzed in terms of the mapping locations of their ends and how their length profile reports on characteristic contacts in chromatin and folded DNA. It can also be used to produce DNA foot-printing data for both DNA-bound proteins and nucleosomes with near single base pair resolution. This technology could increase our knowledge of genetic structure and regulation, advancing both research and clinical treatment-based fields. Stage of research: The method has been used to examine chromatin secondary structure in live cells. Applications: Tool to evaluate chromatin structure in cells for: Fertility medicine- analyze sperm cells for possible defects in the DNA, independent of motility Drug development- evaluate effects of drugs targeting chromatin modification pathways Nanotechnology - analyze the folded structure of nucleic acids in nanoscale devices or therapeutic nucleic acid delivery particles containing DNA or RNA Research regarding transcription factors and regulation of genetic material Advantages: Wide range of uses- this method of analysis can precisely penetrate tightly-condensed DNA, enabling it to investigate a broad range of condensed nucleic acid systems including: Mammalian chromatin Chromatin of eukaryotes and arachaea in general Human sperm Bacterial spores Viral capsids Artificial nucleic acid particles Detailed data – Provides high-resolution three-dimensional information about DNA-DNA contacts over 1-10nm without need for proximity ligation or sample permeabilization Different perspective- Unlike other methods of DNA analysis, it does not rely on enzyme-based cleavage Does not have the biases of nucleases- can be used to validate transcription factor foot printing assays