Rapid and unbiased extraction of chromatin associated RNAs from purified native chromatin

Abstract

An ultra fast and unbiased method that uses salicylic acid coated magnetic nanoparticles (SAMNPs) and magnetophoretic chromatography is developed to extract chromatin associated RNAs (CARs). The SAMNPs were first used for enriching cells from the cell culture media and further used for capturing chromatin after cells were lysed. The formed SAMNPs-chromatin complexes were transferred to a viscous polyethylene glycol (PEG) solution stored in a 200-μL pipette tip. Due to the difference in viscosities, a bi-layer liquid was formed inside the pipette tip. The SAMNPs-chromatin complexes were separated from the free SAMNPs and free RNA-SAMNPs complexes by applying an external magnetic field. The CARs were further extracted from the SAMNP-chromatin complexes directly. The extracted CARs were reverse transcribed as cDNA and further characterized by real-time qPCR. The total assay time taken for cell separation, chromatin purification and chromatin associated RNAs extraction can be accomplished in less than 2h.

Technical advances in global DNA methylation analysis in human cancers

“…While this may in the foreseeable future help clinicians make informed choices pertaining to patient profiling and therapeutic management, standards will have to be developed to decorously interpret the disease risk imparted by global changes of the methylome. We realize that the infrastructural wealth available to scientists in biomedical settings may not be practical in a clinic and in this regards, and to address this challenge our lab and others have used lateral flow techniques that can potentially be used for onsite sensing [ 85 , 86 ] in conjunction with chromatin extraction methods [ 87 ] to addressing this lacunae. Sample preparation will continue to challenge the point of care sensors development.…”