title: 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.
authors.affiliation: Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA; Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA; Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Zhongwu
authors.initials: Z
authors.lastname: Zhou
authors.affiliation: Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA; Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA; Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Stephen F
authors.initials: SF
authors.lastname: Konieczny
authors.affiliation: Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA; Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA; Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA. Electronic address: josephi@purdue.edu.
authors.forename: Joseph M K
authors.initials: JM
authors.lastname: Irudayaraj
mesh_terms: D002843:Chromatin / Q000737:chemistry*; D002845:Chromatography; D005821:Genetic Techniques; D008280:Magnetics; D053758:Nanoparticles; D012313:RNA / Q000302:isolation & purification*; D020156:Salicylic Acid / Q000737:chemistry; D013997:Time Factors
chemical_list: D002843:Chromatin; D012313:RNA; D020156:Salicylic Acid
keywords: Heterochromatin; Magnetic nanoparticle; Magnetophoretic chromatography; Soluble chromatin; Unbiased preparation of chromatin associated RNAs