RNA Antisense Purification (RAP) for Mapping RNA Interactions with Chromatin

  • Jesse Engreitz
  • Eric S. Lander
  • Mitchell Guttman
Part of the Methods in Molecular Biology book series (MIMB, volume 1262)

Abstract

RNA-centric biochemical purification is a general approach for studying the functions and mechanisms of noncoding RNAs. Here, we describe the experimental procedures for RNA antisense purification (RAP), a method for selective purification of endogenous RNA complexes from cell extracts that enables mapping of RNA interactions with chromatin. In RAP, the user cross-links cells to fix endogenous RNA complexes and purifies these complexes through hybrid capture with biotinylated antisense oligos. DNA loci that interact with the target RNA are identified using high-throughput DNA sequencing.

Key words

RNA purification Chromatin Localization lncRNA Hybrid capture 

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Jesse Engreitz
    • 1
    • 5
  • Eric S. Lander
    • 2
    • 3
  • Mitchell Guttman
    • 4
  1. 1.Broad Institute of Harvard and MITCambridgeUSA
  2. 2.Department of BiologyMITCambridgeUSA
  3. 3.Department of Systems BiologyHarvard Medical SchoolBostonUSA
  4. 4.Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUSA
  5. 5.Division of Health Sciences and TechnologyMITCambridgeUSA

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