Mapping Long Noncoding RNA Chromatin Occupancy Using Capture Hybridization Analysis of RNA Targets (CHART).
Capture Hybridization Analysis of RNA Targets (CHART) has recently been developed to map the genome-wide binding profile of chromatin-associated RNAs. This protocol uses a small number of 22-28 nucleotide biotinylated antisense oligonucleotides, complementary to regions of the target RNA that are accessible for hybridization, to purify RNAs from a cross-linked chromatin extract. RNA-chromatin complexes are next immobilized on beads, washed, and specifically eluted using RNase H. Associated genomic DNA is then sequenced using high-throughput sequencing technologies and mapped to the genome to identify RNA-chromatin associations on a large scale. CHART-based strategies can be applied to determine the nature and extent of long noncoding RNA (long ncRNA) association with chromatin genome-wide and identify direct long ncRNA transcriptional targets.
Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK. k.w.vance@bath.ac.uk.
Keith W
KW
Vance
D000818:Animals; D001665:Binding Sites; D002843:Chromatin / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D003432:Cross-Linking Reagents; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009693:Nucleic Acid Hybridization / Q000379:methods*; D016376:Oligonucleotides, Antisense / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D016914:Ribonuclease H / Q000378:metabolism; D017422:Sequence Analysis, DNA
D002843:Chromatin; D003432:Cross-Linking Reagents; D016376:Oligonucleotides, Antisense; D062085:RNA, Long Noncoding; D016914:Ribonuclease H
CHART; Chromatin; Genome-wide binding; Long noncoding RNA; Oligonucleotide capture