Abstract
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.
| Original language | English |
|---|---|
| Title of host publication | Enhancer RNAs |
| Subtitle of host publication | Methods and Protocols |
| Editors | U Andersson Orom |
| Place of Publication | New York, U. S. A. |
| Publisher | Springer |
| Pages | 39-50 |
| Number of pages | 12 |
| ISBN (Print) | 9781493940332 |
| DOIs | |
| Publication status | Published - 24 Sep 2016 |
Publication series
| Name | Methods in Molecular Biology |
|---|---|
| Volume | 1468 |
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Mapping long noncoding RNA chromatin occupancy using capture hybridization analysis of RNA targets (CHART). / Vance, Keith W.
Enhancer RNAs: Methods and Protocols. ed. / U Andersson Orom. New York, U. S. A. : Springer, 2016. p. 39-50 (Methods in Molecular Biology; Vol. 1468).Research output: Chapter in Book/Report/Conference proceeding › Chapter
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TY - CHAP
T1 - Mapping long noncoding RNA chromatin occupancy using capture hybridization analysis of RNA targets (CHART)
AU - Vance, Keith W
PY - 2016/9/24
Y1 - 2016/9/24
N2 - 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.
AB - 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.
UR - http://dx.doi.org/10.1007/978-1-4939-4035-6_5
U2 - 10.1007/978-1-4939-4035-6_5
DO - 10.1007/978-1-4939-4035-6_5
M3 - Chapter
SN - 9781493940332
T3 - Methods in Molecular Biology
SP - 39
EP - 50
BT - Enhancer RNAs
A2 - Andersson Orom, U
PB - Springer
CY - New York, U. S. A.
ER -