Abstract
Recent genome-wide studies have yielded new insights into the biological function of long noncoding RNAs (lncRNAs), predominantly through analysis of their genomic addresses. These studies have revealed that a large number of lncRNAs map to regulatory elements in eukaryotic genome regions known as promoter and enhancer elements. Here, we review the principles of current methodologies for analyzing lncRNAs with high-throughput sequencing approaches. These include (1) direct RNA sequencing, (2) sequencing coupled with transcription, and (3) isolation of protein complexes associated with lncRNAs followed by high-throughput sequencing. Within these categories, we also describe detailed protocols for chromatin-associated RNA sequencing, nascent transcript Global run-on sequencing, and photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation.
| Original language | English (US) |
|---|---|
| Journal | Methods in Enzymology |
| DOIs | |
| State | Accepted/In press - 2016 |
Fingerprint
Keywords
- Cap analysis of gene expression
- Global run-on sequencing
- Long noncoding RNA
- Next-generation sequencing
- Photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation
- RNA immunoprecipitation and sequencing
ASJC Scopus subject areas
- Biochemistry
- Molecular Biology
Cite this
Detection and Analysis of Long Noncoding RNAs. / Lai, F.; Blumenthal, E.; Shiekhattar, Ramin.
In: Methods in Enzymology, 2016.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Detection and Analysis of Long Noncoding RNAs
AU - Lai, F.
AU - Blumenthal, E.
AU - Shiekhattar, Ramin
PY - 2016
Y1 - 2016
N2 - Recent genome-wide studies have yielded new insights into the biological function of long noncoding RNAs (lncRNAs), predominantly through analysis of their genomic addresses. These studies have revealed that a large number of lncRNAs map to regulatory elements in eukaryotic genome regions known as promoter and enhancer elements. Here, we review the principles of current methodologies for analyzing lncRNAs with high-throughput sequencing approaches. These include (1) direct RNA sequencing, (2) sequencing coupled with transcription, and (3) isolation of protein complexes associated with lncRNAs followed by high-throughput sequencing. Within these categories, we also describe detailed protocols for chromatin-associated RNA sequencing, nascent transcript Global run-on sequencing, and photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation.
AB - Recent genome-wide studies have yielded new insights into the biological function of long noncoding RNAs (lncRNAs), predominantly through analysis of their genomic addresses. These studies have revealed that a large number of lncRNAs map to regulatory elements in eukaryotic genome regions known as promoter and enhancer elements. Here, we review the principles of current methodologies for analyzing lncRNAs with high-throughput sequencing approaches. These include (1) direct RNA sequencing, (2) sequencing coupled with transcription, and (3) isolation of protein complexes associated with lncRNAs followed by high-throughput sequencing. Within these categories, we also describe detailed protocols for chromatin-associated RNA sequencing, nascent transcript Global run-on sequencing, and photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation.
KW - Cap analysis of gene expression
KW - Global run-on sequencing
KW - Long noncoding RNA
KW - Next-generation sequencing
KW - Photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation
KW - RNA immunoprecipitation and sequencing
UR - http://www.scopus.com/inward/record.url?scp=84962249936&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84962249936&partnerID=8YFLogxK
U2 - 10.1016/bs.mie.2016.03.010
DO - 10.1016/bs.mie.2016.03.010
M3 - Article
JO - Methods in Enzymology
JF - Methods in Enzymology
SN - 0076-6879
ER -