TY - CHAP
T1 - Detection and Analysis of Long Noncoding RNAs
AU - Lai, F.
AU - Blumenthal, E.
AU - Shiekhattar, R.
N1 - Publisher Copyright:
© 2016 Elsevier Inc.
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
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U2 - 10.1016/bs.mie.2016.03.010
DO - 10.1016/bs.mie.2016.03.010
M3 - Chapter
C2 - 27372765
AN - SCOPUS:84962249936
T3 - Methods in Enzymology
SP - 421
EP - 444
BT - Methods in Enzymology
PB - Academic Press Inc.
ER -