Chapter 15 Co-Immunoprecipitation Techniques for Assessing RNA-Protein Interactions In Vivo

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

From the moment a nascent transcript emerges from an RNA polymerase until its ultimate destruction, an RNA is bound by proteins that govern its fate. Thus, in order to understand posttranscriptional regulation of gene expression, it is essential to ascertain which proteins bind a given RNA in vivo. This chapter describes three immunoprecipitation-based assays designed to query the in vivo makeup of RNA-protein complexes. Two of these, UV cross-linking and RNA immunoprecipitation (RIP), include cross-linking steps that trap complexes formed in vivo. A third, a cell mixing experiment, verifies that an interaction occurs in vivo by controlling for RNA-protein association subsequent to cell lysis. Using these protocols, this chapter presents evidence that the abundant nuclear RNA-binding protein hnRNP C interacts with the Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA in vivo.

Original languageEnglish (US)
Pages (from-to)317-342
Number of pages26
JournalMethods in Enzymology
Volume449
Issue numberC
DOIs
StatePublished - 2008

Fingerprint

Immunoprecipitation
RNA
Nuclear RNA
Proteins
Heterogeneous-Nuclear Ribonucleoproteins
Human Herpesvirus 8
RNA-Binding Proteins
Gene Expression Regulation
DNA-Directed RNA Polymerases
Nuclear Proteins
Protein C
Gene expression
Assays
Association reactions
Messenger RNA
Experiments

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

Chapter 15 Co-Immunoprecipitation Techniques for Assessing RNA-Protein Interactions In Vivo. / Conrad, Nicholas K.

In: Methods in Enzymology, Vol. 449, No. C, 2008, p. 317-342.

Research output: Contribution to journalArticle

@article{fc9e46f5e893475cb09e94e31b808a1c,
title = "Chapter 15 Co-Immunoprecipitation Techniques for Assessing RNA-Protein Interactions In Vivo",
abstract = "From the moment a nascent transcript emerges from an RNA polymerase until its ultimate destruction, an RNA is bound by proteins that govern its fate. Thus, in order to understand posttranscriptional regulation of gene expression, it is essential to ascertain which proteins bind a given RNA in vivo. This chapter describes three immunoprecipitation-based assays designed to query the in vivo makeup of RNA-protein complexes. Two of these, UV cross-linking and RNA immunoprecipitation (RIP), include cross-linking steps that trap complexes formed in vivo. A third, a cell mixing experiment, verifies that an interaction occurs in vivo by controlling for RNA-protein association subsequent to cell lysis. Using these protocols, this chapter presents evidence that the abundant nuclear RNA-binding protein hnRNP C interacts with the Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA in vivo.",
author = "Conrad, {Nicholas K.}",
year = "2008",
doi = "10.1016/S0076-6879(08)02415-4",
language = "English (US)",
volume = "449",
pages = "317--342",
journal = "Methods in Enzymology",
issn = "0076-6879",
publisher = "Academic Press Inc.",
number = "C",

}

TY - JOUR

T1 - Chapter 15 Co-Immunoprecipitation Techniques for Assessing RNA-Protein Interactions In Vivo

AU - Conrad, Nicholas K.

PY - 2008

Y1 - 2008

N2 - From the moment a nascent transcript emerges from an RNA polymerase until its ultimate destruction, an RNA is bound by proteins that govern its fate. Thus, in order to understand posttranscriptional regulation of gene expression, it is essential to ascertain which proteins bind a given RNA in vivo. This chapter describes three immunoprecipitation-based assays designed to query the in vivo makeup of RNA-protein complexes. Two of these, UV cross-linking and RNA immunoprecipitation (RIP), include cross-linking steps that trap complexes formed in vivo. A third, a cell mixing experiment, verifies that an interaction occurs in vivo by controlling for RNA-protein association subsequent to cell lysis. Using these protocols, this chapter presents evidence that the abundant nuclear RNA-binding protein hnRNP C interacts with the Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA in vivo.

AB - From the moment a nascent transcript emerges from an RNA polymerase until its ultimate destruction, an RNA is bound by proteins that govern its fate. Thus, in order to understand posttranscriptional regulation of gene expression, it is essential to ascertain which proteins bind a given RNA in vivo. This chapter describes three immunoprecipitation-based assays designed to query the in vivo makeup of RNA-protein complexes. Two of these, UV cross-linking and RNA immunoprecipitation (RIP), include cross-linking steps that trap complexes formed in vivo. A third, a cell mixing experiment, verifies that an interaction occurs in vivo by controlling for RNA-protein association subsequent to cell lysis. Using these protocols, this chapter presents evidence that the abundant nuclear RNA-binding protein hnRNP C interacts with the Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA in vivo.

UR - http://www.scopus.com/inward/record.url?scp=59649092360&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=59649092360&partnerID=8YFLogxK

U2 - 10.1016/S0076-6879(08)02415-4

DO - 10.1016/S0076-6879(08)02415-4

M3 - Article

C2 - 19215765

AN - SCOPUS:59649092360

VL - 449

SP - 317

EP - 342

JO - Methods in Enzymology

JF - Methods in Enzymology

SN - 0076-6879

IS - C

ER -