Analysis of RNA structure and RNA-protein interactions in mammalian cells by use of terminal transferase-dependent PCR

Hsiu-Hua Chen; Jeanne Lebon; Arthur D Riggs

doi:10.1007/978-1-60327-475-3_21

Analysis of RNA structure and RNA-protein interactions in mammalian cells by use of terminal transferase-dependent PCR

Methods Mol Biol. 2008:488:319-41. doi: 10.1007/978-1-60327-475-3_21.

Authors

Hsiu-Hua Chen¹, Jeanne Lebon, Arthur D Riggs

Affiliation

¹ Beckman Research Institute of the City of Hope, Duarte, California, USA.

PMID: 18982300
DOI: 10.1007/978-1-60327-475-3_21

Abstract

Terminal transferase-dependent polymerase chain reaction (TDPCR) can be used after reverse transcription (RT) to analyze RNA. This method (RT-TDPCR) has been used for study of RNA structure and RNA-protein interactions at nucleotide-level resolution. A detailed protocol of RT-TDPCR is presented here with examples of its use with ribonuclease T1 in mammalian cells for detecting (1) RNA structure and protein footprints of the human ferritin heavy-chain messenger RNA and (2) in vivo structure of exon 4 of human XIST (X chromosome inactivation-specific transcript) RNA.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Base Sequence
Cell Line, Tumor
Humans
Models, Genetic
Molecular Sequence Data
Nucleic Acid Conformation
Nucleotidyltransferases / metabolism*
Protein Binding
Proteins / chemistry
Proteins / genetics
Proteins / metabolism*
RNA / chemistry
RNA / genetics
RNA / metabolism*
Reverse Transcriptase Polymerase Chain Reaction / methods*

Substances

Proteins
RNA
Nucleotidyltransferases

Grants and funding

GM50575/GM/NIGMS NIH HHS/United States