RATA: A method for high-throughput identification of RNA bound transcription factors

Main Article Content

Karyn Schmidt
Frank Buquicchio
Johanna S. Carroll
Robert J. Distel
Carl D. Novina

Keywords

long non-coding RNA, transcription factor, scaffold, MS2 RNA immunoprecipitation

Abstract

Long non-coding RNAs (lncRNAs) regulate critical cellular processes and their dysregulation contributes to multiple diseases. Although only a few lncRNAs have defined mechanisms, many of these characterized lncRNAs interact with transcription factors to regulate gene expression, suggesting a common mechanism of action. Identifying RNA-bound
transcription factors is especially challenging due to inefficient RNA immunoprecipitation and low abundance of many transcription factors. Here we describe a highly sensitive, user-friendly, and inexpensive technique called RATA (RNA-associated transcription factor array), which utilizes a MS2-aptamer pulldown strategy coupled with transcription factor activation arrays for identification of transcription factors associated with a nuclear RNA of interest. RATA requires only ~5 million cells and standard molecular biology reagents for multiplexed identification of up to 96 transcription factors in 2–3 d. Thus, RATA offers significant advantages over other technologies for analysis of RNA-transcription factor interactions.

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