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GRO-seq, A Tool for Identification of Transcripts Regulating Gene Expression

Part of the Methods in Molecular Biology book series (MIMB,volume 1543)

Abstract

The advent of next-generation sequencing (NGS) technologies has revolutionized the way we do research on gene expression. High-throughput transcriptomics became possible with the development of microarray technology, but its widespread application only occurred after the emergence of massive parallel sequencing. Especially, RNA sequencing (RNA-seq) has greatly increased our knowledge about the genome and led to the identification and annotation of novel classes of RNAs in different species. However, RNA-seq measures the steady-state level of a given RNA, which is the equilibrium between transcription, processing, and degradation. In recent years, a number of dedicated RNA-seq technologies were developed to measure specifically transcription events. Global run-on sequencing (GRO-seq) is the most widely used method to measure nascent RNA, and in recent years, it has been applied successfully to study the function and mechanism of action of noncoding RNAs. Here, we describe a detailed protocol of GRO-seq that can be readily applied to investigate different aspects of RNA biology in human cells.

Key words

  • Sequencing
  • GRO-seq
  • Nascent transcription
  • Noncoding RNA
  • Enhancer
  • Running Head: GRO-seq

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Acknowledgment

We would like to specially thank Leighton Core for kindly sharing the GRO-seq protocol with us. RL is supported by the Fundação para a Ciência e Tecnologia de Portugal (SFRH/BD/74476/2010; POPH/FSE).

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Correspondence to Reuven Agami or Gozde Korkmaz .

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Lopes, R., Agami, R., Korkmaz, G. (2017). GRO-seq, A Tool for Identification of Transcripts Regulating Gene Expression. In: Napoli, S. (eds) Promoter Associated RNA. Methods in Molecular Biology, vol 1543. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6716-2_3

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  • DOI: https://doi.org/10.1007/978-1-4939-6716-2_3

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  • Publisher Name: Humana Press, New York, NY

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