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Methods Mol Biol. 2017;1543:45-55. doi: 10.1007/978-1-4939-6716-2_3.

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

Author information

1
Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands.
2
Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands. r.agami@nki.nl.
3
Erasmus MC, Rotterdam University, Rotterdam, The Netherlands. r.agami@nki.nl.
4
Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands. g.korkmaz@nki.nl.

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.

KEYWORDS:

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

PMID:
28349421
DOI:
10.1007/978-1-4939-6716-2_3
[Indexed for MEDLINE]

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