Genome-wide Mapping of Endogenous G-quadruplex DNA Structures by Chromatin Immunoprecipitation and High-throughput Sequencing

Overview

Journal Nat Protoc

Specialties Biology
Pathology
Science

Date 2018 Feb 23

PMID 29470465

Citations 138

Authors

Robert Hansel-Hertsch

Jochen Spiegel

Giovanni Marsico

David Tannahill

Shankar Balasubramanian

Affiliations

Soon will be listed here.

Abstract

G-rich DNA sequences can form four-stranded G-quadruplex (G4) secondary structures and are linked to fundamental biological processes such as transcription, replication and telomere maintenance. G4s are also implicated in promoting genome instability, cancer and other diseases. Here, we describe a detailed G4 ChIP-seq method that robustly enables the determination of G4 structure formation genome-wide in chromatin. This protocol adapts traditional ChIP-seq for the detection of DNA secondary structures through the use of a G4-structure-specific single-chain antibody with refinements in chromatin immunoprecipitation followed by high-throughput sequencing. This technology does not require expression of the G4 antibody in situ, enabling broad applicability to theoretically all chromatin sources. Beginning with chromatin isolation and antibody preparation, the entire protocol can be completed in <1 week, including basic computational analysis.

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