Chromatin Immunoprecipitation-sequencing (ChIP-seq)
Chromatin Immunoprecipitation assays have the ability to capture an image of specific protein to DNA interactions that are occurring in a system and process these interactions using quantitative polymerase chain reaction (qPCR), ChIP-chip, or next generation sequencing (NGS). When paired with next generation sequencing specifically, ChIP-seq is a powerful way to identify genome-wide DNA binding sites for transcription factors and other proteins.
When performing ChIP-seq, chromatin is separated from cells or tissues and is fragmented. Antibodies are used to enrich for specific chromatin fragments and DNA is recovered, sequenced, and aligned to a specific genome to determine protein binding Ioci. Studies using the technology have assisted with remarkable use cases like revealing key genes in prostate cancer and the profiling of breast cancer tumors.
ChIP has been around for a long time, but through the use of next generation sequencing, ChIP-Seq is a significant improvement over even ChIP-chip. Originally, only predetermined original specific sites of a known sequence could be studied with traditional ChIP. ChIP-chip helped to address those concerns, but the mapping precision is lower and the dynamic range of the readout is significantly less than is capable with ChIP-Seq. One study found that 10-30% of functional transcription factor binding sites were lost when ChIP-chip was used, where this isn’t an issue with ChIP-Seq.
ChIP-Seq’s abilities have allowed for population analysis of protein-DNA interactions on a genomic scale. They have also allowed for the investigation of the evolution of transcription factor binding. Both of these use cases would previously have been impossible with previously available methods and has a wide use of research use cases. As a now mature technology with compatibility across various input DNA samples, ChIP-Seq is the preferred method for genome-wide profiling across multiple samples.
The Illumina Platform for ChIP-Seq
Technically, ChIP-Seq can be completed effectively on any Next Generation Sequencing (NGS) platform. The vast majority of papers published so far though have been done on the Illumina platform. Here at Macrogen, we also use the Illumina platform for many of our sequencing needs as well.
Illumina has a very clear workflow that can be found in greater detail here, but essentially it can be explained as:
- TruSeq ChIP Library Preparation – Illumina’s simple, cost-effective kit is utilized to generate ChIP-Seq libraries.
- Sequencing with HiSeq Systems – HiSeq 3000 and 4000 standards are considered the gold standard with unrivaled speed and performance. HiSeq 3000 is a single-flow system that offers low price per sample and quick run times, while HiSeq 4000 is a double-flow system that offers a daily throughput of over 400 Gb. The ChIP prep kit is also compatible though with the HiSeq 1000, 1500, 2000, and 2500 systems. With even greater throughput, Illumina’s NovaSeq Series sets the bar higher.
- Analyze and Store Data – BaseSpace apps can be used to analyze and store data once it’s sequenced. Apps like the ChIP-Seq app, Genomatix Pathway System (GePS), BaseSpace Sequence Hub, and BaseSpace Correlation Engine can all be used in the analysis process.
ChIP-Seq Into the Future
Even as recently as March, two researchers from the University of Tokyo looked at recent advances in ChIP-seq analysis, from quality management to whole-genome annotation. While ChIP-seq is a relatively mature technology, its cost and availability were concerns as recently as a few years ago. As those concerns have gone away, ChIP-Seq has become the primary method used to analyze protein interactions with DNA. ChIP-Seq can be expected to have a major role in epigenetic sequencing and continue to reveal key genes in types of cancers.