AutoRELACS: automated generation and analysis of ultra-parallel ChIP-seq

L Arrigoni,F Ferrari,T Manke,J Weller,C Bella,U Bönisch

doi:10.1038/s41598-020-69443-8

L Arrigoni, F Ferrari + Show 4 more

Open Access

https://doi.org/10.1038/s41598-020-69443-8

Copy DOI

Abstract

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a method used to profile protein-DNA interactions genome-wide. Restriction Enzyme-based Labeling of Chromatin in Situ (RELACS) is a recently developed ChIP-seq protocol that deploys a chromatin barcoding strategy to enable standardized and high-throughput generation of ChIP-seq data. The manual implementation of RELACS is constrained by human processivity in both data generation and data analysis. To overcome these limitations, we have developed AutoRELACS, an automated implementation of the RELACS protocol using the liquid handler Biomek i7 workstation. We match the unprecedented processivity in data generation allowed by AutoRELACS with the automated computation pipelines offered by snakePipes. In doing so, we build a continuous workflow that streamlines epigenetic profiling, from sample collection to biological interpretation. Here, we show that AutoRELACS successfully automates chromatin barcode integration, and is able to generate high-quality ChIP-seq data comparable with the standards of the manual protocol, also for limited amounts of biological samples.

Highlights

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a method used to profile protein-DNA interactions genome-wide
Restriction Enzyme-based Labeling of Chromatin in Situ (RELACS) is a method that enables the high-throughput generation of chromatin immunoprecipitation (ChIP)-seq experiments[9]
To increase the standardization and the scalability of this approach, we have developed AutoRELACS, an automated implementation of the RELACS protocol using the liquid handler Biomek i7

Summary

Introduction

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a method used to profile protein-DNA interactions genome-wide. Over the last ten years, much work has been devoted to address these and other shortcomings[4,5,6,7,8] In line with these efforts, we have recently developed Restriction Enzyme-based Labeling of Chromatin in Situ (RELACS), a method that employs chromatin barcoding to enable high-throughput generation of ChIP-seq e xperiments[9]. While other automated ChIP-seq implementations already e xist[11,12], they still require a large amount of sample material, and they do not utilize the enormous multiplexing potential of barcoded chromatin The scope of these methods is limited to data generation and the lack of an integrated bioinformatics workflow that streamlines standard computational tasks (e.g. QC, DNA-mapping, peak calling). We test the performance of AutoRELACS by assessing (1) the scalability of the chromatin barcode integration step, (2) the quality of the generated data in comparison to the benchmark set by the manual protocol, and (3) the sensitivity of the automated method when working with low (≤ 25,000 cells/sample) and very low Scientific Reports | (2020) 10:12400

Methods

Results

Conclusion