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ATAC-seq in Emerging Model Organisms: Challenges and Strategies.
Duğçar Ebrar Erdoğan1,2, Shadi Karimifard3,4, Mozhgan Khodadadi5
1Department of Developmental Biology, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany.
Optimizing the Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) for new model organisms requires careful attention to nuclei isolation and library amplification. Proper sample preservation, like using homogenate in cell culture medium instead of direct cryopreservation, is crucial for reliable chromatin accessibility data.
Area of Science:
- Genomics
- Molecular Biology
- Epigenetics
Background:
- The Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) is a powerful tool for mapping genome-wide chromatin accessibility.
- Its application in emerging model systems, particularly arthropods, faces challenges related to tissue availability, protocol optimization, and genome quality.
- Adapting ATAC-seq requires addressing specific technical hurdles to ensure high-quality data.
Purpose of the Study:
- To provide detailed guidance on optimizing the ATAC-seq protocol for emerging model organisms.
- To highlight critical steps impacting data quality, including nuclei isolation, transposase incubation, and library amplification.
- To offer insights into bioinformatic quality control and the effects of sample preservation methods on ATAC-seq data.
Main Methods:
- Detailed examination of key ATAC-seq protocol steps: nuclei isolation, Tn5 transposase incubation, and PCR amplification.
- Evaluation of different sample preservation methods (fresh tissue, cryopreservation, homogenate in cell culture medium) on chromatin integrity.
- Bioinformatic analysis of ATAC-seq data with emphasis on quality checkpoints.
Main Results:
- Successful adaptation of ATAC-seq in spider and ant species demonstrates the protocol's versatility.
- Optimal nuclei isolation and library amplification conditions are critical for obtaining high-quality sequencing data.
- Direct cryopreservation of tissue negatively impacts chromatin integrity, while preserving homogenate in cell culture medium mitigates this effect.
Conclusions:
- Careful planning, protocol optimization, and rigorous quality control are essential for successful ATAC-seq implementation in emerging model organisms.
- The study provides practical advice for researchers new to ATAC-seq, particularly those working with non-model species.
- Optimized ATAC-seq can effectively map the regulatory landscape and identify gene regulatory elements in diverse genomes.
