251. ATAC-seq with unique molecular identifiers improves quantification and footprinting
- Author
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Chunjiao Xia, Keyan Liao, Tao Zhu, Weibo Xie, and Rongfang Zhou
- Subjects
Epigenomics ,Computer science ,Sequence analysis ,Pipeline (computing) ,genetic processes ,Arabidopsis ,DNA Footprinting ,Medicine (miscellaneous) ,ATAC-seq ,Computational biology ,Polymerase Chain Reaction ,Sensitivity and Specificity ,Article ,Mobile elements ,General Biochemistry, Genetics and Molecular Biology ,law.invention ,Genomic analysis ,03 medical and health sciences ,0302 clinical medicine ,Dna genetics ,law ,Humans ,natural sciences ,Sensitivity (control systems) ,lcsh:QH301-705.5 ,Transcription factor ,Polymerase chain reaction ,Transposase ,030304 developmental biology ,0303 health sciences ,Reproducibility of Results ,DNA ,Sequence Analysis, DNA ,Footprinting ,Computational biology and bioinformatics ,Chromatin ,Identifier ,HEK293 Cells ,lcsh:Biology (General) ,Chromatin Immunoprecipitation Sequencing ,General Agricultural and Biological Sciences ,Software ,030217 neurology & neurosurgery ,Transcription Factors - Abstract
ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) provides an efficient way to analyze nucleosome-free regions and has been applied widely to identify transcription factor footprints. Both applications rely on the accurate quantification of insertion events of the hyperactive transposase Tn5. However, due to the presence of the PCR amplification, it is impossible to accurately distinguish independently generated identical Tn5 insertion events from PCR duplicates using the standard ATAC-seq technique. Removing PCR duplicates based on mapping coordinates introduces increasing bias towards highly accessible chromatin regions. To overcome this limitation, we establish a UMI-ATAC-seq technique by incorporating unique molecular identifiers (UMIs) into standard ATAC-seq procedures. UMI-ATAC-seq can rescue about 20% of reads that are mistaken as PCR duplicates in standard ATAC-seq in our study. We demonstrate that UMI-ATAC-seq could more accurately quantify chromatin accessibility and significantly improve the sensitivity of identifying transcription factor footprints. An analytic pipeline is developed to facilitate the application of UMI-ATAC-seq, and it is available at https://github.com/tzhu-bio/UMI-ATAC-seq., Tao Zhu et al. present UMI-ATAC-seq, an improved ATAC-seq technique that uses unique molecular identifiers to avoid filtering out true independent - but identical - Tn5 insertion events that would otherwise be treated as PCR duplicates. They apply UMI-ATAC-seq to rice panicle samples and show that their approach improves the quantification of chromatin accessibility and footprinting.
- Published
- 2020