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ATAC-seq with unique molecular identifiers improves quantification and footprinting
- Source :
- Communications Biology, Communications Biology, Vol 3, Iss 1, Pp 1-10 (2020)
- Publication Year :
- 2020
- Publisher :
- Springer Science and Business Media LLC, 2020.
-
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.<br />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.
- 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
Subjects
Details
- ISSN :
- 23993642
- Volume :
- 3
- Database :
- OpenAIRE
- Journal :
- Communications Biology
- Accession number :
- edsair.doi.dedup.....24050e077bcf311d4c6ae05a6242821e