AUTHOR=Seufert Isabelle , Sant Pooja , Bauer Katharina , Syed Afzal P. , Rippe Karsten , Mallm Jan-Philipp TITLE=Enhancing sensitivity and versatility of Tn5-based single cell omics JOURNAL=Frontiers in Epigenetics and Epigenomics VOLUME=1 YEAR=2023 URL=https://www.frontiersin.org/journals/epigenetics-and-epigenomics/articles/10.3389/freae.2023.1245879 DOI=10.3389/freae.2023.1245879 ISSN=2813-706X ABSTRACT=

The analysis of chromatin features in single cells centers around Tn5 transposase and exploits its activity to simultaneously fragment target DNA and integrate adapter sequences of choice. This reaction provides a direct readout in the assay for transposase-accessible chromatin in single cells (scATAC-seq) to map open chromatin loci. However, a current limitation is the sparse coverage of these open sites in a given single cell by droplet-based methods. Thus, enhancing Tn5 activity to improve genomic coverage of scATAC-seq or facilitating multi-omics readouts of chromatin features via Tn5 together with the transcriptome is of great interest. Here, we address these issues by optimizing scATAC-seq for an increased number of integrations per cell. In addition, we provide a protocol that combines mapping of histone modification with scRNA-seq from the same cell by targeting Tn5 to antibody-bound chromatin epitopes. Our experimental workflows improve the results obtained from the downstream data analysis and serve to better resolve epigenetic heterogeneity and transcription regulation in single cells.