Single-cell RNA-seq methods can be used to delineate cell types and states at unprecedented resolution but do little to explain why certain genes are expressed. Single-cell ATAC-seq and multiome (ATAC + RNA) have emerged to give a complementary view of the cell state. It is however unclear what additional information can be extracted from ATAC-seq data besides transcription factor binding sites. Here, we show that ATAC-seq telomere-like reads counter-inituively cannot be used to infer telomere length, as they mostly originate from the subtelomere, but can be used as a biomarker for chromatin condensation. Using long-read sequencing, we further show that modern hyperactive Tn5 does not duplicate 9 bp of its target sequence, contrary to common belief. We provide a new tool, Telomemore, which can quantify nonaligning subtelomeric reads. By analyzing several public datasets and generating new multiome fibroblast and B-cell atlases, we show how this new readout can aid single-cell data interpretation. We show how drivers of condensation processes can be inferred, and how it complements common RNA-seq-based cell cycle inference, which fails for monocytes. Telomemore-based analysis of the condensation state is thus a valuable complement to the single-cell analysis toolbox.

Department of Chemistry Faculty of Science University of South Bohemia Ceske Budejovice 37005 Czech Republic

Department of Chemistry Umeå University Linnaeus väg 10 Umeå universitet 901 87 Umeå Sweden

Department of Clinical Microbiology Umeå University Biomedicinbyggnaden 6M Umeå universitetssjukhus 901 87 Umeå Sweden

Department of Molecular Biology Umeå University Biomedicinbyggnaden 6K och 6L Umeå universitetssjukhus 901 87 Umeå Sweden

Industrial Doctoral School Umeå University Umeå Sweden

Integrated Science Lab Umeå University Naturvetarhuset Universitetsvägen 901 87 Umeå Sweden

Laboratory for Molecular Infection Medicine Sweden Umeå University Biomedicinbyggnaden 6K och 6L Umeå universitetssjukhus 901 87 Umeå Sweden

Sartorius Corporate Research Östra Strandgatan 24 903 33 Umeå Sweden

Umeå Centre for Microbial Research Universitetstorget 4 901 87 Umeå Sweden

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