Stergachis, A. B., Debo, B. M., Haugen, E., Churchman, L. S. & Stamatoyannopoulos, J. A. Single-molecule regulatory architectures captured by chromatin fiber sequencing. Science 368, 1449–1454 (2020).
Google Scholar
Bohaczuk, S. C. et al. Resolving the chromatin impact of mosaic variants with targeted Fiber-seq. Genome Research 34, 2269–2278 (2024).
Google Scholar
Battaglia, S. et al. Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements. Nat. Genet. 54, 1504–1513 (2022).
Google Scholar
Abdulhay, N. J. et al. Massively multiplex single-molecule oligonucleosome footprinting. Elife 9, 1–23 (2020).
Google Scholar
Lee, I. et al. Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing. Nat. Methods 17, 1191–1199 (2020).
Google Scholar
Krebs, A. R. et al. Genome-wide single-molecule footprinting reveals high RNA polymerase II turnover at paused promoters. Mol. Cell 67, 411–422 (2017).
Google Scholar
Shipony, Z. et al. Long-range single-molecule mapping of chromatin accessibility in eukaryotes. Nat. Methods 17, 319–327 (2020).
Google Scholar
Buenrostro, J. D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486–490 (2015).
Google Scholar
Cusanovich, D. A. et al. Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. Science 348, 910–914 (2015).
Google Scholar
He, R. et al. Genome-wide single-cell and single-molecule footprinting of transcription factors with deaminase. Proc. Natl Acad. Sci. USA 121, e2423270121 (2024).
Google Scholar
Yu, T. et al. Deaminase-mediated chromatin accessibility profiling with single-allele resolution. Preprint at bioRxiv https://doi.org/10.1101/2024.12.17.628768 (2024).
Mok, B. Y. et al. A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing. Nature 583, 631–637 (2020).
Google Scholar
Mi, L. et al. DddA homolog search and engineering expand sequence compatibility of mitochondrial base editing. Nat. Commun. 14, 874 (2023).
Google Scholar
Yin, L., Shi, K. & Aihara, H. Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA. Nat. Struct. Mol. Biol. 30, 1153–1159 (2023).
Google Scholar
Mok, B. Y. et al. CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA. Nat. Biotechnol. 40, 1378–1387 (2022).
Google Scholar
Guo, J. et al. A DddA ortholog-based and transactivator-assisted nuclear and mitochondrial cytosine base editors with expanded target compatibility. Mol. Cell 83, 1710–1724 (2023).
Google Scholar
Huang, J. et al. Discovery of deaminase functions by structure-based protein clustering. Cell 186, 3182–3195 (2023).
Google Scholar
Roh, H. et al. Coupling CRISPR scanning with targeted chromatin accessibility profiling using a double-stranded DNA deaminase. Nat. Methods 22, 2083–2093 (2025).
Google Scholar
Kelly, T. K. et al. Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res. 22, 2497–2506 (2012).
Google Scholar
Bintu, L. et al. Transcriptional regulation by the numbers: models. Curr. Opin. Genet. Dev. 15, 116–124 (2005).
Google Scholar
Sherman, M. S. & Cohen, B. A. Thermodynamic state ensemble models of cis-regulation. PLoS Comput. Biol. 8, e1002407 (2012).
Google Scholar
Grasberger, H. et al. STR mutations on chromosome 15q cause thyrotropin resistance by activating a primate-specific enhancer of MIR7-2/MIR1179. Nat. Genet. 56, 877–888 (2024).
Google Scholar
Bernardini, A. et al. The USR domain of USF1 mediates NF-Y interactions and cooperative DNA binding. Int. J. Biol. Macromol. 193, 401–413 (2021).
Google Scholar
Ito, Y., Zhang, Y., Dangaria, S., Luan, X. & Diekwisch, T. G. H. NF-Y and USF1 transcription factor binding to CCAAT-box and E-box elements activates the CP27 promoter. Gene 473, 92–99 (2011).
Google Scholar
Zhu, J., Giannola, D. M., Zhang, Y., Rivera, A. J. & Emerson, S. G. NF-Y cooperates with USF1/2 to induce the hematopoietic expression of HOXB4. Blood 102, 2420–2427 (2003).
Google Scholar
Vollger, M. R. et al. A haplotype-resolved view of human gene regulation. Preprint at bioRxiv https://doi.org/10.1101/2024.06.14.599122 (2024).
Zalusky, M. P. et al. 3-hour genome sequencing and targeted analysis to rapidly assess genetic risk. Genet. Med. Open 2, 101833 (2024).
Google Scholar
Aguet, F. et al. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 369, 1318–1330 (2020).
Google Scholar
Rautiainen, M. et al. Telomere-to-telomere assembly of diploid chromosomes with Verkko. Nat. Biotechnol. https://doi.org/10.1038/S41587-023-01662-6 (2023).
Gonzalez-Pena, V. et al. Accurate genomic variant detection in single cells with primary template-directed amplification. Proc. Natl Acad. Sci. USA 118, e2024176118 (2021).
Google Scholar
Jarvis, E. D. et al. Semi-automated assembly of high-quality diploid human reference genomes. Nature 611, 519–531 (2022).
Google Scholar
Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170–175 (2021).
Google Scholar
Porubsky, D. et al. Human de novo mutation rates from a four-generation pedigree reference. Nature 643, 427–436 (2025).
Google Scholar
Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).
Google Scholar
Cremer, T. & Cremer, C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat. Rev. Genet. 2, 292–301 (2001).
Google Scholar
Monahan, K. et al. Role of CCCTC binding factor (CTCF) and cohesin in the generation of single-cell diversity of protocadherin-α gene expression. Proc. Natl Acad. Sci. USA 109, 9125–9130 (2012).
Google Scholar
Rao, S. S. P. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680 (2014).
Google Scholar
Guo, Y. et al. CRISPR inversion of CTCF sites alters genome topology and enhancer/promoter function. Cell 162, 900–910 (2015).
Google Scholar
ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
Google Scholar
Grubert, F. et al. Landscape of cohesin-mediated chromatin loops in the human genome. Nature 583, 737–743 (2020).
Google Scholar
Dixon, J. R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380 (2012).
Google Scholar
Dixit, A. et al. Perturb-seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens. Cell 167, 1853–1866 (2016).
Google Scholar
Gilbert, L. A. et al. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159, 647–661 (2014).
Google Scholar
Kennedy, S. R. et al. Detecting ultralow-frequency mutations by Duplex Sequencing. Nat. Protoc. 9, 2586–2606 (2014).
Google Scholar
Vogelstein, B. & Kinzler, K. W. Digital PCR. Proc. Natl Acad. Sci. USA 96, 9236–9241 (1999).
Google Scholar
Muyas, F. et al. De novo detection of somatic mutations in high-throughput single-cell profiling data sets. Nat. Biotechnol. 42, 758–767 (2024).
Google Scholar
Dou, J. et al. Single-nucleotide variant calling in single-cell sequencing data with Monopogen. Nat. Biotechnol. 42, 803–812 (2024).
Google Scholar
Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190–1195 (2012).
Google Scholar
Cheng, Y. H. H., Bohaczuk, S. C. & Stergachis, A. B. Functional categorization of gene regulatory variants that cause Mendelian conditions. Hum. Genet. 143, 559–605 (2024).
Google Scholar
Kong, Y. et al. Critical assessment of DNA adenine methylation in eukaryotes using quantitative deconvolution. Science https://doi.org/10.1126/science.abe7489 (2022).
Jha, A. et al. DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools. Genome Res. https://doi.org/10.1101/gr.279095.124 (2024).
Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience https://doi.org/10.1093/gigascience/giab008 (2021).
Tareen, A. & Kinney, J. B. Logomaker: beautiful sequence logos in Python. Bioinformatics 36, 2272–2274 (2020).
Google Scholar
Grant, C. E., Bailey, T. L. & Noble, W. S. FIMO: scanning for occurrences of a given motif. Bioinformatics 27, 1017–1018 (2011).
Google Scholar
Castro-Mondragon, J. A. et al. JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 50, D165–D173 (2022).
Google Scholar
Neph, S. et al. BEDOPS: high-performance genomic feature operations. Bioinformatics 28, 1919–1920 (2012).
Google Scholar
Martin, M. et al. WhatsHap: fast and accurate read-based phasing. Preprint at bioRxiv https://doi.org/10.1101/085050 (2016).
ENCODE Project Consortium et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 583, 699–710 (2020).
Google Scholar
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
Google Scholar
Swanson, E. G. et al. StergachisLab/DAF-seq-Manuscript. Source code. Zenodo https://doi.org/10.5281/zenodo.14563107 (2025).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Google Scholar
Yin, M. et al. Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites. Cell Res. 27, 1365–1377 (2017).
Google Scholar
