DeChIC-seq establishes a conversion-based framework for chromatin profiling that enables mechanistic dissection of TF-driven gene regulation across rare cells, developmental systems, and disease contexts.
Fiber-seq simultaneously profiles chromatin accessibility, DNA methylation, protein footprints, and genetic variation on single molecules at near—base-pair resolution, revealing how genetic and epigenetic features interact to regulate gene expression and provides a powerful new framework for dissecting immune cell func...
Emily A. Madden, James T. Anderson, M. Cowles et al.· Journal of Immunology· 0 citations
SCIENCE-seq is presented, a multimodal single-cell interactomics platform enabling simultaneous detection of RNA–RNA interactions and chromatin DNA–DNA contacts within individual cells and identifies a glioma-specific trans-chromosomal HOX hub driven by five interacting lncRNAs.
Evgeny Deforzh, Yanhong Zhang, H. Mnatsakanyan et al.· bioRxiv· 0 citations
An integrated single-molecule view of regulatory remodeling may support identification of adaptive resistance mechanisms, compensatory regulatory programs, pharmacodynamic biomarkers, and candidate synthetic lethal interactions relevant to epigenetic drug development.
Keith E. Maier, James T. Anderson, Connor P. Frasier et al.· Clinical Cancer Research· 0 citations
A large-scale scATAC-seq resource that substantially improves immune cell annotation and regulatory inference and provides an unprecedented reference for immune cell gene regulatory circuits and a valuable resource for exploring the epigenome of human immune cells is presented.
Sydney Kuhl, Upaasana Krishnan, Andreas Tjaernberg et al.· Journal of Immunology· 0 citations
The results indicate that G-quadruplex-prone sequences represent a common genomic feature associated with a number of human transcription factors and chromatin-associated regulatory proteins and support a model in which G4-rich regions act as selective regulatory scaffolds shaping transcription factor occupancy and gen...
Karolína Drápalová, Michaela Dobrovolná, Filip Kledus et al.· BMC Genomics· 0 citations
A comparative overview of major PDI technologies organized according to the biological scale at which they operate is provided, including sequence- and chromatin-based binding prediction, multi-omics integration, and regulatory network inference.