Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [in vitro footprinting]
Cis-regulatory elements (CREs) control gene expression and are dynamic in their structure and function, reflecting changes to the composition of diverse effector proteins over time. However, methods for measuring the organization of effector proteins at CREs across the genome are limited, hampering efforts to connect CRE structure to their function in cell fate and disease. Here, we developed PRINT, a computational method that identifies footprints of DNA-protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein sizes. Using these multi-scale footprints, we created the seq2PRINT framework, which employs deep-learning to allow precise inference of transcription factor and nucleosome binding and interprets regulatory logic at CREs. Applying seq2PRINT to single-cell chromatin accessibility data from human bone marrow, we observe sequential establishment and widening of CREs centered on pioneer factors across hematopoiesis. We further discover age-associated alterations in the structure of CREs in murine hematopoietic stem cells, including widespread loss of nucleosomes and gain of de novo-identified Ets composite motifs. Collectively, we establish a method for obtaining rich insights into DNA-binding protein dynamics from chromatin accessibility data and reveal the architecture of regulatory elements across differentiation and aging. Overall design: Bacterial artificial chromosome DNA was tagmented by Tn5 in the presence or absence of purified recombinant TF.