Multiscale footprints reveal the organization of cis-regulatory elements
Broad Institute · Harvard University · +4 more institutions
Abstract
. 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 size. Using these multiscale footprints, we created the seq2PRINT framework, which uses 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…
Citation impact
- FWCI
- 28.35
- Percentile
- 100%
- References
- 92
Authors
22- HYHu YanCorresponding
Broad Institute, Harvard University
- MAMax A. Horlbeck
Broad Institute, Boston Children's Hospital, Harvard University
- RZRuochi Zhang
Broad Institute, Harvard University
- SMSai Ma
Broad Institute, Harvard University, Icahn School of Medicine at Mount Sinai
- RSRojesh Shrestha
Broad Institute, Harvard University
Topics & keywords
- Computational biology
- Regulatory science
- Chemistry
- Biology
- Ecology