@article {Kim2020.10.16.342857, author = {Daniel Kim and Viviana Risca and David Reynolds and James Chappell and Adam Rubin and Namyoung Jung and Laura Donohue and Arwa Kathiria and Minyi Shi and Zhixin Zhao and Harsh Deep and Howard Y. Chang and Michael P. Snyder and William J. Greenleaf and Anshul Kundaje and Paul A. Khavari}, title = {The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation}, elocation-id = {2020.10.16.342857}, year = {2020}, doi = {10.1101/2020.10.16.342857}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Transcription factors (TFs) bind DNA sequence motif vocabularies in cis-regulatory elements (CREs) to modulate chromatin state and gene expression during cell state transitions. A quantitative understanding of how motif lexicons influence dynamic regulatory activity has been elusive due to the combinatorial nature of the cis-regulatory code. To address this, we undertook multi-omic data profiling of chromatin and expression dynamics across epidermal differentiation to identify 40,103 dynamic CREs associated with 3,609 dynamically expressed genes, then applied an interpretable deep learning framework to model the cis-regulatory logic of chromatin accessibility. This identified cooperative DNA sequence rules in dynamic CREs regulating synchronous gene modules with diverse roles in skin differentiation. Massively parallel reporter analysis validated temporal dynamics and cooperative cis-regulatory logic. Variants linked to human polygenic skin disease were enriched in these time-dependent combinatorial motif rules. This integrative approach reveals the combinatorial cis-regulatory lexicon of epidermal differentiation and represents a general framework for deciphering the organizational principles of the cis-regulatory code in dynamic gene regulation.HIGHLIGHTSAn integrative multi-omic resource profiling chromatin and expression dynamics across keratinocyte differentiationPredictive deep learning models of chromatin dynamics reveal a high-resolution cis-regulatory DNA motif lexicon of epidermal differentiationModel interpretation enables discovery of combinatorial cis-regulatory logic of homotypic and heterotypic motif combinationsMassively parallel reporter experiments validate temporal dynamics and cis-regulatory logic of the combinatorial motif lexiconCompeting Interest StatementH.Y.C. is a co-founder of Accent Therapeutics, Boundless Bio, and is an advisor to 10x Genomics, Arsenal Biosciences, and Spring Discovery. M.P.S. is a cofounder and on the advisory board of Personalis, SensOmics, January, Filtricine, Qbio, Protos, Mirive and Nimo. M.P.S. is also on the advisory board of Genapsys and Tailai. W.J.G. is a consultant for 10x Genomics who has licensed IP associated with ATAC-seq. W.J.G. has additional affiliations with Guardant Health (consultant) and Protillion Biosciences (co-founder and consultant). A.K. has affiliations with Biogen (consultant), ImmunAI (SAB), RavelBio (scientific co-founder and SAB).}, URL = {https://www.biorxiv.org/content/early/2020/10/17/2020.10.16.342857}, eprint = {https://www.biorxiv.org/content/early/2020/10/17/2020.10.16.342857.full.pdf}, journal = {bioRxiv} }