A cis-regulatory atlas in maize at single-cell resolution.

Cell
Alexandre P MarandRobert J Schmitz

Abstract

cis-regulatory elements (CREs) encode the genomic blueprints of spatiotemporal gene expression programs enabling highly specialized cell functions. Using single-cell genomics in six maize organs, we determined the cis- and trans-regulatory factors defining diverse cell identities and coordinating chromatin organization by profiling transcription factor (TF) combinatorics, identifying TFs with non-cell-autonomous activity, and uncovering TFs underlying higher-order chromatin interactions. Cell-type-specific CREs were enriched for enhancer activity and within unmethylated long terminal repeat retrotransposons. Moreover, we found cell-type-specific CREs are hotspots for phenotype-associated genetic variants and were targeted by selection during modern maize breeding, highlighting the biological implications of this CRE atlas. Through comparison of maize and Arabidopsis thaliana developmental trajectories, we identified TFs and CREs with conserved and divergent chromatin dynamics, showcasing extensive evolution of gene regulatory networks. In addition to this rich dataset, we developed single-cell analysis software, Socrates, which can be used to understand cis-regulatory variation in any species.

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Citations

Jun 5, 2021·Nature Plants·Tobias JoresChristine Queitsch
May 22, 2021·Journal of Experimental Botany·Rachel ShahanPhilip N Benfey
Jun 12, 2021·Current Opinion in Plant Biology·Abbas ShojaeeShao-Shan Carol Huang
Aug 5, 2021·Current Opinion in Biotechnology·Peter A CrispLee T Hickey
Aug 14, 2021·Communications Biology·Benjamin ColeDiane E Dickel
Aug 15, 2021·Current Opinion in Plant Biology·Alexandre P Marand, Robert J Schmitz
Aug 26, 2021·STAR Protocols·Alexandre P MarandRobert J Schmitz
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Sep 18, 2021·Annual Review of Genetics·Kook Hui RyuJohn Schiefelbein
Aug 12, 2021··Xuan ZhangPedro Augusto Braga dos Reis

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