背景回顾：cis-regulatory elements (CREs) encode the genomic blueprints of spatiotemporal gene expression programs enabling highly specialized cell functions. 

主要研究：Using single-cell genomics in six maizeorgans, 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. 

结果1-CREs在基因组特定区域的富集：Cell-type-specific CREs were enriched for enhancer activity and within unmethylated long terminal repeat retrotransposons. 

结果2-表型变异相关热点与人工选择：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. 

结果3-玉米和拟南芥的比较：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. 

结果4-软件开发：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.

 摘 要 

顺式调控元件（CREs）编码时空基因表达程序的基因组蓝图，从而实现高度特化的细胞功能。基于对六种玉米器官的单细胞基因组测序，作者通过转录因子结合图谱鉴定了决定各种细胞类型和协调染色质组织的顺式和反式调控因子，发现了具有非细胞自主性活性的TFs，并且揭示了作用于高阶染色质互作的TFs。细胞类型特异性CREs富集于具有增强子活性和非甲基化长末端重复序列逆转录转座子区域。此外，作者还发现细胞类型特异性CREs是表型相关遗传变异的热点区，并且在现代玉米的育种过程中受到选择，表明了CRE图谱具有非常重要的生物学意义。通过比较玉米和拟南芥的发育轨迹，作者鉴定了二者之间具有分化和保守染色质动态的CREs，展示了基因调控网络的广泛演化。除了提供了玉米宝贵的数据，作者还开发了单细胞分析软件Socrates，可以用于任意物种的顺式调控原件变异的检测与鉴定。