研究绘制出单细胞分辨率的玉米顺式调控图谱
2021-05-14   阅读:331   来源:细胞

近日,美国佐治亚大学Robert J. Schmitz、Alexandre P. Marand等研究人员合作绘制出单细胞分辨率的玉米顺式调控图谱。这一研究成果于2021年5月7日在线发表在国际学术期刊《细胞》上。

通过六种玉米器官中的单细胞基因组学,研究人员鉴定了顺式和反式调节因子,这些因子定义了不同的细胞身份,并介导了染色体组织。细胞类型特异的顺式调控元件(CRE)富含增强子活性,并在未甲基化的长末端重复逆转录转座子中富集。此外,研究人员发现特定于细胞类型的CRE是表型相关遗传变异的热点,并且在现代玉米育种过程中被选择作为目标,从而突出了这个CRE图谱的生物学意义。

通过比较玉米和拟南芥的发育轨迹,研究人员确定了具有保守和不同染色质动力学的TF和CRE,并显示了基因调控网络的广泛进化。除了这个丰富的数据集外,研究人员还开发了单细胞分析软件Socrates,该软件可用于了解任何物种的顺式调控变异。

据悉,CRE编码时空基因表达程序的基因组蓝图,可实现高度专业化的细胞功能。

附:英文原文

Title: A cis-regulatory atlas in maize at single-cell resolution

Author: Alexandre P. Marand, Zongliang Chen, Andrea Gallavotti, Robert J. Schmitz

Issue&Volume: 2021-05-07

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

DOI: 10.1016/j.cell.2021.04.014

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