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PNAS:拟南芥超级增强子的鉴定及功能验证

已有 798 次阅读 2022-11-23 22:49 |个人分类:每日摘要|系统分类:论文交流

Identification and functional validation of super-enhancers in Arabidopsis thaliana

第一作者Hainan Zhao

第一单位密歇根州立大学

通讯作者Jiming Jiang


 Abstract 

背景回顾Super-enhancers (SEs) are exceptionally large enhancers and are recognized to play prominent roles in cell identity in mammalian species. 


主要发现We surveyed the genomic regions containing large clusters of accessible chromatin regions (ACRs) marked by deoxyribonuclease (DNase) I hypersensitivity in Arabidopsis thaliana


结果1-超级增强子鉴定及特征分析We identified a set of 749 putative SEs, which have a minimum length of 1.5 kilobases and represent the top 2.5% of the largest ACR clusters. We demonstrate that the genomic regions associating with these SEs were more sensitive to DNase I than other nonpromoter ACRs. The SEs were preferentially associated with topologically associating domains. Furthermore, the SEs and their predicted cognate genes were frequently associated with organ development and tissue identity in A. thaliana. Therefore, the A. thaliana SEs and their cognate genes mirror the functional characteristics of those reported in mammalian species. 


结果3-超级增强子的验证We developed CRISPR/Cas-mediated deletion lines of a 3,578-bp SE associated with the thalianol biosynthetic gene cluster (BGC). Small deletions (131–157 bp) within the SE resulted in distinct phenotypic changes and transcriptional repression of all five thalianol genes. In addition, T-DNA insertions in the SE region resulted in transcriptional alteration of all five thalianol genes. 


结论Thus, this SE appears to play a central role in coordinating the operon-like expression pattern of the thalianol BGC.


image.png

A representative SE that spans 6.8 kb and is located between two well-studied TFs (AP2 and SPT) related to flower development.


 摘 要 

超级增强子是一类作用非常强的增强子,在哺乳动物的细胞身份决定方面发挥重要作用。作者通过脱氧核糖核酸酶DNase I调查了拟南芥中包含大段开放染色质区域聚集的基因组区域。作者共鉴定了749个假定的超级增强子,长至少1.5Kb,代表了开放染色质区域集群的top 2.5%。作者发现相比于其它非启动子的开放染色质区域,与这些超级增强子相关的基因组区域对于DNase I的敏感性更强。另外,超级增强子偏向于与拓扑结构域(TAD)相关。此外,超级增强子及其预测靶基因经常与拟南芥的器官发育和组织特性有关。因此,拟南芥超级增强子及其靶基因具有类似于哺乳动物中所报道的功能性特征。作者进一步通过CRISPR/Cas技术敲除了与三萜类化合物生物合成基因簇相关的超级增强子(长3,578 bp)。对于该超级增强子短片段(131–157 bp)的删除会导致不同的表型变化,并且会导致所有的5个三萜类化合物生物合成基因表达被抑制。另外,在该超级增强子上进行T-DNA插入会导致所有的5个三萜类化合物生物合成基因的转录紊乱。因此,这一超级增强子似乎在协调三萜类化合物生物合成基因簇的类操纵子表达模式方面发挥重要作用。




** Jiming Jiang **


个人简介:

1993年,堪萨斯州立大学,博士。


研究方向

1. 植物响应环境胁迫的分子调控机制;

2. 马铃薯遗传改良。 


doi: https://doi.org/10.1073/pnas.221532811


Journal: PNAS

Published date: November 21, 2022


Cite:
Hainan Zhao, Mingyu Yang, Jade Bishop, Yuhan Teng, Yingxue Cao, Brandon D. Beall, Shuanglin Li, Tongxin Liu, Qingxi Fang, Chao Fang, Haoyang Xin, Hans-Wilhelm Nützmann, Anne Osbourn, Fanli Meng, Jiming Jiang. Identification and functional validation of super-enhancers in Arabidopsis thaliana. PNAS, 2022, 119(48): e2215328119. DOI: https://doi.org/10.1073/pnas.2215328119



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