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启动子捕获Hi-C技术鉴定拟南芥中与启动子相关的环和喷泉结构。

Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis.

作者信息

Wang Dingyue, Xiao Suxin, Shu Jiayue, Luo Lingxiao, Yang Minqi, Calonje Myriam, He Hang, Song Baoxing, Zhou Yue

机构信息

State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.

Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC), Avenida Américo Vespucio 49, 41092, Seville, Spain.

出版信息

Genome Biol. 2024 Dec 31;25(1):324. doi: 10.1186/s13059-024-03465-7.

DOI:10.1186/s13059-024-03465-7
PMID:39741350
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11686913/
Abstract

BACKGROUND

Promoters serve as key elements in the regulation of gene transcription. In mammals, loop interactions between promoters and enhancers increase the complexity of the promoter-based regulatory networks. However, the identification of enhancer-promoter or promoter-related loops in Arabidopsis remains incomplete.

RESULTS

Here, we use promoter capture Hi-C to identify promoter-related loops in Arabidopsis, which shows that gene body, proximal promoter, and intergenic regions can interact with promoters, potentially functioning as distal regulatory elements or enhancers. We find that promoter-related loops mainly repress gene transcription and are associated with ordered chromatin structures, such as topologically associating domains and fountains-chromatin structures not previously identified in Arabidopsis. Cohesin binds to the center of fountains and is involved in their formation. Moreover, fountain strength is positively correlated with the number of promoter-related loops, and the maintenance of these loops is linked to H3K4me3. In atxr3 mutants, which lack the major H3K4me3 methyltransferases in Arabidopsis, the number of promoter-related loops at fountains is reduced, leading to upregulation of fountain-regulated genes.

CONCLUSIONS

We identify promoter-related loops associated with ordered chromatin structures and reveal the molecular mechanisms involved in fountain formation and maintenance.

摘要

背景

启动子是基因转录调控的关键元件。在哺乳动物中，启动子与增强子之间的环状相互作用增加了基于启动子的调控网络的复杂性。然而，拟南芥中增强子-启动子或启动子相关环状结构的鉴定仍不完整。

结果

在此，我们使用启动子捕获Hi-C技术鉴定拟南芥中的启动子相关环状结构，结果表明基因体、近端启动子和基因间区域可与启动子相互作用，可能作为远端调控元件或增强子发挥作用。我们发现启动子相关环状结构主要抑制基因转录，并与有序的染色质结构相关，如拓扑相关结构域和喷泉状染色质结构，后者是拟南芥中以前未鉴定出的。黏连蛋白结合在喷泉状结构的中心并参与其形成。此外，喷泉状结构强度与启动子相关环状结构的数量呈正相关，且这些环状结构的维持与H3K4me3有关。在缺乏拟南芥主要H3K4me3甲基转移酶的atxr3突变体中，喷泉状结构处启动子相关环状结构的数量减少，导致喷泉状结构调控基因上调。

结论

我们鉴定了与有序染色质结构相关的启动子相关环状结构，并揭示了喷泉状结构形成和维持所涉及的分子机制。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99cc/11686913/012edeff756d/13059_2024_3465_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99cc/11686913/4175e0ab2776/13059_2024_3465_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99cc/11686913/afaaa76df3b9/13059_2024_3465_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99cc/11686913/785f57c84cbd/13059_2024_3465_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99cc/11686913/e5de1858230a/13059_2024_3465_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99cc/11686913/7472c3b4d639/13059_2024_3465_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99cc/11686913/012edeff756d/13059_2024_3465_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99cc/11686913/4175e0ab2776/13059_2024_3465_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99cc/11686913/afaaa76df3b9/13059_2024_3465_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99cc/11686913/785f57c84cbd/13059_2024_3465_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99cc/11686913/e5de1858230a/13059_2024_3465_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99cc/11686913/7472c3b4d639/13059_2024_3465_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/99cc/11686913/012edeff756d/13059_2024_3465_Fig6_HTML.jpg

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