Identification and functional validation of super-enhancers in Arabidopsis thaliana

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

Research output: Contribution to journalArticlepeer-review

14 Citations (SciVal)


Super-enhancers (SEs) are exceptionally large enhancers and are recognized to play prominent roles in cell identity in mammalian species. We surveyed the genomic regions containing large clusters of accessible chromatin regions (ACRs) marked by deoxyribonuclease (DNase) I hypersensitivity in Arabidopsis thaliana. 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. 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. Thus, this SE appears to play a central role in coordinating the operon-like expression pattern of the thalianol BGC.

Original languageEnglish
Article numbere2215328119
Pages (from-to)e2215328119
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number48
Early online date21 Nov 2022
Publication statusPublished - 29 Nov 2022

Bibliographical note

Funding Information:
ACKNOWLEDGMENTS.F.M.was supported by the National Key R & D Program of China (2021YFF1001202) and the National Natural Science Foundation of China (32172032).J.B.and H.-W.N.were supported by the University of Bath and a Royal Society University Research Fellowship (UF160138).J.J.was supported by NSF grants MCB-1412948 and ISO-2029959 and MSU startup funds. A.O’s lab is supported by the John Innes Foundation and the BBSRC Institute Strategic Programme Grant ‘Molecules from Nature - Products and Pathways (BBS/E/J/00PR9790).

Publisher Copyright:
Copyright © 2022 the Author(s). Published by PNAS.


  • biosynthetic gene cluster
  • CRISPR/Cas
  • enhancer
  • super-enhancer
  • transcriptional regulation

ASJC Scopus subject areas

  • General


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