The characterization of Mediator 12 and 13 as conditional positive gene regulators in Arabidopsis

Liu, Qikun; Bischof, Sylvain; Harris, C. Jake; Zhong, Zhenhui; Zhan, Lingyu; Nguyen, Calvin; Rashoff, Andrew Q.; Barshop, William D.; Sun, Fei; Feng, Suhua; Potok, Magdalena E.; Gallego-Bartolomé, Javier; Zhai, Jixian; Wohlschlegel, James A.; Carey, Michael; Long, Jeffrey A.; Jacobsen, Steven E.

doi:10.1038/s41467-020-16651-5

Cited by 27 publications

(31 citation statements)

References 71 publications

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“…Therefore, it is possible that the termination of Pol II elongation at − 60 nt is caused by a unique chromatin status at the tRNA gene promoter. To test this scenario, we analyzed published data of MNase-seq [ 61 ], ChIP-seq (H3K4me3, H3K36me3, H3K27me3, H3K9me2) [ 62 ], and the CG, CHG, and CHH DNA methylation level to check the chromatin status at the two tRNA loci showed in Fig. 4 , including nucleosome positioning, histone modification, and DNA methylation (Additional file 1 , Fig.…”

Section: Resultsmentioning

confidence: 99%

Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing

Liu

Hong

et al. 2021

Genome Biol

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Background The dynamic process of transcription termination produces transient RNA intermediates that are difficult to distinguish from each other via short-read sequencing methods. Results Here, we use single-molecule nascent RNA sequencing to characterize the various forms of transient RNAs during termination at genome-wide scale in wildtype Arabidopsis and in atxrn3, fpa, and met1 mutants. Our data reveal a wide range of termination windows among genes, ranging from ~ 50 nt to over 1000 nt. We also observe efficient termination before downstream tRNA genes, suggesting that chromatin structure around the promoter region of tRNA genes may block pol II elongation. 5′ Cleaved readthrough transcription in atxrn3 with delayed termination can run into downstream genes to produce normally spliced and polyadenylated mRNAs in the absence of their own transcription initiation. Consistent with previous reports, we also observe long chimeric transcripts with cryptic splicing in fpa mutant; but loss of CG DNA methylation has no obvious impact on termination in the met1 mutant. Conclusions Our method is applicable to establish a comprehensive termination landscape in a broad range of species.

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Section: Resultsmentioning

confidence: 99%

Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing

Liu

Hong

et al. 2021

Genome Biol

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“…Analyses of loss-of-function mutants in Mediator subunits revealed that the plant Mediator complex regulates transcription in a specific manner. Whereas the Mediator subunits might not be all required for general gene transcription, they are implicated in the control of various pathways (Kidd et al, 2009;Elfving et al, 2011;Hemsley et al, 2014;Ruiz-Aguilar et al, 2020;Liu et al, 2020). So far, Mediator subunits have been reported to play roles in organ and tissue development, hormone signaling, flowering transition, immune response, and abiotic stresses (Kidd et al, 2009;Wang et al, 2011;Bendía-Monreal and Gillmor, 2016;Crawford et al, 2020;Zhu et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

TheArabidopsismediator complex subunit 8 regulates oxidative stress responses

Denecker

Kelen

et al. 2021

The Plant Cell

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Signaling events triggered by hydrogen peroxide (H2O2) regulate plant growth and defense by orchestrating a genome-wide transcriptional reprogramming. However, the specific mechanisms that govern H2O2-dependent gene expression are still poorly understood. Here we identify the Arabidopsis Mediator complex subunit MED8 as a regulator of H2O2 responses. The introduction of the med8 mutation in a constitutive oxidative stress genetic background (catalase-deficient, cat2) was associated with enhanced activation of the salicylic acid pathway and accelerated cell death. Interestingly, med8 seedlings were more tolerant to oxidative stress generated by the herbicide methyl viologen and exhibited transcriptional hyperactivation of defense signaling, in particular salicylic acid- and jasmonic acid-related pathways. The med8-triggered tolerance to methyl viologen was manipulated by introduction of secondary mutations in salicylic acid and jasmonic acid pathways. In addition, analysis of the Mediator interactome revealed interactions with components involved in mRNA processing and microRNA biogenesis, hence expanding the role of Mediator beyond transcription. Notably, MED8 interacted with the transcriptional regulator NEGATIVE ON TATA-LESS, NOT2, to control the expression of H2O2-inducible genes and stress responses. Our work establishes MED8 as a component regulating oxidative stress responses and demonstrates that it acts as a negative regulator of H2O2 -driven activation of defense gene expression.

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“…S15 ). To further test the hypothesis that up-regulation of ATXR6 expression may be sufficient to suppress the atxr5/6 phenotype, we crossed atxr5/6 (W) with mediator12 ( med12 ) ( 23 ), which has pleiotropic effects on gene expression. Loss of MEDIATOR12 increased ATXR6 expression and suppressed the TE up-regulation and extra DNA phenotypes of atxr5/6 (W) ( SI Appendix , Fig.…”

Section: Resultsmentioning

confidence: 99%

The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis

Potok

Zhong

Picard

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis. Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements (TEs), chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. How loss of ATXR5/6 and H3K27me1 leads to these phenotypes remains unclear. Here we provide extensive characterization of the atxr5/6 hypomorphic mutant by comprehensively examining gene expression and epigenetic changes in the mutant. We found that the tissue-specific phenotypes of TE derepression and excessive DNA in this atxr5/6 mutant correlated with residual ATXR6 expression from the hypomorphic ATXR6 allele. However, up-regulation of DNA damage genes occurred regardless of ATXR6 levels and thus appears to be a separable process. We also isolated an atxr6-null allele which showed that ATXR5 and ATXR6 are required for female germline development. Finally, we characterize three previously reported suppressors of the hypomorphic atxr5/6 mutant and show that these rescue atxr5/6 via distinct mechanisms, two of which involve increasing H3K27me1 levels.

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The characterization of Mediator 12 and 13 as conditional positive gene regulators in Arabidopsis

Cited by 27 publications

References 71 publications

Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing

Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing

TheArabidopsismediator complex subunit 8 regulates oxidative stress responses

The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis

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