MED25 connects enhancer–promoter looping and MYC2-dependent activation of jasmonate signalling

Wang, Hang; Li, Shuyu; Li, Yan'an; Xu, Yiran; Wang, Yunhao; Zhang, Ruoxi; Sun, Wenjing; Chen, Qian; Wang, Xiu‐Jie; Li, Chuanyou; Zhao, Jiuhai

doi:10.1038/s41477-019-0441-9

Cited by 97 publications

(79 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In Arabidopsis (Arabidopsis thaliana), JA triggers a genome-wide transcriptional program that is largely regulated by MYC2 (Boter et al, 2004;Lorenzo et al, 2004;Dombrecht et al, 2007;Fernández-Calvo et al, 2011;Kazan and Manners, 2013;Zhai et al, 2013;Chini et al, 2016;Zhai et al, 2017). The activity of this master transcription factor depends on its physical and functional interactions with MED25, a subunit of the plant Mediator transcriptional coactivator complex (Çevik et al, 2012;Chen et al, 2012;An et al, 2017;Zhai et al, 2018;Wang et al, 2019). At the resting stage, a group of JASMONATE ZIM-DOMAIN (JAZ) proteins physically interact with MYC2, thereby repressing the expression of JA-responsive genes (Chini et al, 2007;Thines et al, 2007;Yan et al, 2007;Pauwels et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Mediator Subunit MED25 Couples Alternative Splicing of JAZ Genes with Fine-Tuning of Jasmonate Signaling

Deng

Zhai

et al. 2019

Plant Cell

Self Cite

View full text Add to dashboard Cite

JASMONATE ZIM-DOMAIN (JAZ) transcriptional repressors are key regulators of jasmonate (JA) signaling in plants. At the resting stage, the C-terminal Jas motifs of JAZ proteins bind the transcription factor MYC2 to repress JA signaling. Upon hormone elicitation, the Jas motif binds the hormone receptor CORONATINE INSENSITIVE1, which mediates proteasomal degradation of JAZs and thereby allowing the Mediator subunit MED25 to activate MYC2. Subsequently, plants desensitize JA signaling by feedback generation of dominant JAZ splice variants that repress MYC2. Here we report the mechanistic function of Arabidopsis (Arabidopsis thaliana) MED25 in regulating the alternative splicing of JAZ genes through recruiting the splicing factors PRE-mRNA-PROCESSING PROTEIN 39a (PRP39a) and PRP40a. We demonstrate that JA-induced generation of JAZ splice variants depends on MED25 and that MED25 recruits PRP39a and PRP40a to promote the full splicing of JAZ genes. Therefore, MED25 forms a module with PRP39a and PRP40a to prevent excessive desensitization of JA signaling mediated by JAZ splice variants.

show abstract

Section: Introductionmentioning

confidence: 99%

Mediator Subunit MED25 Couples Alternative Splicing of JAZ Genes with Fine-Tuning of Jasmonate Signaling

Deng

Zhai

et al. 2019

Plant Cell

Self Cite

View full text Add to dashboard Cite

show abstract

“…1b, lower panel). The association of transcription regulators with both TSS and TTS was also observed in ChIP-seq analyses of WRKY (Birkenbihl et al, 2017) and Myelocytomatosis 2 (MYC2) (Wang et al, 2019) TFs. Thus, we concluded that the TPR1-chromatin association profile generally resembles binding profiles of TFs.…”

Section: Resultsmentioning

confidence: 72%

Genome-wide chromatin binding of transcriptional corepressor Topless-related 1 inArabidopsis

Griebel

Lapin

Kracher

et al. 2020

Preprint

View full text Add to dashboard Cite

1 Timely and specific regulation of gene expression is critical for plant responses to 2 environmental and developmental cues. Transcriptional coregulators have emerged 3 as important factors in gene expression control, although they lack DNA-binding 4 domains and the mechanisms by which they are recruited to and function at the 5 chromatin are poorly understood. Plant Topless-related 1 (TPR1), belonging to a 6 family of transcriptional corepressors found across eukaryotes, contributes to 7 immunity signaling in Arabidopsis thaliana and wild tobacco. We performed 8 chromatin immunoprecipitation and sequencing (ChIP-seq) on an Arabidopsis TPR1-9 GFP expressing transgenic line to characterize genome-wide TPR1-chromatin 10 associations. The analysis revealed ~1400 genes bound by TPR1, with the majority 11 of binding sites located at gene upstream regions. Among the TPR1 bound genes, 12 we find not only regulators of immunity but also genes controlling growth and 13 development. To support further analysis of TPR1-chromatin complexes and other 14 transcriptional corepressors in plants, we provide two ways to access the processed 15 ChIP-seq data and enable their broader use by the research community.16 17 Plant materials and growth conditions 121 Stable transgenic lines pTPR1:TPR1-GFP Col-0 (TPR-GFP) and pTPR1:TPR1-HA 122 #3 Col-0 (TPR1-HA) were described previously (Zhu et al., 2010). Plants were grown 123 on soil with a daily 10 h light period (150-200 µE/m 2 s) at 22 °C and 60 % relative 124 humidity. Plant leaf material was harvested after 6 weeks of growth. 125 126 Chromatin immunoprecipitation assays and sequencing (ChIP-seq) 127 ChIP was performed on 2 g leaf tissues of 6-week-old plants according to Gendrel et 128 al. (2005) with modifications (Birkenbihl et al., 2012). Leaf samples were cross-linked 129 twice by infiltration with 1% formaldehyde under a vacuum for 2x 7.5 minutes. Nuclei 130 were disrupted by sonication 10 times for 30 s each and 30 s of cooling in a 131 Bioruptor (Diagenode). IPs were performed using α-GFP (Ab6556, Abcam) 132 antibodies and Protein A agarose beads (Sigma). After elution of immune 133 complexes, cross-linking was reversed with an overnight incubation at 65°C in 134 200 mM NaCl followed by proteinase K digestion. DNA was extracted with phenol-135 chloroform and precipitated with ethanol in the presence of 0.3 M sodium acetate 136 (pH=5.2) and 10 µg/mL glycogen (overnight at -20°C). After centrifugation, DNA 137 pellets were washed with 70% ethanol, air-dried and resuspended in water before 138 PCR. MiniElute PCR Purification Kit (Qiagen, Germany) was used for cleaning ChIP 139 DNA and two rounds of in vitro transcription by T7 RNA polymerase followed 140 according to a linear DNA amplification (LinDA) protocol (Shankaranarayanan et al.

show abstract

“…Reprogramming of the epigenome is an integral part of development and environmental stimulus-induced gene expression (Feng et al, 2010, Xiao et al, 2017). For example, activation of the transcriptional JA response requires the formation of MYC2/MED25-mediated chromatin looping (Wang et al, 2019). To investigate the extent of JA-induced changes in chromatin architecture and the regulatory importance of MYC2 in this response, we conducted ChIP-seq assays to profile the genome wide occupancy of the histone modification H3K4me3 and the histone variant H2A.Z in untreated/JA-treated (4 h) Col-0 and myc2 seedlings.…”

Section: Resultsmentioning

confidence: 99%

Integrated Multi-omic Framework of the Plant Response to Jasmonic Acid

Zander

Lewsey

Clark

et al. 2019

Preprint

View full text Add to dashboard Cite

27Understanding the systems-level actions of transcriptional responses to hormones provides 28 insight into how the genome is reprogrammed in response to environmental stimuli. Here, we 29 investigate the signaling pathway of the hormone jasmonic acid (JA), which controls a plethora of 30 critically important processes in plants and is orchestrated by the transcription factor MYC2 and 31 its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the 32 response to JA that spans from the activity of master and secondary-regulatory transcription 33 factors, through gene expression outputs and alternative splicing to protein abundance changes, 34 protein phosphorylation and chromatin remodeling. We integrated time series transcriptome 35 analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These 36 enable us to predict previously unknown points of crosstalk from JA to other signaling pathways 37 and to identify new components of the JA regulatory mechanism, which we validated through 38 targeted mutant analysis. These results provide a comprehensive understanding of how a plant 39 hormone remodels cellular functions and plant behavior, the general principles of which provide 40 a framework for analysis of cross-regulation between other hormone and stress signaling 41 pathways. 42 43 44 45 46 47 48 49 50 51 52 5 2004, Fernandez-Calvo et al. , 2011). myc3 and myc4 single mutants behave like wildtype with 104 regards to JA-induced root growth inhibition. However, in combination with the myc2 mutant, 105 myc2 myc3 double mutants exhibit an increased JA hyposensitivity, almost as pronounced as in 106 myc2 myc3 myc4 triple mutants (Fernandez-Calvo et al., 2011). We consequently selected MYC3 107 for an in-depth analysis. 108In order to better understand how the master TFs MYC2 and MYC3 control the JA-109 induced transcriptional cascade, we determined their genome-wide binding sites using chromatin 110 immunoprecipitation sequencing (ChIP-seq). Four biological replicates of JA-treated (2 hours) 111 three-day-old etiolated Arabidopsis seedlings that express a native promoter-driven and epitope 112 (YPet)-tagged version of MYC2 and three biological replicates of MYC3 (Col-0 MYC2::MYC2-113 Ypet, Col-0 MYC3::MYC3-Ypet) were used (Gimenez-Ibanez et al., 2017). The genome-wide 114distributions of MYC2 and MYC3 binding sites were highly similar (Fig. 1c, d). We identified 6,736 115 MYC2 and 3,982 MYC3 binding sites of high confidence, equating to 6,178 MYC2 and 4,092

show abstract

MED25 connects enhancer–promoter looping and MYC2-dependent activation of jasmonate signalling

Cited by 97 publications

References 47 publications

Mediator Subunit MED25 Couples Alternative Splicing of JAZ Genes with Fine-Tuning of Jasmonate Signaling

Mediator Subunit MED25 Couples Alternative Splicing of JAZ Genes with Fine-Tuning of Jasmonate Signaling

Genome-wide chromatin binding of transcriptional corepressor Topless-related 1 inArabidopsis

Integrated Multi-omic Framework of the Plant Response to Jasmonic Acid

Contact Info

Product

Resources

About