<i>Arabidopsis</i>Topless-related 1 mitigates physiological damage and growth penalties of induced immunity

Griebel, Thomas; Lapin, Dmitry; Locci, Federica; Kracher, Barbara; Bautor, Jaqueline; Qiu, Jianhui; Concia, Lorenzo; Benhamed, Moussa; Parker, JE

doi:10.1101/2021.07.07.451397

Cited by 4 publications

(5 citation statements)

References 97 publications

(187 reference statements)

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“…This indicates that MORC7A peaks are associated with TF binding sites. We also re-analyzed three factors in particular because published ChIP-seq data was available, PIF4 [19], ARF6 [20], and TPR1 [21]. Metaplot analysis showed that with ChIP-seq data for MORC7A-unique, MORC7B-unique, MORC7-Pol V Common, and Pol V-unique regions showed the strongest co-localization with MORC7A (Fig.…”

Section: Resultsmentioning

confidence: 99%

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MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions

Zhong

Xue

Harris

et al. 2022

Preprint

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Background: The Microrchidia (MORC) proteins are a family of evolutionarily conserved GHKL-type ATPases involved in chromatin compaction and gene silencing. Arabidopsis MORC proteins act in the RNA-directed DNA methylation (RdDM) pathway, where they act as molecular tethers to ensure the efficient establishment of RdDM and de novo gene silencing. However, MORC proteins also have RdDM-independent functions; although, their underlying mechanisms are unknown. Results: In this study, we examined regions of MORC binding where RdDM does not occur in order to shed light on the RdDM-independent functions of MORC proteins. We found that MORC proteins compact chromatin and reduce DNA accessibility to transcription factors (TFs), thereby repressing gene expression. We also found that MORC-mediated repression of gene expression was particularly important under conditions of stress. We showed that MORC proteins regulate TFs through either direct or indirect interactions, and these TFs can in some cases regulate their own transcription, resulting in feedforward loops. Conclusions: Our findings provide insights into the molecular mechanisms of MORC-mediated chromatin compaction and transcription regulation.

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Section: Resultsmentioning

confidence: 99%

“…Metaplot of ARF6 ChIP-seq data [20] over MORC7A-unique, MORC7B-unique, MORC7-Pol V Common, and Pol V-unique regions. Metaplot of TPR1 ChIP-seq data [21] over MORC7A-unique, MORC7B-unique, MORC7-Pol V Common, and Pol V-unique regions. c .…”

Section: Supplementary Figuresmentioning

confidence: 99%

MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions

Zhong

Xue

Harris

et al. 2022

Preprint

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“…As gene expression coregulators, TPL/TPRs have many downstream targets (33). To further confirm the possibility that FER regulates gene expression by interacting with TPL/TPRs, we performed TF enrichment analysis in the iGRN and PlantTFBD databases (see Materials and Methods).…”

Section: Resultsmentioning

confidence: 99%

“…Therefore, certain DEGs in the low-differentiation cells from the WT and fer-4 were likely regulated by TPL/TPRs. We also analyzed the transcriptomic overlap of fer-4 (36) and tpltpr1tpr4 (33). In total, 1908 overlapping genes among the DEGs of tpltpr1tpr4 and fer-4 were identified (Fig S6C).…”

Section: Resultsmentioning

confidence: 99%

Wounding promotes root regeneration through a cell wall integrity sensor, the receptor kinase FERONIA

Xie

Chen

et al. 2022

Preprint

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Wounding caused by various stresses is the initial event of plant regeneration. However, the mechanisms underlying the early wounding responses to promote plant regeneration remain largely unknown. Here, we report that the receptor kinase FERONIA (FER) interacts with Topless/Topless-related proteins (TPL/TPRs) to regulate the expression of regeneration-related genes to modulate root tip regeneration. One ligand of FER, rapid alkalinization factor 33 (RALF33), is stimulated by wounding and functions together with FER to promote regeneration. Single-cell sequencing data showed that the low-differentiation cell types in the stele may account for the enhanced regeneration ability in the fer mutant, especially in the columella and quiescent center (QC). Further interaction assays and analysis of the gene expression patterns in low-differentiation cell types confirmed that FER interacts with TPL/TPRs to regulate the expression of downstream regeneration-related genes. One of their downstream targets, an essential transcription factor (TF) in root regeneration, ERF115, acts downstream of FER-TPL/TPRs to control regeneration. Our results suggested a signaling pathway between the early wounding response and regeneration processes in roots.One-sentence summaryRALF33-FER serves as an early signaling module between wounding and regeneration by functioning with TPL/TPRs in roots.

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“…A D S 3 / F A D 5 e n c o d e s p l a s t i d i c p a l m i t o y lmonogalactosyldiacylglycerol D7 desaturase, which is responsible for the synthesis of 16:1 fatty acid from galactolipids and sulfolipids (Smith et al, 2013). WSIP2 is involved in physiological damage and plant immunity (Griebel et al, 2023). It is thus clear that the regulation of the formation of branching angles in rapeseed is complicated.…”

Section: Discussionmentioning

confidence: 99%

Identification of a major QTL and candidate genes analysis for branch angle in rapeseed (Brassica napus L.) using QTL-seq and RNA-seq

Lei,

Chen,

Liang

et al. 2024

Front. Plant Sci.

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IntroductionBranching angle is an essential trait in determining the planting density of rapeseed (Brassica napus L.) and hence the yield per unit area. However, the mechanism of branching angle formation in rapeseed is not well understood.MethodsIn this study, two rapeseed germplasm with extreme branching angles were used to construct an F2 segregating population; then bulked segregant analysis sequencing (BSA-seq) and quantitative trait loci (QTL) mapping were utilized to localize branching anglerelated loci and combined with transcriptome sequencing (RNA-seq) and quantitative real-time PCR (qPCR) for candidate gene miningResults and discussionA branching angle-associated quantitative trait loci (QTL) was mapped on chromosome C3 (C3: 1.54-2.65 Mb) by combining BSA-seq as well as traditional QTL mapping. A total of 54 genes had SNP/Indel variants within the QTL interval were identified. Further, RNA-seq of the two parents revealed that 12 of the 54 genes were differentially expressed between the two parents. Finally, we further validated the differentially expressed genes using qPCR and found that six of them presented consistent differential expression in all small branching angle samples and large branching angles, and thus were considered as candidate genes related to branching angles in rapeseed. Our results introduce new candidate genes for the regulation of branching angle formation in rapeseed, and provide an important reference for the subsequent exploration of its formation mechanism.

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ArabidopsisTopless-related 1 mitigates physiological damage and growth penalties of induced immunity

Cited by 4 publications

References 97 publications

MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions

MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions

Wounding promotes root regeneration through a cell wall integrity sensor, the receptor kinase FERONIA

Identification of a major QTL and candidate genes analysis for branch angle in rapeseed (Brassica napus L.) using QTL-seq and RNA-seq

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