Structure of the
            <i>Arabidopsis</i>
            TOPLESS corepressor provides insight into the evolution of transcriptional repression

Martín-Arevalillo, Raquel; Nanao, Max H.; Larrieu, Antoine; Vinos-Poyo, Thomas; Mast, David; Galván‐Ampudia, Carlos; Brunoud, Géraldine; Vernoux, Teva; Dumas, Renaud; Parcy, François

doi:10.1073/pnas.1703054114

Cited by 89 publications

(113 citation statements)

References 38 publications

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“…The JMJ14 dataset includes two NAC transcription factors NAC50 and NAC52 that have previously been identified to interact with JMJ14 (Ning et al, 2015). TPL co-precipitates all other TOPLESS-related (TPR) proteins, supporting recent finding that TPL/TPR proteins form tetramers (Martin-Arevalillo et al, 2017). These examples confirm that our MS-IP strategy identifies bona fide JMJ14-and TPL-interacting proteins.…”

Section: Dissection Of the Microprotein Repressor Complex By Mass Spesupporting

confidence: 77%

Dissection of the microProtein miP1 floral repressor complex in Arabidopsis

Rodrigues

Dolde

Straub

et al. 2018

Preprint

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SUMMARYMicroProteins have emerged as potent regulators of transcription factor activity. Here we use a combination of forward genetics and proteomics to dissect the miP1a/b microProtein complex that acts to delay the floral transition in Arabidopsis. The microProteins miP1a and miP1b can bridge an interaction between the flowering promoting factor CONSTANS (CO) and the TOPLESS (TPL) co-repressor protein to represses flowering. We find that the JUMONJI14 (JMJ14) histone demethylase is part of this repressor complex that can initiate chromatin changes in FLOWERING LOCUS T (FT) gene, the direct target of CO. Plants with mutations in JMJ14 exhibit an early flowering phenotype that is largely dependent on the activity of CO, supporting a role for CO in this repressive complex. When mis-expressed at the shoot apex, CO can induce early flowering only in the jmj14 background. Our results indicate that the repressor acts in the shoot apical meristem to keep it in an undifferentiated state until the leaf-derived florigen signal induces the conversion into a floral meristem.

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Section: Dissection Of the Microprotein Repressor Complex By Mass Spesupporting

confidence: 77%

Dissection of the microProtein miP1 floral repressor complex in Arabidopsis

Rodrigues

Dolde

Straub

et al. 2018

Preprint

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“…TPL/TPR co‐repressors bind EAR domains via their C‐terminal to LisH (CTLH) domains found near their N‐termini (Long et al., ). Recent structural analyses of the TPL N‐terminal domain have highlighted the precise interaction interface between TPL and AUX/IAA EAR domains, as well as the TPL‐TPL dimerization and tetramerization motifs (Ke et al., ; Martin‐Arevalillo et al., ). The residues required for higher order multimers of TPL tetramers have also been identified (Ma et al., ).…”

Section: Supplemental Analysesmentioning

confidence: 99%

Accelerating structure‐function mapping using the ViVa webtool to mine natural variation

et al. 2019

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Thousands of sequenced genomes are now publicly available capturing a significant amount of natural variation within plant species; yet, much of these data remain inaccessible to researchers without significant bioinformatics experience. Here, we present a webtool called ViVa (Visualizing Variation) which aims to empower any researcher to take advantage of the amazing genetic resource collected in the Arabidopsis thaliana 1001 Genomes Project ( http://1001genomes.org ). ViVa facilitates data mining on the gene, gene family, or gene network level. To test the utility and accessibility of ViVa, we assembled a team with a range of expertise within biology and bioinformatics to analyze the natural variation within the well‐studied nuclear auxin signaling pathway. Our analysis has provided further confirmation of existing knowledge and has also helped generate new hypotheses regarding this well‐studied pathway. These results highlight how natural variation could be used to generate and test hypotheses about less‐studied gene families and networks, especially when paired with biochemical and genetic characterization. ViVa is also readily extensible to databases of interspecific genetic variation in plants as well as other organisms, such as the 3,000 Rice Genomes Project ( http://snp-seek.irri.org/ ) and human genetic variation ( https://www.ncbi.nlm.nih.gov/clinvar/ ).

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“…Significant peaks (MACS2 summit q val ≤ 10 -10 ) are marked by horizontal bars, with the color saturation proportional to the -log 10 q value (as for the narrowPeak file format in ENCODE). Direct TFL1-FD targets include mediator complex subunit ( MED ), which links to Pol II transcription 65 , co-repressor complexes linked to histone de-acetylation such as SEUSS-LIKE ( SLK ) and TOPLESS-RELATED ( TPR ) 66 and HISTONE DEACETYLASE 18 ( HDA18 ). BRAHMA ( BRM ) is a SWI/SNF chromatin remodeler 66 , REPRESSOR OF SILENCING 4 ( ROS4 ) a histone acetyltransferase 67 , EMBRYONIC FLOWER 1 ( EMF1 ) and PICKLE RELATED 1 ( PKR ) are linked to Polycomb repression 68 , ASH1-RELATED 3/SET DOMAIN GROUP 4 ( AHR3/SDG4 ) is a histone methyltransferase 69 , METHYL-CPG-BINDING DOMAIN 10 and 11 ( MBD10/11 ) are putative methyl-DNA binding proteins 70 .…”

Section: Supplementary Figuresmentioning

confidence: 99%

Florigen family chromatin recruitment, competition and target genes

Zhu

Klasfeld

et al. 2020

Preprint

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17Plants monitor seasonal cues, such as day-length, to optimize life history traits including 18 onset of reproduction and inflorescence architecture 1-3 . Florigen family transcriptional 19 co-regulators TERMINAL FLOWER 1 (TFL1) and FLOWERING LOCUS T (FT) 20 antagonistically regulate these vital processes 4-6 yet how TFL1 and FT execute their 21 roles and what the mechanism is for their antagonism remains poorly understood. We 22 Main 35Plant development occurs after embryogenesis and is plastic, this allows modulation of 36 the final body plan in response to environmental cues to enhance growth and 37 reproductive success 7,8 . Of particular importance for species survival is the timing of the 38 formation of flowers that give rise to seeds which occurs in response to the seasonal 39 cues photoperiod and temperature 1,3,9 . For example, in plants that flower only once, like 40Arabidopsis and most crops, an early switch to flower formation allows rapid completion 41 of the life-cycle in a short growing season, but reduces total seed set or yield 10-12 . By 42 contrast, delaying flower formation supports formation of more seeds, but extends the 43 time to seed set. In many plant species, these alternative developmental trajectories are 44 tuned in response to daylength in antagonistic fashion by two members of the florigen 45 family of proteins 12,13 . FT promotes onset of the reproductive phase and flower 46 formation (determinacy), while TFL1 promotes vegetative development and branch fate 47 (indeterminacy) 4-6,13 . In Arabidopsis, which flowers in the spring, FT accumulates only 48 when the daylength exceeds a critical threshold, while TFL1 is present in both short-day 49 and long-day conditions 1,3,14 . A key unanswered question is how FT and TFL1 50 modulate plant form -what are the downstream processes they set in motion and what 51 is molecular basis for their antagonism? 52 53Accumulating evidence points to roles of FT and TFL1, which lack ability to bind DNA, 54 in transcriptional activation and repression, respectively, by forming complexes with a 55 bZIP transcription factor, FLOWERING LOCUS D (FD) 12,15-19 , although non-nuclear 56 functions for both proteins have also been described 20,21 . Mechanistic insight into 57 florigen activity has been hampered by their low protein abundance. To overcome this 58 limitation and to test the role of TFL1 in the nucleus, we conducted TFL1 chromatin 59 immunoprecipitation followed by sequencing (ChIP-seq). Towards this end, we first 60 generated a biologically active, genomic GFP-tagged version of TFL1 (gTFL1-GFP tfl1-61 1) (Supplementary Fig. 1a, b). Next, we enriched for TFL1 expressing cells by isolating 62 shoot apices from 42-day-old short-day-grown inflorescences just prior to onset of 63 flower formation (Fig. 1a). Finally, we optimized low abundance ChIP by combining 64 eight individual ChIP reactions per ChIP-seq replicate. We conducted FD ChIP-seq in 65 4 analogous fashion using a published 22 , biologically active ( Supplementary Fig. 1c), 66 genomic...

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Structure of the Arabidopsis TOPLESS corepressor provides insight into the evolution of transcriptional repression

Cited by 89 publications

References 38 publications

Dissection of the microProtein miP1 floral repressor complex in Arabidopsis

Dissection of the microProtein miP1 floral repressor complex in Arabidopsis

Accelerating structure‐function mapping using the ViVa webtool to mine natural variation

Florigen family chromatin recruitment, competition and target genes

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