GARNet Research Roundup: July 17th 2020

This edition of GARNet Research Roundup begins with a remarkable four papers that include work from Caroline Dean’s lab at the John Innes Centre. The first two papers are collaborations with members of Martin Howard’s lab and look at the molecular mechanisms that control long-term cold sensing or the antisense regulation of FLC respectively. The third paper looks at the function of the ICU1-associated PRC2 complex while the final ‘Dean-lab’ paper is a collaboration with Judith Irwin and looks at regulation of flowering time in Brassica napus.

The next three papers also feature authors from the John Innes Centre. The first looks at the role of mRNA methylation in the control of leaf organogenesis; the second paper investigates how AXR1 functions in the methylation of transposable elements and the final paper characterises a new method for the automated measurement of seeds.

The first non-JIC paper in this Roundup is led by Robert Caine from the University of Sheffield and characterises stomatal development in Physcomitrium patens. Andrea Harper at the University of York leads the next paper that applies an associative transcriptomics approach to the genome of Brassica juncea.

The next paper includes co-authors from Aberystwyth and characterises a molecular interaction from pollen tubes that can stimulate ectopic programmed cell death. The final two papers include co-authors from the University of Oxford. Firstly Paul Jarvis is involved with a Japanese study that looks at chloroplast autophagy and ubiquitination. Finally Nick Harberd is co-author on a Chinese study looking at iron accumulation in Arabidopsis seeds.


Zhao Y, Antoniou-Kourounioti RL, Calder G, Dean C, Howard M (2020) Temperature-dependent growth contributes to long-term cold sensing Nature; 10.1038/s41586-020-2485-4. doi:10.1038/s41586-020-2485-4

Yusheng Zhao is first author on this work from the Howard and Dean labs at the John Innes Centre. They reveal a molecular mechanism that underpins the ability of plants to sense the winter period. They show that abundance of the transcription factor NTL8 is critical for the control of expression of the VERNALIZATION INSENSITIVE 3 protein, which in turn epigenetically silences FLC throughout the winter.

https://www.nature.com/articles/s41586-020-2485-4

Fang X, Wu Z, Raitskin O, et al (2020) The 3′ processing of antisense RNAs physically links to chromatin-based transcriptional control Proc Natl Acad Sci U S A. 2020;202007268. doi:10.1073/pnas.2007268117

Open Access

Xiaofeng Feng works with the Howard and Dean labs at the John Innes Centre and is lead author on this research. The authors provide molecular detail to the complex control of antisense RNA regulation of the FLC locus, which provides a link to epigenetic silencing via the Polycomb Repressive Complex 2.


Bloomer RH, Hutchison CE, Bäurle I, et al (2020) The Arabidopsis epigenetic regulator ICU11 as an accessory protein of Polycomb Repressive Complex 2 Proc Natl Acad Sci U S A. 2020;201920621. doi:10.1073/pnas.1920621117 Open Access

Rebecca Bloomer is first author on this collaboration between researchers at the John Innes Centre and the University of Edinburgh. They identify INCURVATA11 (ICU11) as a Polycomb Repressive Complex 2 (PRC2) accessory protein that co-localises with the core components of the PRC2. The ICU1-associated PRC2 complex controls H3K36me3 demethylation at the FLC locus, revealing an additional mechanism for the control of flowering time.


Tudor EH, Jones DM, He Z, et al (2020) QTL-seq identifies BnaFT.A02 and BnaFLC.A02 as candidates for variation in vernalization requirement and response in winter oilseed rape (Brassica napus) Plant Biotechnol J. 2020;10.1111/pbi.13421. doi:10.1111/pbi.13421 Open Access

Eleri Tudor is first author on this work from the Dean and Irwin labs at the John Innes Centre. They characterise the key floral regulators FLOWERING LOCUS C (BnaFLC.A02) and FLOWERING LOCUS T (BnaFT.A02) in Brassica napus, showing that allelic variation at these loci is importance for the close-association between vernalisation and flowering time.

https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.13421

Arribas-Hernández L, Simonini S, Hansen MH, et al (2020) Recurrent requirement for the m6A-ECT2/ECT3/ECT4 axis in the control of cell proliferation during plant organogenesis Development. doi:10.1242/dev.189134 Open Access

Laura Arribas-Hernández is lead author on this Danish-UK collaboration that includes Sara Simonini and Lars Ostergaard from the John Innes Centre as co-authors. They look at the role of YTH-domain proteins ECT2, ECT3 and ECT4 during leaf development. They show that the methylated mRNA (m6A)-binding site of these proteins is essential for their function, highlighting the m6A-ECT2/ECT3/ECT4 axis as an important module to stimulate plant organogenesis.

https://dev.biologists.org/content/early/2020/06/30/dev.189134.long

Christophorou N, She W, Long J, et al (2020) AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization PLoS Genet. 16(6):e1008894. doi:10.1371/journal.pgen.1008894 Open Access

This collaboration between Université Paris-Saclay and the John Innes Centre includes Nicolas Christophorou as first author. They investigate the role of the well-characterised NEDD8/RUB1 E1 ligase AXR1 in DNA methylation of transposable elements. This links the role of AXR1 with its previously characterised effects in hormone signalling and in the control of the formation of meiotic crossovers.


Colmer J, O’Neill CM, Wells R, et al (2020) SeedGerm: a cost-effective phenotyping platform for automated seed imaging and machine-learning based phenotypic analysis of crop seed germination New Phytol. 10.1111/nph.16736. doi:10.1111/nph.16736 Open Access

This UK-Chinese-Dutch collaboration is led by Joshua Colmer and introduces a new phenotyping platform that was tested against a diverse panel of Brassica napus varieties. This SeedGerm hardware and software measures seed germination, automates seed imaging and is a platform for machine-learning based phenotypic analysis. This will hopefully be a useful tool for the investigation of critical seed phenotypes.

https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.16736

Caine RS, Chater CCC, Fleming AJ, Gray JE (2020) Stomata and Sporophytes of the Model Moss Physcomitrium patens. Front Plant Sci. 2020;11:643. doi:10.3389/fpls.2020.00643 Open Access

Bobby Caine from the University of Sheffield is lead author on this research that characterises stomatal development in the model moss species Physcomitrium patens. Although they show key differences in stomatal development between Physcomitrium and Arabidopsis, key regulators of this process in higher plants also functions in mosses, providing important evolutionary insights.

https://www.frontiersin.org/articles/10.3389/fpls.2020.00643/full

Harper AL, He Z, Langer S, et al (2020) Validation of an Associative Transcriptomics platform in the polyploid crop species Brassica juncea by dissection of the genetic architecture of agronomic and quality traits Plant J. 2020;10.1111/tpj.14876. doi:10.1111/tpj.14876  Open Access

GARNet committee member Andrea Harper from the University of York leads this research that employs associative transcriptomics analysis in Brassica juncea. To generate this analysis platform they mapped transcriptome data from a diverse panel of B. juncea accessions to produce a pan-transcriptome reference. This will be a useful research for the mapping of loci involved in important agronomic traits.


Lin Z, Xie F, Trivino M, et al. (2020) Ectopic expression of a self-incompatibility module triggers growth arrest and cell death in vegetative cells Plant Physiol. doi:10.1104/pp.20.00292 Open Access

Zongcheng Lin is first author on this Belgium-led study that includes Marina Trivino and Maurice Bosch from IBERS, Aberystwyth University as co-authors. They look at the interaction between cognate PrsS and PrpS proteins that are involved in the pollen self-incompatibility response in poppy. By ectopic expression in Arabidopsis roots they show that this interaction can cause programmed cell death (PCD) in vegetative tissues. This signalling module may become an important tool for inducible PCD in other developmental contexts.

http://www.plantphysiol.org/content/early/2020/06/19/pp.20.00292.long

Kikuchi Y, Nakamura S, Woodson JD, et al (2020) Chloroplast autophagy and ubiquitination combine to manage oxidative damage and starvation responses Plant Physiol. 2020;pp.00237.2020. doi:10.1104/pp.20.00237 Open Access

Paul Jarvis from the University of Oxford is a co-author on this Japanese study led by Yuta Kikuchi. This work demonstrates that autophagy and chloroplast-associated ubiquitin ligase E3s cooperate for protein turnover, management of ROS accumulation, and adaptation to starvation.


Sun Y, Li JQ, Yan JY, et al (2020) Ethylene promotes seed iron storage during Arabidopsis seed maturation via ERF95 transcription factor J Integr Plant Biol. 10.1111/jipb.12986. doi:10.1111/jipb.12986

Nick Harberd from the University of Oxford is a co-author on this Chinese study led by Ying Sun at Zhejiang University in Hangzhou. In this work they show that the ERF95 transcription factor regulates Arabidopsis seed Fe accumulation and through a series of investigations they are able to conclude that the gaseous hormone ethylene promotes seed Fe accumulation during seed maturation via an EIN3-ERF95-FER1-dependent signaling pathway.



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