Daniel Pass talks to GARNet

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Published on: October 16, 2017

Daniel Pass (Cardiff University) discusses his recent paper published in PLoS Genetics entitled ‘Genome-wide chromatin mapping with size resolution reveals a dynamic sub- nucleosomal landscape in Arabidopsis’. Dan highlights his Github page where the code for the novel graphics in this paper are held.

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006988

https://github.com/ChromatinCardiff/DanielPassProcessingPipelines

Miriam Gifford talks to GARNet

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Published on: October 9, 2017

Miriam Gifford talks to GARNet about a recent Large Scale Biology paper in The Plant Cell entitled ‘Root architecture shaping by the environment is orchestrated by dynamic gene expression in space and time’.
http://www.plantcell.org/content/early/2017/09/11/tpc.16.00961
More on the eFP browser here: http://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi

Arabidopsis Research Roundup: October 5th

After a brief hiatus the UK Arabidopsis Research Roundup returns with eight papers that focus on different aspects of Arabidopsis cell biology.

Firstly GARNet PI Jim Murray leads a study that performs a genome-wide analysis of sub-nucleosomal particles whilst Phil Wigge’s lab at SLCU conducts a more focused study on G-box regulatory sequences.

Thirdly Veronica Grieneisen (JIC) and co-workers have modelled the process of boron transport in the root, revealing exciting insights into how traffic jams might form.

Fourthly is a large scale biology paper led by Miriam Gifford (University of Warwick) that looks at the temporal and spatial expression patterns that control lateral root development.

Next Alexander Ruban (QMUL) investigates how low-light acclimated plants respond to high light.

The sixth and seventh studies are led by Alison Baker (Leeds) or Bill Davies (Lancaster) and look at phosphate or hormone signaling respectively.

Finally Gareth Jenkins (University of Glasgow) compares the UV-B signaling module in lower plants with that in Arabidopsis.


Pass DA, Sornay E, Marchbank A, Crawford MR, Paszkiewicz K, Kent NA, Murray JAH (2017) Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis. PLoS Genet. doi: 10.1371/journal.pgen.1006988

Open Access

GARNet PI Jim Murray is the corresponding author on this study that performs a whole-genome scan of sub-nucleosomal particles (subNSPs) that have been identified using differential micrococcal nuclease (MNase) digestion. They link the position of subNSPs with RNAseq data taken from plants grown in different light conditions. They show that this new technique is able to discriminate regulatory regions that have been obscured by previous experimental procedures and therefore represents a very useful experimental method.


Ezer D, Shepherd SJ, Brestovitsky A, Dickinson P, Cortijo S, Charoensawan V, Box MS, Biswas S, Jaeger K, Wigge PA (2017) The G-box transcriptional regulatory code in Arabidopsis. Plant Physiol. 10.1104/pp.17.01086

Open Access

Phil Wigge (SLCU) is the corresponding author of this study that investigates the sequence elements that are linked to the conserved G-box regulatory motifs. They identify a set of bZIP and bHLH transcription factors that predict the expression of genes downstream of perfect G-boxes. In addition they have developed a website that provide visualisations of the G-box regulatory network (araboxcis.org).


Sotta N, Duncan S, Tanaka M, Takafumi S, Marée AF, Fujiwara T, Grieneisen VA (2017) Rapid transporter regulation prevents substrate flow traffic jams in boron transport. Elife. doi: 10.7554/eLife.27038

Open Access

Veronica Grieneisen (JIC) is the lead author on this detailed analysis of the regulatory circuits that are established during boron uptake in Arabidopsis roots. They used mathematical modelling to show that during boron uptake, swift regulation of transport activity is needed to prevent toxic accumulation of the metal. This system has analogy to the way in which traffic jams of nutrient flow might form and has relevance for regulatory systems outside of plant science. https://www.sciencedaily.com/releases/2017/09/170905104358.htm


Walker L, Boddington C, Jenkins D, Wang Y, Grønlund JT, Hulsmans J, Kumar S, Patel D, Moore JD, Carter A, Samavedam S, Bomono G, Hersh DS, Coruzzi GM, Burroughs NJ, Gifford ML (2017) Root architecture shaping by the environment is orchestrated by dynamic gene expression in space and time. Plant Cell. doi: 10.1105/tpc.16.00961

Open Access

Miriam Gifford (University of Warwick) leads this broad consortium that has taken a systems biology approach to better define the environmental factors that control dynamic root architecture. They track transcriptional responses during lateral root development in remarkable detail, looking at individual transcripts. They confirm the idea that the activity of a gene is not simply a function of its amino acid sequence but rather the temporal and spatial regulation of its expression.


Tian Y, Sacharz J, Ware MA, Zhang H, Ruban AV (2017) Effects of periodic photoinhibitory light exposure on physiology and productivity of Arabidopsis plants grown under low light. J Exp Bot. doi: 10.1093/jxb/erx213. Open Access

Alexander Ruban (QMUL) is the corresponding author on this collaboration with Chinese colleagues that examined the effect of high-light stress on low-light acclimated Arabidopsis plants. Initially these plants showed significant photo-inhibition but that they recovered rapidly and after 2 weeks of treatment there was no change in photosynthetic yield. In addition high light acclimated plants showed accelerated reproductive phase change that coincided with higher seed yield.


Qi W, Manfield IW, Muench SP, Baker A (2017) AtSPX1 affects the AtPHR1 -DNA binding equilibrium by binding monomeric AtPHR1 in solution. Biochem J. doi: 10.1042/BCJ20170522 Open Access

Alison Baker (University of Leeds) leads this research that focusses on the binding of the Phosphate Starvation Response 1 (PHR1) transcription factor to regulatory P1BS DNA sequences. They show a tandem P1BS sequence is bound more strongly than a single P1BS site. Ultimately they demonstrate tight regulation of phosphate signaling both by the concentration of phosphate as well as the activity of the interacting SPX protein.


Li X, Chen L, Forde BG, Davies WJ (2017) The Biphasic Root Growth Response to Abscisic Acid in Arabidopsis Involves Interaction with Ethylene and Auxin Signalling Pathways. Front Plant Sci. doi: 10.3389/fpls.2017.01493 Open Access

Bill Davies and Brian Forde (Lancaster University) lead this work that investigates the effect on ethylene and auxin on the biphasic response to ABA during root elongation. They used a range of hormone signalling mutants to show that the response to high ABA is via both ethylene and auzin signalling. In contrast the response to low ABA does not require ethylene signalling.


Soriano G, Cloix C, Heilmann M, Núñez-Olivera E, Martínez-Abaigar J, Jenkins GI (2017) Evolutionary conservation of structure and function of the UVR8 photoreceptor from the liverwort Marchantia polymorpha and the moss Physcomitrella patens. New Phytol. doi: 10.1111/nph.14767

Gareth Jenkins (University of Glasgow) is the corresponding author of this work that looks at the role of the UVR8 UV-B receptor in lower plants. They expressed the versions of UVR8 from a moss or a liverwort in Arabidopsis and showed that although there appears to be differences in the regulation of this protein, the mechanism of UV-B signaling is evolutionarily conserved

SEB/GARNet meeting on Post Translational Modifications.

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Published on: October 5, 2017

GARNet are co-organising this exciting symposium and workshop on plant signalling with post-translational modifications held in Edinburgh 11-13 December 2017.
Abstract deadline: 20 October 2017

Early-bird registration deadline: 3 November 2017

http://www.sebiology.org/events/event/from-proteome-to-phenotype

KEYNOTE SPEAKERS

Matthias Mann (Max Planck Institute of Biochemistry

Ron Hay (University of Dundee)

DYNAMIC PHOSPHORYLATION

Cyril Zipfel (The Sainsbury Laboratory)

Gitta Coaker (UC Davis)

John Christie (University of Glasgow)

PROTEIN SUMOYLATION

Ari Sadanandom (Durham University)

Andreas Bachmair (University of Vienna)

Maria Lois (CRAG Spain)

EMERGING PTMS

Piers Hemsley (University of Dundee)

Markus Wirtz (University of Heidelberg)

Stéphane Ravanel (INRA/CNRS)

UBIQUITIN-MEDIATED PROTEASOME

Steven Spoel (University of Edinburgh)

Luz Irina Calderon-Villalobos (IPB Leipniz)

Emmanuelle Graciet (Maynooth University)

REDOX-BASED PTMS

Gary Loake (University of Edinburgh)

Frank van Breusegem (VIB Ghent)

Daniel Gibbs (University of Birmingham)

TECHNOLOGICAL ADVANCES

Alex Jones (University of Warwick, UK)

Frank Menke (The Sainsbury Laboratory, UK)

Katja Baerenfaller (ETH Zurich, Switzerland)

 

GARNET WORKSHOP ON PLANT PROTEOMICS (13 Dec 2017)

Learn about new technologies and available software for analysis of

proteome samples in a workshop led by Dr. Alex Jones (University of

Warwick). FREE for attendees of the symposium but only 30 spaces

available!!

 

Organising committee: Steven Spoel (University of Edinburgh & GARNet),

Geraint Parry (GARNet), Cyril Zipfel (The Sainsbury Laboratory).

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