Arabidopsis Research Round-up

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Published on: January 21, 2015

Lots of new and interesting papers to catch up on from the New Year break this week. Fans of proteomics will be happy as we have three proteomics papers fromEdinburgh, Cambridge and Birmingham! The John Innes Centre and University of Warwick also have an update for us on how histone dynamics affect transcription;Norwich and Sainsbury Lab Cambridge-based researchers tell us more about ELF3; Rothamsted scientists reveal roles for CER2-LIKE proteins; and Donna Bond andProfessor Sir David Baulcombe reveal how virus-induced gene silencing can be used to study transposable elements.


  • Krahmer J, Hindle MM, Martin SF, Le Bihan T and Millar AJ. Sample preparation for phosphoproteomic analysis of circadian time series in Arabidopsis thaliana. Methods in Enzymology, 26 December 2014. DOI: 10.1016/bs.mie.2014.10.022.

This useful review from former GARNet PI Andrew Millar and team discusses methods used in phosphoproteomics – the study of post-translational protein phosphorylations.


  • Rosa S, Ntoukakis V, Ohmido N, Pendle A, Abranches R and Shaw P. Cell differentiation and development in Arabidopsis are associated with changes in histone dynamics at the single cell level. The Plant Cell, 30 December 2014. DOI: 10.1105/tpc.114.133793. [Open Access]

In this really interesting Plant Cell paper, researchers including those from the John Innes Centre and the University of Warwick, provide evidence to suggest that stem cells have relatively mobile histones, whereas as cells differentiate, the histones become acetylated and thus more and more ‘fixed’ to the chromatin. This helps to explain how stem cells have the propensity to generate cells with different gene expression profiles, and why differentiated cells of a given type all express genes in a coordinated manner.


  • Box MS, Huang E, Domijan M, et al. ELF3 controls thermoresponsive growth in Arabidopsis. Current Biology, 30 December 2014. DOI: 10.1016/j.cub.2014.10.076.

Published just a little too late for Christmas (!), this paper comes from a collaboration between mostly Norwich Research Park-based scientists and those at the The Sainsbury Lab in Cambridge. The paper explores the role and function of the transcriptional regulator ELF3 (EARLY FLOWERING3). This gene encodes a protein that rapidly and reversibly binds to transcriptional targets in a temperature-dependent mechanism, thus regulating cell elongation in response to changes in ambient temperature.


  • Marondedze C, Wong A, Groen A, Serrano N, Jankovic B, Lilley K, Gehring C and Thomas L. Exploring the Arabidopsis proteome: influence of protein solubilization buffers on proteome coverage. International Journal of Molecular Science, 31 December 2014. DOI: 10.3390/ijms16010857. [Open Access]

Led by a Saudi Arabian team but involving the work of Arnoud Groen and Kathryn Lilley from the University of Cambridge, here’s another paper on the subject of methods in proteomics. In this work, using Arabidopsis thaliana as a model, the group assesses how variations in techniques and detergents used as the solubilisation buffer can affect the results of a proteomic study.


  • Roitinger E, Hofer M, Köcher T, Pichler P, Novatchkova M, Yang J, Schlögelhofer and Mechtler K. Quantitative phosphoproteomics of the ATM and ATR dependent DNA damage response in Arabidopsis thaliana. Molecular & Cellular Proteomics, 5 January 2015. DOI: 10.1074/mcp.M114.040352. [Open Access]

More proteomics! Jianhua Yang from the University of Birmingham is an author on this Austrian-led paper, in which a novel mass spec-based phosphoproteomics approach to study DNA damage repair in Arabidopsis thaliana is described. The approach allowed identification of nearly 11,000 proteins and 15,500 unique phosphopeptides, of which 134 ATM/ATR-dependent phosphopeptides were up-regulated, and 38 were down-regulated. Both known and novel targets of ATM/ATR were found.


  • Bond DM and Baulcombe DC. Epigenetic transitions leading to heritable, RNA-mediated de novo silencing in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the USA, 5 January 2015. DOI: 10.1073/pnas.1413053112. [Open Access]

This PNAS offering is from Donna Bond and David Baulcombe from the University of Cambridge. Investigating the mechanisms by which RNA-directed DNA methylation (RdDM) is achieved to silence transposable elements, the authors wondered whether DNA methylation can be induced de novo at naïve sites, or whether it can only re-establish epigenetic silencing of active transposable elements. Using virus-induced epigenetic silencing (VIGS)-RdDM, it is demonstrated that epigenetic silencing can be achieved in a genetic mutant plant, mediated via virus-derived small RNAs. This has great potential for use as a tool in gene silencing studies.


  • Haslam T, Haslam RP, Thoraval D, et al. CER2-LIKE proteins have unique biochemical and physiological functions in very-long-chain fatty acid elongation. Plant Physiology, 14 January 2015. DOI: 10.1104/pp.114.253195. [Open Access]

This article, which involved the work of Richard Haslam, Frédéric Beaudoin and Johnathan Napier from Rothamsted Research, explores the functionality of the enzyme CER2 and its homologues; required for the elongation of fatty acids with chains longer than 28 carbons. Three CER2-LIKE proteins are shown to have unique effects on the substrate specificity of the same condensing enzyme (required to catalyse the first step of the fatty acid elongation process), and furthermore are important in cuticle formation and pollen coat function.

Arabidopsis Information Portal at PAGXXIII

Last Monday the Arabidopsis community gathered for the Arabidopsis Information Portal workshop at PAG XXIII. The Arabidopsis Informatics Portal (AIP) was funded by NSF and BBSRC to move beyond the Arabidopsis genome resource provided by TAIR toward linking the genome to the epigenome, proteome, transcriptome and interactome.

AraportThe first talk was a short update from Eva Huala, formerly of TAIR and now of Phoenix Bioinformatics, the nonprofit company she started in order to keep TAIR going. Huala explained that after TAIR’s NSF funding ended, the pay-to-access model was chosen over the alternative pay-to-submit (open access) approach. This means TAIR is focussed on ensuring the subscribers get the best possible value for money by providing the best possible database curation, manual annotation and user experience. Most TAIR subscription fees are paid by libraries, as if it was a journal, but researchers from institutions whose libraries do not pay the fee will be able to access TAIR’s manual annotation after a year’s embargo.

Next, Sean May (NASC, University of Nottingham) explained that NASC is a module of AIP and is currently integrating with the ABRC. He is consulting the community about the development of NASC, so make sure you have your say in the NASC Strategy Survey:

Chia-yi Cheng (JCVI) gave an overview of Araport, the online home of the AIP. Araport federates diverse datasets from other places, for example TAIR, UniProt and BAR, and maintains the Col-0 ‘gold standard’ annotation. It uses JBrowse as the default genome browser and hosts datasets including the CoGe epigenomics resource, which I blogged about last week. (more…)

To tweet or not to tweet?

Here at GARNet, we’re pretty big fans of social media, and Twitter in particular. You can find me, for example @GARNetweets, Charis is @weedinggems, and Ruth has the enviable Twitter handle @plantscience. We regularly post links to news, journal papers, job posts etc., tweet from conferences, and encourage live-tweeting at our own events too.

Left behind at GARNet Towers while my colleagues attended the Plant & Animal Genome conference in San Diego last week, I followed events virtually, via the Twitter hashtag #PAGXXIII – thanks to everyone who tweeted for keeping me up to speed!

Though once upon a time it would have been considered rude to sit tapping away at your phone during a plenary lecture, in today’s WiFi-enabled world, more and more people are using social media during conferences. As John Innes Centre (@JohnInnesCentre) student Amelia Frizell (@AmeliaFrizell) points out in this blog post, there are many advantages to live-tweeting: it’s a great way to make notes, stay engaged with the speaker, increase your Twitter follower numbers and network with peers.

But there’s an ongoing debate, known as “Twittergate”, about whether it’s appropriate to tweet during a conference, what should and should not be tweeted, and what, exactly, the “twetiquette” is when engaging with social media during live events.

A Twitter account I follow recently retweeted a link to quite an old blog post on The Guardian website, which reminds us that there is a certain level of responsibility involved in live-tweeting. At academic conferences in particular, there are unwritten rules that should be followed. I recommend reading the article as there are some very useful tips and things to bear in mind.

You see, although many of us are fully subscribed to the idea of Twitter as a way to quickly give and receive snippets of news and information, not everyone feels the same way. Not everyone is aware of what Twitter is, how it works, or just how public a channel it is. Many distrust it and are sceptical. Some academics, for example, are comfortable with presenting unpublished work to an audience of peers in the room, but less happy to have it instagrammed and summarised in 140 characters or less and whizzed around the Twitterverse for anyone to read.

Having been lucky enough to attend quite a few conferences last year, it was interesting to note the uptake, or not, of Twitter in different places. At UKPSF (@UKPSF) Plant Sci 2014 and ASPB’s (@ASPB) Plant Biology 2014, for example, tweeting was encouraged and I was among a handful or two of other delegates all using the official conference hashtags. At ICAR 2014 (@ICAR2014) however, Charis, Ruth and I were practically the only ones online.

At SEB (@SEBiology) 2014 in Manchester there were noticeably more ‘tweeps’ in the plant science sessions than there were in the animal or cell biology talks, while at SpotOn London (@SpotOnLondon), a science communication conference I attended at the end of 2013, there were so many people tweeting and using electronic devices that it was a scrum to find available plug sockets to recharge during the lunch break!

Like Amelia, I think – when used responsibly – Twitter is brilliant for conference and workshop communication, and as Anne Osterrieder (@anneosterrieder) and others testify, social media is a great science outreach tool, too. Like it or not, Twitter is a ‘thing’ now. And it’s not just a frivolous plaything for younger students or early career researchers, it’s a bona fide tool for communicating and sharing news and joining in online conversations.

Speakers: don’t be offended if people spend more time looking down at their iPads than up at your slides. If they’re tweeting or live-blogging about your work, they are helping you to communicate your science to far more people than just those in the room. If you’re presenting something you’d rather not have published on the internet, or don’t want your photo taken, just say so during your talk – the twitterati will respect your wishes.

Embrace Twitter. Why not set up your own Twitter account and start posting links to your papers or research websites? Follow people you’re interested in (like us?!) and retweet what they have to say. Tweet about what you get up to in your lab. Put your Twitter handle on your conference presentations so people can @mention you in their tweets, or even start your own catchy hashtag? Who knows, you could end up trending!

EBI resources at PAGXXIII

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Published on: January 15, 2015

I spent Sunday morning wandering in and out of the ‘Tools and Resources from EBI’ session here at PAG. Some EBI resources for plant science will be very familiar to some of our community, but the presenters gave accessible talks that included some news and advice, so I thought I’d round them up for you.

Maria Keays presented ArrayExpress and ExpressionAtlas. These are the functional genomics tools from EBI. Keays defined functional genomics as the study of gene expression, gene function and gene regulation – these tools certainly aren’t just for microarray data!

Users submit their data to ArrayExpress via the Annotare submission tool, which encourages inclusion of information about how the samples were grown all the way through to data generation. Keays acknowledged that a user may encounter an error message they can’t get around, and assured us that emails sent to the helpdesk ( are responded to quickly. Once submitted, the dataset and associated metadata is checked by a human curator before the user can upload it. The data can stay private until publication because two logins are provided; one for the submitter and one for the reviewer of the paper they hope to publish.

We’ve been encouraging our community to share data on NCBI GEO because it is able to disseminate almost any data type. But for functional genomics data, ArrayExpress is just as acceptable to journals as GEO, and the Annotare submission tool requires more extensive metadata and more stringent standards than GEO. (more…)

Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up
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Published on: January 14, 2015

Back after our Christmas/New Year break, here’s a catch-up of the some of the new Arabidopsis papers to be published before Christmas. Today’s round-up features new work by scientists from the Universities of York, Leicester, Cambridge, Edinburgh and Leeds, and from the institutes Rothamsted Research and the James Hutton Institute.


  • Delker C, Sonntag L, James GV, et al. The DET1-COP1-HY5 pathway constitutes a multipurpose signaling module regulating plant photomorphogenesis and thermomorphogenesis. Cell Reports, 18 December 2014. DOI: 10.1016/j.celrep.2014.11.043. [Open Access]

Though it has been known for some time that the transcription factor PHYTOCHROME INTERACTING FACTOR4 (PIF4) regulates the growth response of Arabidopsis thaliana to elevated ambient temperature by activating hormonal modules, it is not known how, exactly, temperature regulates PIF4 activity. Using a forward genetic approach, this group of German researchers – with the help of Seth J. Davis from the University of York – provide evidence to suggest that seedling growth in response to elevated temperature is transcriptionally regulated by the DE-ETIOLATED 1 (DET1)-CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1)-ELONGATED HYPOCOTYL 5 (HY5)-dependent photomorphogensis pathway.


  • Park GT, Frost JM, Park J-S, Kim TH, Lee JS, Oh SA, Twell D, Brooks JS, Fischer RL and Choi Y. Nucleoporin MOS7/Nup88 is required for mitosis in gametogenesis and seed development in Arabidopsis. Proceedings of the National Academy of Sciences of the USA, 8 December 2014. DOI: 10.1073/pnas.1421911112. [Open Access]

Working with Korean and American colleagues, David Twell from the University of Leicester was involved in this fascinating study of the mos7-5 mutant line of Arabidopsis thaliana. mos7-5  mutants experience ovule and pollen abortion in MOS7/mos7-5 heterozygous plants, and preglobular statge lethality in homozygous mos7-5 seeds. This study shoes that MOS7 is localized to the nuclear membrane but associated with the spindle apparatus during postmeiotic mitosis; in MOS7/mos7-5 heterozygotes, abortion is accompanied by a failure of spindle formation, cell fate specification and phragmoplast activity. These findings provide an important advance on current knowledge for plant scientists, but because the regulation of mitosis is highly conserved between plants and animals, it could be significant for animal researchers too.


  • Landrein B, Refahi Y, Besnard F, Hervieux N, Mirabet V, Boudaoud A, Vernoux T and Hamant O. Meristem size contributes to the robustness of phyllotaxis in Arabidopsis. Journal of Experimental Botany, 11 December 2014. DOI: 10.1093/jxb/eru482. [Open Access]

Led by a French team, this J Ex Bot paper included work by Yassin Refahi of the Sainsbury Laboratory at Cambridge. Using Arabidopsis, the group studied the relationship between day length, the size of the shoot apical meristem, and the robustness of phyllotactic patterns. Among several patterns identified was the overall finding that robustness of the phyllotactic pattern is not optimal in the wild type plant, suggesting that it is regulated by day length; a new example of the link between plant patterning and its environment.


  • Bielecka M, Watanabe M, Morcuende R, Scheible WR, Hawkesford MJ, Hesse H and Hoefgen R. Transcription and metabolome analysis of plant sulphate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulphur, nitrogen and phosphorus nutritional responses in Arabidopsis. Frontiers in Plant Science, 22 December 2014. DOI: 10.3389/fpls.2014.00805. [Open Access]

This Frontiers in Plant Science paper advances our basic understanding of the transcriptional effects of short-term sulphur starvation and re-supply in Arabidopsis thaliana; in turn this could have significance down the line for crop improvement. An international collaboration including Malcolm Hawkesford from Rothamsted Researchused a combination of transcriptomics and metabolomics analysis to not only identify the differential expression of 21 transcription factors in response to sulphur levels, but also to predict their downstream gene targets.


  • Hu X, Kong X, Wang C, et al. Proteasome-mediated degradation of FRIGIDA modulates flowering time in Arabidopsis during vernalization. The Plant Cell, 23 December 2014. DOI: 10.1105/tpc.114.132738.

Gary Loake from the University of Edinburgh was involved in this Plant Cell paper, in which the mostly Chinese team identify that FRIGIDA – a scaffold protein involved in the recruitment of chromatin modifiers that cause epigenetic changes to regulate flowering genes – is degraded in a proteasome-mediated mechanism. The proteolysis mechanism is induced by WRKY34 and is dependent upon CULLIN3A.


  • Taylor-Teeples M, Lin L, de Lucas M, et al. An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature, 24 December 2014. DOI: 10.1038/nature14099.

Led by the Brady lab at UC Davis, this Nature paper also involved the work of Cambridge-based theoretical biophysicist, Sebastian Ahnert. The paper presents a novel protein–DNA network model showing the interactions between Arabidopsis thaliana transcription factors and secondary cell wall metabolite genes. This model allowed the group to develop and validate new hypotheses about secondary cell wall gene regulation under abiotic stress.


  • Foyer CH, Verrall SR and Hancock RD. Systematic analysis of phloem-feeding insect-induced transcriptional reprogramming in Arabidopsis highlights common features and reveals distinct responses to specialist and generalist insects. Journal of Experimental Botany, 24 December 2014.DOI: 10.1093/jxb/eru491.

In terms of immunity, plants may respond very differently to phloem-feeding insects (PFIs) compared to chewing insects. Here, Christine Foyer from the University of Leeds, and Susan Verrall and Robert Hancock from the James Hutton Institute, provide a comprehensive transcriptomic analysis of Arabidopis thaliana when infested withMyzus persicae, Bemisa tabaci or Brevicoryne brassicae. Though an increase in transcripts associated with WRKY transcription factor genes is a common feature of PFI infestation, there is significant divergeance in secondary metabolism depending on the species of PFI. Nevertheless, this research suggests that plants recognize and respond to perturbations in the cell wall during PFI infestation.


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Published on: January 11, 2015

Happy New Year! We at GARNet enjoyed a long Christmas break and some of us have returned to work via California! Ruth, Jim and I are in San Diego this week for the Plant and Animal Genome Conference (PAG).

PAG is an enormous conference – take a look at the Twitter stream (PAGXXIII) for an idea of how many sessions run at any one time. Yesterday I went to sessions on Ontologies, Brassica and Tritaceae, and I thought I’d quickly update our blog readers about a workshop about the CoGe online tool. I mentioned CoGe in this post about the EPIC conference and it’s also featured in the June 2013 edition of GARNish.

Eric Lyons, one of the creators of CoGe, began the session by explaining that CoGe is a platform for managing, visualising, analysing and comparing genomes. It can deal with unlimited numbers of genomes of unlimited size—though there is a limit for the number of annotations per genome—and while there are tools set up for ease of use, users can perform custom, on-the-fly analysis too.

Throughout the session, Lyons was clear that CoGe is ‘Powered by iPlant.’ It uses iPlant middleware to enable data storage, universal log-in and much more functionality that the user might not be aware of but which makes their experience smooth and relatively stress-free. (more…)

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