The Arabidopsis Epitranscriptome

Lead Research Organisation: University of Dundee
Department Name: School of Life Sciences

Abstract

Working with pea plants in his monastery garden, the Austrian monk Gregor Mendel discovered that they inherit from their parents, what we now know to be genes, which control how they grow. Like peas, the genes in the DNA of our chromosomes have the code for life. But what is that code exactly? DNA is comprised of long chains of chemicals of four different types: A, C, G and T. The genetic code is copied into a related molecule called RNA that is the messenger of this code. RNA is comprised of almost the same chemicals, A, C, and G, but U replaces T. Cellular machines called ribosomes, take the message and use it to build proteins corresponding to this code.

Interestingly, the RNA chemicals can be altered, and by far the most common modification within the messenger RNA chain is m6A. Consequently, messenger RNA is effectively comprised of five different chemicals: A, C, G, U and m6A. You never heard of it? It is surprising how little attention it has had because if humans, flies or plants don't have it, they die. Recently, a human gene called FTO, which is linked to several human diseases, was found to encode a protein able to convert m6A back to A. This revealed that m6A levels in RNA could be controlled, and if this was disrupted, disease could result. It seems that m6A doesn't change the genetic code itself, but it does affect the message and so affects how the code is used in everyday life. This project is all about m6A in plants, but based on what we have done so far, it should tell us about animals and people as well.

Like Mendel, our project results from discoveries we have made with plants. While studying a protein that naturally helps plants flower, Gordon Simpson's team discovered it controlled where messages end. Using a specially developed technique, they discovered that this protein is found close together with enzymes that make m6A. This made some sense because Rupert Fray, an RNA methylation expert, had previously shown that m6A is mostly found near the end of messages. So, using the same techniques to see what proteins were closely associated with the enzymes that make m6A, Gordon Simpson worked with Rupert Fray, and together, they discovered several proteins that were highly related across lots of different plants and animals, that helped these enzymes make m6A not only in plants but in humans as well.

The aim of this project is to understand m6A a lot better by using plants. Plants are vital to our food and energy security so it is important that we know how they work. Because we can make mutant plants in the lab that still live but have altered levels of m6A, we can study them more simply and use that knowledge to try to understand why plants and animals use m6A in the message of their genetic code.

First, we want to know which messages have m6A and where in the message is this found. We want to know if this changes in different situations such as in flowers compared to leaves or when the plant is stressed. Second, we want to know how m6A is made by the factors that help the enzymes we have found. Do they do it to all genes, or only some and only in specific parts of some messages? How do they talk about what they are doing to all the other parts of the cell that are making and reading the code as well? Third, we want to understand exactly what goes wrong when m6A is changed. What happens to individual messages? Finally, we'd like to begin to understand how the m6A code is read. Proteins with YTH domains apparently bind m6A, they are found in plants but we don't know what they do.

We form a hugely experienced team in this area and we hope to learn very basic knowledge about the message of our genetic code. This work will provide state-of-the-art training for early career scientists working as a team on plants, genetics, RNA, proteins and computational analysis of large sequencing datasets - assembling the skills modern plant science needs to ensure future food and energy security.

Technical Summary

The most prevalent internal modification of eukaryotic mRNA is the methylation of adenosine at the N6 position (m6A) and there are writers, readers and erasers of this epitranscriptome code. The enzyme that writes this code (MTA in Arabidopsis) is essential for life in Arabidopsis, flies and humans, and specific functions for RNA methylation are emerging. Working with Arabidopsis, we used in vivo interaction proteomics to identify a core set of conserved factors that co-purify with MTA. We have shown that these proteins are required for mRNA methylation in Arabidopsis and HeLa cells, and refer to them as the m6A writer-complex. These breakthroughs suggest that Arabidopsis can be a generally usefully model system for understanding the role and impact of RNA methylation.

The aims of this proposal are to define the Arabidopsis epitranscriptome, determine how it is regulated and assess the impact on gene expression of disrupting individual writer-complex components.

We will use Me-RIP-seq to identify sites of mRNA methylation. We will test whether m6A is dynamically controlled by quantifying shifts in m6A in different tissues and in response to stress. We will examine functional conservation of m6A by Me-RIP-seq of the crop plants rice and tomato. We will assess regulatory roles of the writer-complex by identifying in vivo targets (ChIP-Seq), the impact of disrupted writer-complex component function on specific m6A modifications (Me-RIP) and identify in vivo protein partners. We will analyse the consequences for gene expression in these functionally compromised backgrounds by quantitative RNA-seq. Finally we will begin the first characterization of Arabidopsis YTH domain proteins that can bind m6A.

This collaboration combines expertise in RNA methylation (Fray), the molecular and proteomic analysis of RNA processing (Simpson) and quantitative analysis of high throughput sequencing data (Barton).

Planned Impact

1. Cultural Life. Our work defines a new area of science connected to the very nature of the genetic code. This curiosity-led discovery of new knowledge is a feature that the UK public expect of their scientists as GGS experienced when he spoke about non-coding antisense RNAs at a BBSRC organized public engagement event at the Edinburgh International Science Festival.

2. Agricultural Industry. Our work benefits the development of world agriculture in several distinct ways. First GGS and RGF are training a new generation of plant scientists familiar with working with genetics, making crosses and phenotyping plants. Second, we are training biologists used to working in multi-disciplinary teams, combining the iterative interaction of bench scientists with computational biologists. Third, through analysis of huge sequencing datasets we are drawing into plant biology, scientists from mathematical and physics backgrounds, who bring with them quite different skill-sets and insight that can be highly beneficial to understanding plant biology and hence crop science. By establishing cross-link based in vivo interaction proteomics, we are optimizing a relatively neglected research tool for the plant biology community. In light of the relative challenges in extracting proteins from living plants compared to human cell lines, this development may be particularly beneficial to plant biologists. Finally, the link between mRNA methylation and translatability under stress conditions identified by RGF's group may benefit the agricultural industry by aiding selection/breeding programmes. For example, knowledge of how plants survive hypoxic conditions could lead to crops better able to withstand flooding and waterlogging.

3. World Economy. Dundee takes the training of PhD and Post-Doctoral scientists particularly seriously and has a specific department called "OPD" that delivers "non-bench" training in, for example, public speaking and public engagement. Both Dundee and Nottingham provide a highly international working environment with staff from over 60 different nationalities. Dundee houses the 3rd largest biotech cluster in the UK, whilst Nottingham University is a founding partner in BioCity Nottingham - one of Europe's largest bioscience incubators. Together, these aspects of research life provide rounded, highly skilled and educated employees to the international work-force. Among recent alumni from GGS's and GJB's BBSRC-funded work who came to Dundee from overseas, C. Hornyik has gone on to hold a P.I. position in crop science in the UK, L. Terzi a managerial position in a Swiss pharmaceutical company and Alexander Sherstnev analyses RNA-Seq data for Glaxo Smith Kline in Hertfordshire. Alumni from RGF's lab include University faculty (G. Kahka and S. Zhong) and staff scientists in industry (J. Button, MedImmune).

4. Society Through Public Engagement. This proposal relates to fundamental understanding of the genetic code. The GM controversy highlights the importance of public understanding and support for the research we do. GGS became responsible for Dundee Plant Sciences impact activities in 2010 and since then the Division has successfully developed valuable links with Dundee's Botanic Garden, a hands-on DNA extraction activity to communicate information about plants having genes and a sustainable "Genetics Garden". In this proposal we describe a computer generated animation of the epitranscriptome and social media tools that we will use to communicate our research interests in gene expression to the general public. The work of our groups in public engagement is not unique, but part of the culture of Dundee University College of Life Sciences, reflected by the fact that Dundee won the inaugural BBSRC "Excellence with Impact" competition and are participants in the current competition.
 
Description 1. We met the original objectives of our proposal.
2. Identification of the proteins that write m6A in plants.
We developed a method to purify protein complexes from plants and devised a new data analysis approach to interpret the findings. Using this approach, we identified a set of proteins required to write m6A in the model plant Arabidopsis. Previous attempts to purify the m6A writer complex from plants had failed to identify several of the components that we discovered, revealing the power of our new approach.
3. Identification of the proteins that read m6A.
We applied our method for purifying proteins in a collaboration with a group in France to identify the proteins that co-purify with proteins that read m6A. This led to the funding of a collaborative award to pursue the function of these proteins during plant stress responses funded by the French Research agency, ANR-Heat-EpiRNA: ANR-17-CE20-0007-04.
4. Mapping the complexity of RNA using nanopore direct RNA sequencing.
We used a conventional approach to study gene regulation in our study called RNA-Seq, but we also pioneered the use of another technology called nanopore direct RNA sequencing that was released towards the end of our funding period. The major distinction between these technologies is that in RNA-Seq, RNA is fragmented into small pieces for sequencing and then computationally reconstructed. This is a difficult and unsolved problem. The advantage of the nanopore approach is that full-length RNA molecules can be sequenced. We modified the technique developed by Oxford Nanopore Technologies to reveal multiple feature of RNA processing in full-length RNA molecules. Our work on validating our findings was published in the open access journal eLIFE.
5. Mapping of the sites of m6A using nanopore direct RNA sequencing.
We developed a new technique to map m6A. We were the first to develop an approach to map m6A using a technique called nanopore direct RNA sequencing. This enabled us to map the position of m6A much more precisely than before. This work was published in the open access journal eLIFE.
6. We discovered that m6A is required for the proper control of circadian rhythms in plants.
Having mapped m6A, in full-length RNA molecules, we could investigate what impacts it had on biology. We discovered that the expression of genes that control the circadian clock of plants were disrupted. We collaborated with Anthony Hall (Earlham Institute) and Peter Gould (University of Liverpool) to show that the circadian rhythms of plants with reduced levels of m6A were extended. Hence, although the circadian clock has been the subject of intense study in Arabidopsis for around 30 years, we were able to reveal a completely different layer of gene regulation required for its control.
7. The major impact of m6A is on when mRNAs end.
When genes are switched on, the DNA is copied into a related molecule called RNA. The RNA copy can be stopped at different sites in the gene, so that different parts of the gene are copied - this is an important level at which genes can be controlled and is a process found widely in nature, including in humans too. We found that in the absence of m6A, the copies of 1000s of genes stopped earlier than normal. These findings suggest that one of the major functions of m6A is to control where gene copies end. The process of ending gene copies is controlled by a multi-protein complex that is made up of related proteins in very different species. However, one component of this complex in plants has a domain which reads m6A, whereas humans, for example, do not. Our findings provide an explanation for the evolution of this domain in this protein specifically in plants.
8. The approach that we have used to map m6A has already been adopted and adapted by others.
The approach that we developed to map m6A has already been adopted and adapted to map m6A in adenovirus, demonstrating the potential for this approach to be more widely useful. We anticipate that this approach could be used to study m6A in different species and in different conditions eg during stress.
9. The experience we developed in analysing RNA we have applied to transform the annotation of orphan crops.
The investment we made in detailed characterisation of the properties of nanopore direct RNA sequencing in revealing the complexity of RNA processing demonstrated its utility in genome annotation. We used this as background data to win funding from GCRF to transform the annotation of orphan crops. We have collaborated with the African Orphan Crops Consortium in this new programme. Our first study, targeting water yam, has already been released https://phytozome-next.jgi.doe.gov/info/Dalata_v2_1.
10. Insight into a group of disease-causing animals.
Aside from plants, the only other species to have evolved a reader domain in the equivalent protein that controls where RNAs end is in the apicomplexa, a group of parasitic protozoa that cause diseases in animals and human such as toxoplasmosis and malaria. Consequently, the insight and approaches used by us, could be translated to alternative drug targets to treat important diseases.
11. A press release relating to the publication of our work in eLIFE is available here:
https://www.lifesci.dundee.ac.uk/news/2020/jan/16/new-approach-revealing-complexity-rnas-genomes-really-encode
12. A podcast interview of people who worked on the mapping of m6A study is available here
http://blog.garnetcommunity.org.uk/matthew-parker-kasia-knop-and-anya-sherwood-talk-to-the-garnet-community-podcast/
13. A press release of our work with nanopore direct RNA sequencing in orphan crops is available here
https://www.lifesci.dundee.ac.uk/news/2020/jan/21/uncovering-genome-sequence-water-yam-orphan-crop
Exploitation Route 1. The approach that we have used to map m6A has already been adopted and adapted by others.
The approach that we developed to map m6A has already been adopted and adapted to map m6A in adenovirus, demonstrating the potential for this approach to be more widely useful. We anticipate that this approach could be used to study m6A in different species and in different conditions eg during stress.
2. The experience we developed in analysing RNA we have applied to transform the annotation of orphan crops.
The investment we made in detailed characterisation of the properties of nanopore direct RNA sequencing in revealing the complexity of RNA processing demonstrated its utility in genome annotation. We used this as background data to win funding from GCRF to transform the annotation of orphan crops. We have collaborated with the African Orphan Crops Consortium in this new programme. Our first study, targeting water yam, has already been released https://phytozome-next.jgi.doe.gov/info/Dalata_v2_1.
3. Insight into a group of disease-causing animals.
Aside from plants, the only other species to have evolved a reader domain in the equivalent protein that controls where RNAs end is in the apicomplexa, a group of parasitic protozoa that cause diseases in animals and human such as toxoplasmosis and malaria. Consequently, the insight and approaches used by us, could be translated to alternative drug targets to treat important diseases.
Sectors Agriculture, Food and Drink,Environment,Pharmaceuticals and Medical Biotechnology

URL https://www.lifesci.dundee.ac.uk/news/2020/jan/16/new-approach-revealing-complexity-rnas-genomes-really-encode
 
Description British Council Newton Bhabha Fund
Amount £5,000 (GBP)
Organisation British Council 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2018 
End 08/2018
 
Description Marie Sklodowska-Curie Actions
Amount € 183,455 (EUR)
Organisation European Union 
Sector Public
Country European Union (EU)
Start 03/2017 
End 02/2019
 
Description Project de Recherche collaborative (PRC) appel a project générique 2017 (collaborative research project, call 2017)
Amount € 508,572 (EUR)
Funding ID ANR-Heat-EpiRNA: ANR-CE20-0007-04 
Organisation National Agency for Research 
Sector Public
Country France
Start 02/2018 
End 01/2022
 
Description Royal Society Newton Advanced Fellowship
Amount £30,000 (GBP)
Organisation The Royal Society 
Sector Charity/Non Profit
Country United Kingdom
Start 12/2017 
End 11/2018
 
Description Wellcome Trust ISSF Interdisciplinary Research Fund
Amount £10,893 (GBP)
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2016 
End 07/2017
 
Description Brian Gregory 
Organisation University of Pennsylvania
Country United States 
Sector Academic/University 
PI Contribution Supply of low methylation plant material for collaborative RNA processing and structure analysis.
Collaborator Contribution Partners have undertaken detailed analysis of mRNA secondary structures and processing changes that take place as a result of reduced RNA methylation.
Impact Submitted joint publication.
Start Year 2015
 
Description Perpignon group 
Organisation The Plant Genome and Development Laboratory (LGDP)
Country France 
Sector Academic/University 
PI Contribution Supply of transgenic plant lines and and analysis of methylation levels of mRNA from heat stressed plants grown by our collaborator.
Collaborator Contribution Preparation of mRNA from heat treated Arabidopsis lines.
Impact Ongoing application grant application to French government by Perpignan Group "Reading the plant epitranscriptome: molecular and physiological functions of m6A readers in Arabidopsis thaliana". We are named as partners in this application. Conference invitation (Summer 2016)
Start Year 2014
 
Description Poznan - m6A mapping 
Organisation Adam Mickiewicz University in Poznan
Country Poland 
Sector Academic/University 
PI Contribution Training given to visiting researcher in methodologies for detecting m6A methylation in primary micro RNAs.
Collaborator Contribution Partner provided RNA samples from control plants and from our low methylation lines. Partner also carried out quantification of specific transcripts after m6A pulldown in Nottingham.
Impact Generation of data for future joint publication.
Start Year 2017
 
Title RATs - Relative Abundance of Transcripts 
Description Who it is for Anyone working in transcriptomics, analysing gene expression and transcript abundances. What it does It provides a method to detect changes in the abundance ratios of transcript isoforms of a gene. This is called Differential Transcript Usage (DTU). RATs is workflow-agnostic. Quantification quality details are left to the quantification tools; RATs uses only the transcript abundances. This makes it suitable for use with alignment-free quantification tools like Kallisto or Salmon. It is also compatible with DTE output from Sleuth. RATs is able to take advantage of the bootstrapped quantifications provided by the alignment-free tools. These bootstrapped data are used by `RATs to assess how much the technical variability of the heuristic quantifications affects differential transcript usage and thus provide a measure of confidence in the DTU calls. What it needs This is an R source package, and will run on any platform with a reasonably up-to-date R environment. As input, RATs requires transcript abundance estimates with or without bootstrapping. For convenience, these can also be extracted directly from the output of Sleuth. RATs also requires a look-up table matching transcript identifiers to respective gene identifiers. This can be obtained through various means, one of them being extracting this info from a GTF file. RATs makes use of the data.table and matrixStats packages, as well as ggplot2 and shiny for visualisations. All these are available from CRAN. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact RATs has generated a lot of interest in the community of people interested in differential transcript identification. A paper describing RATs and its evalutation is in final draft. 
URL https://github.com/bartongroup/RATS
 
Title Relative Abundance of Transcripts (RATS) 
Description Relative Abundance of Transcripts (rats) Description Who it is for Anyone working in transcriptomics, analysing gene expression and transcript abundances. What it does It provides a method to detect changes in the abundance ratios of transcript isoforms of a gene. This is called Differential Transcript Usage (DTU). RATs is workflow-agnostic. Quantification quality details are left to the quantification tools; RATs uses only the transcript abundances, which you can obtain using any tool you like. This makes it suitable for use with alignment-free quantification tools like Kallisto or Salmon. RATs is able to take advantage of the bootstrapped quantifications provided by the alignment-free tools. These bootstrapped data are used by RATs to assess how much the technical variability of the heuristic quantifications affects differential transcript usage and thus provide a measure of confidence in the DTU calls. What it needs This is an R source package, and will run on any platform with a reasonably up-to-date R environment. A few third-party R packages are also required (see below). As input, RATs requires transcript abundance estimates with or without bootstrapping. The format either way is tables with the samples as columns and the transcripts as rows. An extra column holds the transcript IDs. Some functionality to create these from Salmon or Kallisto quantification files is provided by RATs. RATs also requires a look-up table matching the transcript identifiers to the respective gene identifiers. This can be obtained through various means, one of them being extracting this info from a GTF file using functionality provided by RATs. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact RATS allows transcript abundance to be estimated from short read (Illumina) data. It is unique in providing a confidence estimate for such analyses. 
 
Title Relative Abundance of Transcripts (rats) 
Description Description Who it is for Anyone working in transcriptomics, analysing gene expression and transcript abundances. What it does It provides a method to detect changes in the abundance ratios of transcript isoforms of a gene. This is called Differential Transcript Usage (DTU). RATs is workflow-agnostic. Quantification quality details are left to the quantification tools; RATs uses only the transcript abundances, which you can obtain using any tool you like. This makes it suitable for use with alignment-free quantification tools like Kallisto or Salmon. RATs is able to take advantage of the bootstrapped quantifications provided by the alignment-free tools. These bootstrapped data are used by RATs to assess how much the technical variability of the heuristic quantifications affects differential transcript usage and thus provide a measure of confidence in the DTU calls. What it needs This is an R source package, and will run on any platform with a reasonably up-to-date R environment. A few third-party R packages are also required (see below). As input, RATs requires transcript abundance estimates with or without bootstrapping. The format either way is tables with the samples as columns and the transcripts as rows. An extra column holds the transcript IDs. Some functionality to create these from Salmon or Kallisto quantification files is provided by RATs. RATs also requires a look-up table matching the transcript identifiers to the respective gene identifiers. This can be obtained through various means, one of them being extracting this info from a GTF file using functionality provided by RATs. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact This allows the analysis of alternative transcripts from RNA-seq data and has been used by a number of groups in their research. 
URL https://github.com/bartongroup/RATS
 
Title RoSA 
Description RoSA: a tool for the Removal of Spurious Antisense In stranded RNA-Seq experiments we have the opportunity to detect and measure antisense transcription, important since antisense transcripts impact gene transcription in several different ways. Stranded RNA-Seq determines the strand from which an RNA fragment originates, and so can be used to identify where antisense transcription may be implicated in gene regulation. However, spurious antisense reads are often present in experiments, and can manifest at levels greater than 1% of sense transcript levels. This is enough to disrupt analyses by causing false antisense counts to dominate the set of genes with high antisense transcription levels. The RoSA (Removal of Spurious Antisense) tool detects the presence of high levels of spurious antisense transcripts, by: analysing ERCC spike-in data to find the ratio of antisense:sense transcripts in the spike-ins; or using antisense and sense counts around splice sites to provide a set of gene-specific estimates; or both. Once RoSA has an estimate of the spurious antisense, expressed as a ratio of antisense:sense counts, RoSA will calculate a correction to the antisense counts based on the ratio. Where a gene-specific estimate is available for a gene, it will be used in preference to the global estimate obtained from either spike-ins or spliced reads. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact This tool has improved the ability to interpret RNA-seq data for antisense analysis. 
 
Title RoSA: a tool for the Removal of Spurious Antisense 
Description In stranded RNA-Seq experiments we have the opportunity to detect and measure antisense transcription, important since antisense transcripts impact gene transcription in several different ways. Stranded RNA-Seq determines the strand from which an RNA fragment originates, and so can be used to identify where antisense transcription may be implicated in gene regulation. However, spurious antisense reads are often present in experiments, and can manifest at levels greater than 1% of sense transcript levels. This is enough to disrupt analyses by causing false antisense counts to dominate the set of genes with high antisense transcription levels. The RoSA (Removal of Spurious Antisense) tool detects the presence of high levels of spurious antisense transcripts, by: analysing ERCC spike-in data to find the ratio of antisense:sense transcripts in the spike-ins; or using antisense and sense counts around splice sites to provide a set of gene-specific estimates; or both. Once RoSA has an estimate of the spurious antisense, expressed as a ratio of antisense:sense counts, RoSA will calculate a correction to the antisense counts based on the ratio. Where a gene-specific estimate is available for a gene, it will be used in preference to the global estimate obtained from either spike-ins or spliced reads. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact It has enabled a number of groups to identify spurious antisesnse in their RNA-seq data. 
URL https://doi.org/10.5281/zenodo.2661378
 
Title profDGE48 (2016 Update) - Code base for profiling highly replicated differential gene expression RNA-seq 
Description profDGE48 is the code that has been used to understand the relationship between replication and power in RNA-seq analysis. The code also allows the comparison of different methods of calling differential gene expression (DGE) by RNA-seq. This code was central to the high-impact work on RNA-seq published in the journal RNA (Schurch et al). This version includes bug fixes and updates to the work from 2015. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact The software enabled work on RNA-seq to be completed and underpins our understanding of the technique for experimental design decisions made in this grant and all subsequence Simpson/Barton collaborative grants. The principles set out by the software have been widely adopted by the academic community. 
URL https://github.com/bartongroup/profDGE48
 
Description Dec 2016 Oxford: Seminar at WTCHG/SGC: Identification of novel functional sites in protein domains from the analysis of human variation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact This was an invited seminar at the Oxford SGC and WTCHG institutes in the Department of Medicine. The seminar described work that covered most of our funded research activities.
Year(s) Of Engagement Activity 2016
URL https://talks.ox.ac.uk/talks/id/7b03765b-6d8a-45c0-bbb1-e570a70377ff/
 
Description Fascination o fPlants Day - "Plant Power" Dundee Botanic Garden 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact We host scientific engagement activities run by scientists in the Division of Plant Sciences. In recent years we have invited staff from The James Hutton Institute to be involved. We have a day of activities, but in addition, we have long lasting displays that include a "Genetics Garden" where we have planted barley mutant along a chromosome, wild ancestors and modern day cultivated varieties of barley, Mendel's original pea mutants. The garden and associated information boards are visible for most of the year. The garden is funded in part by my BBSRC grants. The Garden itself has been profiled on BBC Scotland. The Botanic garden receives 80,000 visitors per year, and the open day activities attract between 650-1500 people per event.
Year(s) Of Engagement Activity 2012,2013,2014,2015,2016,2017
 
Description Feb 2017: Seattle: What can human variation tell us about protein structure? 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This was an invited talk at the genevariation3d workshop at the Institute of Systems Biology which brought together scientists from the genomics/personalised medicine field and the field of protein structure analysis. I presented on our work at this interface that is built on Jalview and the Dundee Resource and inspired by our research in plant biology.
Year(s) Of Engagement Activity 2017
URL http://genevariation3d.org/
 
Description Gatsby Charitable Trust Plant Science Master Class 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact I organised a Masterclass for local schoolchildren S% and S6 on "New technologies" with talks on RNA-Seq analysis, proteomics, with a tour of the proteomics facility. Members of my lab, Geoff Barton's lab and the proteomics facility were involved.The Dundee series of Plant Science Master Classes has been used as a case study by the Gatsby Charitable Trust for the success of the programme as a whole.
Year(s) Of Engagement Activity 2017
 
Description Genetics Garden 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact As part of the pathways to Impact of this proposal we said we would work together with Dundee University Botanic Garden to develop a "Genetics Garden" for public engagement. With funding from Dundee University College of Life Sciences BBSRC Excellence with Impact award we have developed this garden. THis was opened to the public on 27th June 2013.

I developed a Genetics Garden as a hub for Plant Sciences Public Engagement Activity (which I lead). Since its creation in 2013 we have directly engaged 1000s of members of the public in Plant Science. BBC Scotland's Beechgrove Garden was introduced from our Genetics Garden when it was first planted in 2013, and in 2015 Jim McColl met me to plan a special feature on the Genetics Garden. The 8 minute piece was broadcast on BBC2 in August 2015. The recorded number of visitors to Dundee University Botanic Garden the following weekend quadrupled relative to the corresponding weekend of the previous year.

no actual impacts realised to date
Year(s) Of Engagement Activity 2013,2014,2015
URL http://www.bbc.co.uk/programmes/b0674xf1
 
Description Mar 2017: Seminar at Newcastle University: Identification of novel functional sites in protein domains from the analysis of human variation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact This was an invited seminar to the Centre for Health and Bioinformatics at Newcastle University. I presented work at the interface between genomics/transcriptomics and protein structure which relied heavily on the software tools we develop and other resources.
Year(s) Of Engagement Activity 2017
URL http://www.ncl.ac.uk/chabi/events/pastevents/item/eventgeoffbarton.html
 
Description Nov 2016: Talk by Kimon Froussios at RNA Discussion Meeting, James Hutton Institute 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact This was a talk on techniques developed in our group for the analysis of transcript abundance in Arabidopsis and other species. A short talk was given presenting a new computational tool to an audience composed of researchers most likely to use such tools. Discussions ensued with regards to its capabilities and comparison to existing similar tools.
Year(s) Of Engagement Activity 2016
 
Description Oct 2016 Poster: GRE Symposium: with Kimon Froussios: Transcript isoform switching in RNA-seq data 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Poster describing techniques developed to analyse isoform switching in Arabidopsis and other complex Eukaryotes.
Year(s) Of Engagement Activity 2016
 
Description Presentation to Central South University, Changsha, China 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact I gave a talk about our recent research to a mixed audience of scientists and students at CSU, Changsha.
Year(s) Of Engagement Activity 2017
 
Description Seminar at Garvan Institute, Sydney, Australia 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Presented recent research work to staff at the Garvan Institute and others in the region.
Year(s) Of Engagement Activity 2017
 
Description Seminar at Newcastle University, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Presented recent research from my group to Research Group Leaders, Postdocs, Ph.D. Students, Undergraduates.
Year(s) Of Engagement Activity 2017
 
Description Seminar at Sydney University, Australia 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Presentation about my group's research to the University of Sydney.
Year(s) Of Engagement Activity 2017
 
Description Seminar at Wellcome Trust Centre for Human Genetics, University of Oxford 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Seminar describing wide range of research from my group.
Year(s) Of Engagement Activity 2016
URL https://talks.ox.ac.uk/talks/id/7b03765b-6d8a-45c0-bbb1-e570a70377ff/
 
Description Seminar to Free Univesrity of Amsterdam, Netherlands 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Presented recent research from my group to Research Group Leaders, Postdocs, Ph.D. Students, Undergraduates.
Year(s) Of Engagement Activity 2017
 
Description Sept 2015: Invited Seminar at TGAC, Norwich 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact I presented a broad range of our research at an invited seminar at The Genome Analysis Centre (TGAC) now, the Earlham Institute.
Year(s) Of Engagement Activity 2015
 
Description Talk on GM to growers 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Talk to G's vegetable growers and retailers. Guest dinner speaker and chair of GM debate held by their graduate training programme.
Year(s) Of Engagement Activity 2014