Dynamic re-programming of the cold transcriptome in Arabidopsis

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

Abstract

Genes are the repositories of hereditary information; proteins are the machines that carry out the functions of living cells. Gene expression usually refers to the process by which a gene gives rise to a protein. In eukaryotes, gene expression is complex and when such protein-coding genes are expressed, the DNA sequence is first copied into a precursor messenger RNA (pre-mRNA) by transcription. The pre-mRNA undergoes several processing steps to form the mature messenger RNAs (mRNAs) which direct synthesis of the corresponding protein (translation). In this project we focus on an extremely important RNA processing step called alternative splicing (AS). AS generates different mRNA transcripts from the same gene and thereby can modulate transcript and protein levels and functions.

Plants experience continual changes in environmental conditions and have evolved systems to cope with stress-causing conditions and to survive the stress. In this project we are focussed on the response of plants (Arabidopsis) to low temperature and the role of temperature-dependent AS in the plant response to cold. The overall expression of a plant at any particular time is called the transcriptome and it the collection of all of the gene transcripts being expressed. It is determined by 1) transcription (turning genes on or off, up or down) and 2) AS (making >1 transcript from a gene). The high quality of our data allows networks of transcription and AS to be constructed. This will identify key factors which regulate transcriptional and AS responses and the re-programming of the transcriptome when plants are exposed to low temperatures. We will characterise such genes for their effect on sensitivity or tolerance to low temperature thereby identifying candidate genes for improving cold tolerance in crop species.

In this research we will address five main objectives by exploiting our expertise in alternative splicing and circadian clock analyses.

(1) In the dynamic transcript expression profiles that we have already obtained, we observe changes in the rhythmic expression/AS of many genes at low temperature, including genes that lose or gain rhythmicity. This suggests that the circadian clock may be involved in the regulation of these genes and by analysing the transcriptomes of plants grown at 20C and 4C we will identify those genes whose altered expression/AS is controlled by the clock.

(2) We see some AS responses that occur very rapidly after the onset of cooling, suggesting activation of pre-existing splicing factors (SFs) rather than formation of new ones, with phosphorylation as a likely mechanism. We will investigate immediate/early AS and phosphorylation of SFs to identify candidate SFs that may be involved in these rapid responses to cooling.

(3) A major part of the research will be the characterisation of novel cold response genes which show significant AS changes in response to low temperature. Mutant, over-expression and complementation lines will be assessed for cold sensitivity/tolerance and acclimation.

(4) We are now able to generate high resolution data enabling us to build transcription and splicing factor networks and identify and validate key SFs (and transcription factors) that regulate cold-induced AS. The data also gives the opportunity to integrate transcription and AS networks providing a much better understanding to how the transcriptome is dynamically altered.

(5) For future network modelling, knowledge of RNA-binding sites of SFs is essential. We will characterise the RNA-binding sites of key SFs identified here as a first step to developing a splicing code.

Technical Summary

Our experimental approaches and bioinformatics developments demonstrate that dynamic changes in the transcriptome depend on both transcription and AS and that AS forms an important part of re-programming of the transcriptome.

We will continue to use ultra-deep RNA-seq of time-courses of plants treated with low temperatures and exploit our developments in RNA-seq analysis. The dynamic transcript-specific profiles allow network modelling at both the gene (transcriptional) and splicing (AS) levels and, significantly, gives the opportunity to integrate these different layers of regulation. The most up-to-date approaches in network analysis will be applied to existing data and the new data (constant light; first 3 h at 4C) allowing causal inferences in the networks to be predicted.

Key hub genes (genes with many connections to other genes) are likely to be important in re-programming the cold transcriptome. Selected genes will be characterised for their physiological (freezing tolerance and acclimation) and molecular phenotypes (validation of network connections - effects on AS target genes of mutants/over-expression lines).

Immediate/early effects on AS may be important to priming the plant (transcriptome) for temperature change before establishing the full low temperature response. We will therefore exploit the extensive expertise in phosphoproteomics at Dundee to investigate immediate/early phosphorylation of splicing factors in response to low temperatures and will investigate specific kinases involved in cold signalling.

Finally, genes with AS events important in establishing the cold transcriptome and tolerant/acclimation are expected to show an altered phenotype when knocked out. Also, the different transcript isoforms (which may code for different protein isoforms) may be responsible for the phenotype. We will express specific AS isoforms in mutant backgrounds to demonstrate the functionality of specific AS isoforms.

Planned Impact

The impact of this work will be the novel information on how gene expression is reprogrammed at the transcript, gene and network levels and how to apply the current technologies to perform such analyses in different plant and crop species. These approaches can be used by plant scientists examining gene function and gene expression of development, responses to external stimuli, metabolic pathways, biotechnology approaches, plant breeding etc.. In particular, the approaches will benefit many areas of crop genomics and biology but translation to crops requires an understanding of the potential and action to focus on generation of the transcriptomic resources. As such the main beneficiaries and users are the research sector, both academic and industrial.

The main challenge to maximising impact is to raise awareness of its potential and utility with the people who are most likely to use it and benefit their research. This needs to be done in a timely fashion so that other researchers can plan and design RNA-seq experiments with the goal of analysing data using comprehensive RTDs and the best available programmes to quantify transcript levels and establish network models.

The main Impact Objectives are to:

- Publicise the value of transcript-specific expression and understanding the dynamic transcriptome
- Encourage the development of RTDs for other plant/crop species.
- Engage with crop scientists and industry

To achieve these objectives:
1) The PIs/Co-Is will ensure community awareness by contacting research groups in the plant community with details of the project and how it will benefit them

2) The PIs/Co-Is will present regular updates of progress at national and international conferences and meetings on plant biology and genomics such as SEB, ICAR conferences etc as well as through more focussed meetings on RNA splicing, gene networks and the circadian clock. The PIs/Co-Is will also present their findings at invited seminars.

4) The PI/Co-Is will develop a strategy for interacting with crop scientists developing genomics approaches and engaging with industry.

5) Tools and resources for RNA-seq and network analysis will be released on the most appropriate websites for rapid uptake; a "cold" expression website will be established where users can examine expression profiles of their gene of interest in our time-course series.

6) Results will be published in timely fashion.

6) Public engagement activities.

7) Training and mentoring of the PDRAs.
 
Description By detailed analysis of the time-series data of plants grown at 20C and the the temperature lowered to 4C, we have investigated the dynamics of the alternative splicing and transcriptional response. This has allowed us to identify transcription and splicing factors whose expression changes very quickly in response to cold. We are examining the speed and sensitivity of some AS to reductions in temperature. Mutants of some of these genes are being screened for cold tolerance.

We have now conducted an expanded RNA-seq analysis of the first three hours of lower temperature and show that many genes are significantly differentially expressed or differentially alternatively spliced in 20-40 minutes after the temperature starts to fall.

We have used the original dataset to build both gene and splicing networks. We have validated the gene network against previously published data on the cold response. We have separated subnetowrks associated with cold-induced transcription factors CBF2 and CBF1/CBF3 on the basis of timing of changes in expression in response to cold. We show that the well-charactersied CBf regulon is mainly associated with CBF1/CBF3. We have identified a novel sub-network upstream of CBF2 and CBF1/CBF3 called the early cold response sub-network which contains many of the earliest responding genes. The majority of clock genes map the the CBF2 and CBF1/CBF3 subnetworks highlighting the integral connections between the clock and cold response.We furtehr define clusters of genes which are down-regulated in the cold again at different times of exposure to cold. A sub-network of genes enriched for ribosomal proteins and ribosome biogenesis factors (cytoplasmic, chloroplastic and mitochondrial) is up-regulated in the cold. The gene network allows us to asscoiate transcription factors to the regulation of gene clusters. The splicing network reflects the largely very rapid changes in AS with cold. However, around a third of the 2,400 transcripts in the network are in clusters which have rapid changes in rhythmic alternative splicing suggesting a key connection with the clock and changes in expression and function of the clock. By connecting the gene and splicing network we can predict clock genes which potentially trigger changes in expression and alternative splicing to drive the changes in the plant to survive and acclimate.
Exploitation Route Given the extensive research on the cold response in Arabidopsis, the gene network represents the most advancedand high resolution network to have been produced to date. The splicing network is entirely unique. Linking the gene and splicing networks brings added information and overall the network for a fundamental framework for future cold response analyses. The networks provide a means to identify the earliest events in gene expression changes in response to a fall in temperature and predict key events and regulators.

Our advances in RNA-seq analysis speed and accuracy are being recognised by other groups and we will endeavour to spread our expertise.
Sectors Agriculture, Food and Drink,Environment

 
Title 3D RNA-seq 
Description 3D RNA-seq is a program for accurate measurement of differential gene and transcript expression, differential alternative splicing, differential transcript usage and isoform switches from RNA-seq data. It is designed for use by biologists to overcome issues of access to bioinformaticians and to improve the accuracy of analysis over other available programs. The program already has had excellent uptake and excellent reviews (on social media). A paper has recently been submitted for publication. 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? Yes  
Impact 3D has the potential to revolutionise RNA-seq analysis. Impact is measured by the growing number of users and requests from scientists for information and help in running. 
URL https://github.com/wyguo/ThreeDRNAseq
 
Title 3D RNA-seq - a program for biologists for easy and effective RNA-seq analysis 
Description RNA-seq analysis usually relies on bioinformaticians to find the time and will to analyse data generated by bench scientists. The analyses are not always optimum if the bioinformaticians do not fully understand what the biologists want. The time taken for getting such analyses done is a major source of frustration for biologists. We developed methods to analyse RNA-seq accurately and effectively. To meet the needs of biologists, we have developed an easy-to-use RNA-seq analysis program which can be used by biologists with minimal bioinformatics expertise or by bioinformaticians with limited experience in analysing gene expression. The program does the analysis and generates automatically the tables of differentially expressed, genes and transcripts, differentially alternatively spliced genes and differential transcript usage. The prototype was launched at the Cyverse Workshop at the Earlham Institute in December 2018. The updated version will be released in March/April 2019. 
Type Of Material Data analysis technique 
Year Produced 2019 
Provided To Others? No  
Impact The program will be made widely available soon. We expect it to have major impact. 
 
Title New program to detect significant isoform switches in time-series data -Time-Series Isoform Switch (TSIS) 
Description One aspect of alternative splicing (AS) is isoform switching where the relative abundance of different isoforms of the same genes switches under different conditions. For example, isoform switches are used in cancer diagnostics. There are three programs to identify isoform switches in pairwise sample comparisons. TSIS is the only program which can identify significantly different isoform switches in time-series RNA-seq data. 
Type Of Material Data analysis technique 
Year Produced 2017 
Provided To Others? Yes  
Impact To date there are a small number of citations. However, it's application is clearly demonstrated in the Calixto et al (2018) paper and we expect more uptake. 
 
Description Cold tolerance and acclimation phenotyping of mutants of cold responsive splicing factors/RNA-binding proteins 
Organisation Durham University
Country United Kingdom 
Sector Academic/University 
PI Contribution We have identified splicing factors/RNA-binding proteins which rapidly change their expression or alternative splicing in response to low temperatures. We have obtained homozygous mutants of selected genes. The mutants are then tested for their ability to tolerate freezing temperatires and to acclimate to cold in the lab of Dr. Heather Knight.
Collaborator Contribution The partners have helped to perform the analyses and have trained post-docs in the techniques
Impact Freezing sensitivity of a U2B"-like mutant was demonstrated and published in Calixto et al (2018) Plant Cell.
Start Year 2016
 
Description 3D RNA-seq training workshops at University of Leeds (October) and Nottingham (November) - presented by Runxuan Zhang, Wenbin Guo, JC Entizne. 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Study participants or study members
Results and Impact We have developed 3D RNA-seq in oreder to analyse the RNA-seq data generated in time-courses of Arabidopsis plants exposed to cold. 3D RNA-seq is an analysis program for RNA-seq data analysis designed for use by biologists with minimal bioinformatics experience. The program is an easy-to-use tool that provides accurate differential gene and transcript expression and differential alternative splicing. It can be used for RNA-seq data from eukaryotes and has been successfully used with plants (Arabidopsis, potato, barley etc) and animals (human, mouse etc). It won the University of Dundee School of Life Sciences Best Innovation award in 2019. 3D RNA-seq was launched in May 2019 with publication in bioRxiv and has had great success with nearly 2,500 users. To help to have uptake in the UK, we have run training courses in the University of Leeds (supported by GARNet and the University of Nottingham. In addtion, we have trained individuals from human and medical sciences.
Year(s) Of Engagement Activity 2019
 
Description Alternatively spliced genes as novel cold responsive genes in Arabidopsis (Cristiane Calixto/ASPB Hawaii/2017) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk in RNA Biology session of ASPB Plant Biology meeting Hawaii, USA 2017
Year(s) Of Engagement Activity 2017
 
Description Co-organiser of session on "Impact and function of Alternative Splicing" at the SEB Sevilee in July 2019 - John W S Brown - Co-organiser. 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Co-organised the session on Alternative splicing at SEB Seville.
Year(s) Of Engagement Activity 2019
 
Description Interplay between gene expression and alternative splicing determines cold acclimation in Arabidopsis (John Brown/Cambridge University/November 2017) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Invited seminar - Plant Sciences, University of Cambridge
Year(s) Of Engagement Activity 2017
 
Description Invited talk at SEB Seville "Rapid Cold-Induced Expression and Alternative Splicing in Arabidopsis Involves Complex Networks of Regulators". Given by John W S Brown 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented new data on gene expression and alternative splicing in Arabidopsis in response to cold and preliminary data on gene and splicing networks. Great deal of discussion with many scientists.
Year(s) Of Engagement Activity 2019
 
Description Plant Power 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact The public engagement aims of the School of Life Sciences are to:
1. Build on our creative partnerships to deliver a high quality, innovative engagement programme.
2. Engage a range of people with our research.
3. Collaborate with our local communities to meet their needs and widen our reach.
4. Promote and support a culture of active participation in public engagement within our life sciences community. This includes students, research and non-research staff.

In the Division of Plant Sciences, research includes topics such as genetic modification, food security and sustainability. "Plant Power" is an annual event that takes place in collaboration with and at the University of Dundee Botanical Gardens where various different groups and organisations participate with plant related activities/shows. A science strand was delivered by researchers from the Division of Plant Sciences at the University of Dundee and the James Hutton Institute. The aim of the science strand is to engage the general public, mainly family groups, to learn about the plant research taking place locally and why this research is important. Topics such as genetic modification, food security and sustainability are covered. As a division wide event, it addresses our School strategy aim of promoting and supporting a culture of active participation in public engagement within our life sciences community. This includes students, research and non-research staff.

The researchers presented different (12 in total) interactive hands-on outreach activities related to their respective groups' research to the visitors. These activities are either brand new or have been developed by researchers over a number of years at various events. Various modes were used to communicate the research as shown by the diversity of activities undertaken such as the use of simple games (Jumping Genes & 1,000 year Old Farm); craft activities (flower felting & Mendelian Genetics); and accessible science experiments (DNA extraction from raspberries & detection of microbes on the roots of plants).

My research was represented in this program of work by aiding in the demonstration of DNA extraction and where possible, with adults, talking about DNA-RNA-protein to expand on the basic understanding of DNA that many people have.

Over 1000 people came to the Botanical Gardens for the event. They are generally family groups with young children (below 10 years of age). We estimate that around 200-250 people visited our science strand area.
Feedback from the public indicated that they enjoyed all the activities and learned lots of new plant related facts. Feedback comments included:
- Learnt about multicoloured corn - I did not know it existed.
- I did not know corn could be multicoloured.
- I've learnt where bananas and pineapples come from.
- I learnt about potatoes
- Learnt about microbes on roots

Legacy: Follow on plans are for the activities developed for Plant Power to become formal educational borrow boxes for teachers to utilise for an in-class learning resource. An overall Plant Sciences box aligned with the Curriculum for Excellence for Scottish schools and investigating formally sharing activities via publications would be a subsequent step.
Year(s) Of Engagement Activity 2018
URL https://www.eveningtelegraph.co.uk/fp/dundee-people-children-gets-down-to-roots-at-dundees-plant-pow...
 
Description Plant Power 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Plant Power is an annual event that takes place at the University of Dundee Botanic Garden where various different groups and organisations participate with plant related activities/shows. A science strand is delivered by researchers from the Division of Plant Sciences at the University of Dundee and the James Hutton Institute. They presented different interactive hands-on activities related to their respective groups research to the visitors. These activities are either brand new or have been developed over a number of years at various events. The aim is to allow the public to learn about the research taking place locally and why this research is important. Various modes were used to communicate the research as shown by the diversity of activities e.g. use of games (pin the plant & botany trail); craft activities (chromosome modelling & lino printing); science experiments (raspberry DNA extraction); art (animating science).

Approximately 970 people came to the Botanic Garden for the event. They are generally family groups with young children (below 10 years of age). We estimate that around 200-250 people visited our activities.

We talked to members of the public and answered questions from how to stop slugs eating hostas to the safety of GM food.

Feedback from the public indicated that they enjoyed all the activities. Researchers fed back the questions and statements from the public asked while interacting with them.
Year(s) Of Engagement Activity 2019
 
Description Poster at SEB Seville - "RNA-binding proteins involved in gene expression and alternative splicing in Arabidopsis under cold stress" presented by Nikoleta Tzioutziou. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented our latest data on RNA-binding proteins in the cold response in Arabidopsis.
Year(s) Of Engagement Activity 2019
 
Description Presentaion at Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Germany - Rapid and dynamic alternative splicing impacts the cold response transcriptome in Arabidopsis - given by Prof John W S Brown 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited seminar at IPK-Gatersleben; multiple discussions with different group leaders and interested parties
Year(s) Of Engagement Activity 2018
 
Description Presentaion at Molecular Cell Physiology Department, University of Bielefeld, Bielefeld, Germany - Rapid and dynamic alternative splicing impacts the cold response transcriptome in Arabidopsis - given by Prof. John W S Brown 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited seminar - discussions with PhD students and research groups interested in our advanced approaches.
Year(s) Of Engagement Activity 2018
 
Description Presentation at 6th UK RNA Splicing Workshop - Rapid cold-induced alternative splicing in Arabidopsis involves a complex network of regulators - given by Prof John W S Brown 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presentation covered our research on cold-induced changes in expression and alternative splicing. Also presented a new method/tool of RNA-seq analysis designed for biologists. massive interest in this.
Year(s) Of Engagement Activity 2018
 
Description Presentation at GARNet2018:a plant science showcase at University of York - in Large Scale Biology section - "Genome-wide alternative splicing" - given by Dr Cristane Calixto 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Invited to speak about oue genome-wide methods for analysis of RNA-seq for gene expression and alternative splicing
Year(s) Of Engagement Activity 2018
 
Description Presentation at SEB Annual Meeting, Florence - Rapid cold-induced alternative splicing in Arabidopsis involves a complex network of regulators - given by Dr Nikoleta Tzioutziou 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation in section: Plant Temperature responses: Shaping Development and Enhancing Survival?

Presented out novel RNA-seq analysis methods for time-course analysis (paper published in Plant Cell - Calixto et al 2018.
Year(s) Of Engagement Activity 2018
 
Description Public Engagement for Plant Power Day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Our lab members asisted the organisation of the open day "Plant Power Day" that took place in the Dundee Botanic Garden, part of the University of Dundee. The garden was open to public and various activities aimed to engage the puplic (children and adults) with plant research related to the Division of Plant Sciences and The James Hutton Institute in Dundee.
Year(s) Of Engagement Activity 2017
 
Description Rapid and dynamic alternative splicing impacts the Arabidopsis cold response (Cristiane Calixto/IGC Symposium - Lisbon/2017) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited talk at the IGC Symposium 2017 - Plant RNA Biology. Lisbon, 27-28 September 2017 (talk given by Cristiane Calixto)
Year(s) Of Engagement Activity 2017
 
Description Rapid and dynamic alternative splicing impacts the cold response transcriptome in Arabidopsis (John Brown/Humboldt University, Berlin/January 2018) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited seminar at Humboldt University, Berlin, Germany
Year(s) Of Engagement Activity 2018
 
Description Rapid and dynamic alternative splicing impacts the cold response transcriptome in Arabidopsis (John Brown/Max Planck Institute, Golm, Germany/January 2018) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited seminar at MPI Golm, Germany
Year(s) Of Engagement Activity 2018
 
Description School visit (Quenn Victoria School, Dunblane) (John Brown, January, 2018) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Visit to the school to talk about careers in life sciences
Year(s) Of Engagement Activity 2018
 
Description Strategic discussion on plant alternative splicing community following sessions at SEB Seville on "Impact and functions of alternative splicing" 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The appreciation of the importance of alternative splicing continues to grow. A number of research groups have studied many aspects of alternative splicing for over 10 years and our efforts have been responsible for raising such awareness. The potential difficulty is that it becomes accepted without the realisation that there is still an immense amount to be learned. The discussion was about how the plant alternative splicing community (many of whom were at the meeting) should try and alter their outlook to maintain excellent basic research in this area. In addition, over the last 7-8 years 3-4 groups have co-ordinated activities across the European and an International groups but at least two of these groups are coming to an end with the retirement of the group leaders and there was discussion about others taking on the responsibility for maintaining momentum.
Year(s) Of Engagement Activity 2019