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PhD Project: Where Does COOLAIR RNA Go in the Cold? Visualising RNA in Plant Cells

Project 1799 · John Innes Centre · Graduate Programme

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Save this opportunity and prepare around its actual requirements. Confirm deadlines and eligibility at the original source.

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Country or region
United Kingdom
Application deadline
2026-11-30 (confirm the exact time with the source)
Funding
Eligible international applicants compete for four years of tuition and a UKRI-minimum stipend; £21,805 is the 2026/27 reference, with 2027/28 to be confirmed. The £5,000 annual RTSG is research funding. International awards are capped at 30% of the NRPDTP annual cohort, not this project or personal odds. October 2027 entrants may claim up to £3,500 for their own visa and IHS costs after registration against evidence; dependants are excluded. The advert says “shortlisted” while Funding Notes say “awarded”; the individual award awaits formal confirmation.

The research opportunity

PhD Project: Where Does COOLAIR RNA Go in the Cold? Visualising RNA in Plant Cells

Research question and doctoral work

Winter vernalisation progressively represses FLOWERING LOCUS C (FLC), a flowering regulator in Arabidopsis. COOLAIR is a family of antisense long non-coding RNAs transcribed from the FLC locus. Existing research links RNA structure and abundance with cold responses, but neither measurement answers where individual isoforms occur inside plant cells or how localisation relates to FLC regulation.

The PhD will combine plant RNA imaging, advanced fluorescence microscopy, quantitative image analysis and bioinformatics. It will compare the spatial organisation of COOLAIR isoforms under constant and fluctuating winter temperatures, including freezing events, and use natural genetic variation plus mutants affecting COOLAIR transcription and processing to investigate localisation mechanisms and their influence on FLC regulation and flowering. The analysis must distinguish biological redistribution from differences in RNA abundance, cell size, background signal or image segmentation; association alone does not establish causation. Conservation in Brassica crops motivates longer-term relevance, but the advert assigns no crop experiment or field validation.

Host, training and career fit

The research host is the John Innes Centre (JIC), within a University of East Anglia (UEA) registration framework; the student's formal registration unit and degree title depend on the offer. Professor Yiliang Ding is the primary supervisor, Dr Susan Duncan provides day-to-day co-supervision, and Professor Caroline Dean is named as a collaborator, with formal co-supervisor status unconfirmed. This is a four-year full-time NRPDTP project with a mandatory three-month professional internship (PIPS) outside the direct thesis topic.

Training spans RNA and molecular biology, plant genetics, microscopy, quantitative image analysis and bioinformatics. Those skills could transfer to plant-science research, microscopy, image-analysis and biological-data roles; PIPS can broaden exposure beyond academic research. These are plausible pathways inferred from the training, not promised jobs or salaries.

Eligibility and application

The project requires an obtained or expected first-class, upper-second or equivalent Honours degree in biology, biochemistry, molecular biology, plant science, genetics or a related subject; a Master's is not universally required. NRPDTP may consider lower-second applicants who also have a School-accepted relevant Master's or substantial relevant research/non-academic experience. The lower-second degree condition remains, and experience alone does not replace all academic requirements. UEA assesses overseas qualifications individually; the saved material sets no China-specific institution list or PhD percentage threshold.

Science doctoral English requirements are IELTS 6.5 overall with 6.0 in each component; PTE 61 overall and 60 in each component; TOEFL iBT 88 (Reading 20, Writing 19, Listening 19, Speaking 21); or the TOEFL iBT 26 scale, 4.5 overall (Reading, Writing and Listening 3.5 each; Speaking 4), including the Special Home Edition. Tests must be within two years of the course start. China is not on the listed nationality/degree-country exemption route, and a Chinese English-medium degree is not an automatic waiver. NRPDTP permits English to remain an offer condition; UEA makes the final decision.

Apply through UEA using the NRPDTP Personal Statement and Research Statement templates, with a separate application for each project and a maximum of three. The saved guidance asks for qualifications/transcripts and official translations, applicable post-Bachelor study records, a 1–2-page CV, two referees including at least one academic, and passport/visa evidence where applicable. Proposed supervisors and friends or relatives cannot be referees. The saved material does not specify which non-English documents trigger translation; confirm the scope. The linked templates still carry 2026 filenames, so confirm the 2027 versions. Partner institutions state that selection is without regard to gender, marital/civil-partnership status, disability, race, nationality, ethnic origin, religion or belief, sexual orientation, age or social background. Bespoke statement templates are intended to help applicants from under-represented groups give examples and evidence. The advert does not describe individual adjustments following disability disclosure.

The saved October 2026 schedule lists a 30 November 2026 deadline, shortlist notices from the week of 18 January 2027, interviews on 2–4 February, outcome notices from the week of 22 February and a 1 October 2027 start. No deadline hour or time zone is stated, and current application status has not been checked. Contact Yiliang.Ding@jic.ac.uk about the research; confirm application requirements and templates with the admissions team.

Funding

Eligible international applicants can compete for four years of tuition, a UKRI-minimum living stipend and £5,000 per year in Research Training Support Grant (RTSG). RTSG is research funding, not personal living income. International awards are capped at 30% of the entire NRPDTP annual cohort, not this project's places or an applicant's personal odds. £21,805 is the 2026/27 stipend reference; the 2027/28 amount requires the award terms. For October 2027 entrants, up to £3,500 toward the student's own visa and Immigration Health Surcharge (IHS) costs is reimbursed after enrolment/registration against evidence; dependants are excluded, and this is not an upfront waiver. The project text says “shortlisted for funding” while its Funding Notes say “awarded”; individual admission and funding remain subject to the formal outcome.

Sources

NRPDTP project page · FindAPhD listing · NRPDTP website

Research and application brief

Report generated: . This date does not confirm that recruitment remains open.

Information updated: . Recheck the original notice before applying.

Show report contents

PhD Project: Where Does COOLAIR RNA Go in the Cold? Visualising RNA in Plant Cells

Project Assessment

Strong but verify fit. This is a plant RNA cell-biology doctorate at the John Innes Centre (JIC), combining a specific flowering-regulation question with quantitative microscopy. Its distinctive asset is the complementary Ding–Duncan–Dean expertise, rather than an already demonstrated agricultural product. Saved October 2026 project information lists Home and Overseas applicants as eligible to apply. The NRPDTP offers a competitive four-year funded route, with a network-wide international cap; admission and an individual award remain selection outcomes. The listed deadline is 30 November 2026, without a published hour or time zone, for 1 October 2027 entry. Current application status has not been checked. The useful first step is a discussion with Yiliang Ding about the initial biological question, imaging training and supervisory arrangements. Exact NRPDTP COOLAIR 2027 project NRPDTP current four-year international funding NRPDTP current 2027 key dates

Research Problem and Doctoral Work

COOLAIR is a family of antisense long non-coding RNAs associated with FLOWERING LOCUS C (FLC), a regulator of flowering. Existing work connects RNA structure and antisense transcription with winter responses. This project asks a more spatial question: where do different COOLAIR isoforms occur within individual Arabidopsis cells, and when does their location matter for FLC regulation? Amount, molecular conformation and cellular position are related observations, but they are not interchangeable measurements. Yang et al. 2022 single-molecule COOLAIR structural diversity Nielsen et al. 2024 COOLAIR and PRC2 parallel FLC silencing

The advertised work combines plant RNA imaging, advanced fluorescence microscopy, quantitative image analysis and bioinformatics. It compares isoform organisation under constant and fluctuating winter conditions, including freezing events, and uses natural genetic variation plus mutants affecting COOLAIR transcription and processing to investigate localisation mechanisms and their effects on FLC regulation and flowering. Brassica conservation motivates longer-term crop relevance; the advertisement does not establish crop performance, field robustness or an assigned Brassica work package. Exact NRPDTP COOLAIR 2027 project

The principal analytical difficulty is separating biological redistribution from changes in transcript abundance, cell size, background fluorescence or image segmentation. Duncan's quantitative-imaging study demonstrates why calibration and the sampled cellular context matter. A convincing thesis could therefore explain which spatial features are reproducible, which correlate with FLC output and which support a mechanistic interpretation. These are possible scientific contributions whose results remain to be established. Duncan Johansson Ding 2023 quantitative RNA imaging reference genes

The programme is also a substantial conceptual commitment to basic plant biology. A brighter RNA signal would not alone establish altered flowering control; an association between a location and FLC expression would not alone identify direction of causation. Conversely, a well-supported finding that apparent localisation differences disappear after accounting for cell size or abundance could still be scientifically valuable. This distinguishes hypothesis testing from producing an attractive image or confirming a predetermined climate-resilience claim. Yang et al. 2022 single-molecule COOLAIR structural diversity Duncan Johansson Ding 2023 quantitative RNA imaging reference genes Nielsen et al. 2024 COOLAIR and PRC2 parallel FLC silencing

School, Programme and Field Context

JIC is the research host; the relevant university registration framework is the University of East Anglia (UEA). The current NBI Graduate School chair explicitly oversees on-site JIC and neighbouring-institute doctoral students registered at UEA. The final offer should identify this student's formal registration unit and degree title. Participation by the Norwich Research Park partners and collaboration with Dean do not create a joint degree. NBI Graduate School and UEA registration

This is a single main research project within a four-year NRPDTP degree, supplemented by cohort development and a mandatory three-month professional internship (PIPS) outside the direct thesis topic. It is not the separate JIC rotation programme. Initial training-needs assessment and a Personal Development Plan guide specialist and transferable-skills choices. PIPS provides a structured way to explore careers; its organisation, host and timing are not an already allocated job or placement. NRPDTP individual and cohort training NRPDTP four-year project and professional internship

RNA imaging, quantitative image analysis, plant genetics and bioinformatics could transfer to plant-science research, microscopy and image-analysis roles, or research teams needing plant molecular and data skills. PIPS can expose students to work outside the thesis topic. These are plausible career fits inferred from the training, not advertised jobs, salaries or employment outcomes.

The subject case is stronger than an overall university ranking can show: the relevant environment brings together RNA structure, quantitative imaging and a sustained FLC/vernalization research programme. UEA's School of Biological Sciences describes molecular, developmental and plant-biological research within the Faculty of Science and collaboration across the park. This supports the wider academic setting, while the exact departmental registration remains an offer-level check. Yiliang Ding JIC group leader Susan Duncan JIC senior scientist Caroline Dean JIC group leader UEA School of Biological Sciences research context

QS places UEA at joint 381 in its 2027 overall World University Rankings. That is a university-wide measure, not a JIC, plant-science or supervisor ranking. Here the fit between the scientific question, the three named researchers and the local microscopy infrastructure is more informative than treating the overall number as a verdict on the narrow research area. The NRPDTP facility inventory includes light, confocal and advanced fluorescence microscopy, but does not establish this student's access priority or training schedule. QS UEA 2027 overall university rank NRPDTP bioimaging and research facilities

Supervisors and Recent Research

Yiliang Ding is a Professor and JIC Group Leader whose programme examines RNA structure, processing and environmental responses. Susan Duncan is a Senior Scientist, with experience in quantitative single-RNA imaging and model-connected plant imaging; the project explicitly assigns her day-to-day co-supervision. Caroline Dean is a Group Leader and Royal Society Professor studying FLC and epigenetic memory. The advert calls her role collaboration, so formal co-supervisor status should not be assumed. Ding's other AI and RNA-design interests do not automatically become work packages in this PhD. Yiliang Ding JIC group leader Susan Duncan JIC senior scientist Caroline Dean JIC group leader Exact NRPDTP COOLAIR 2027 project

Three independent recent originals provide a useful reading route:

Yang and Colleagues (2022): RNA Structural Diversity

Yang et al., Nature 2022, DOI 10.1038/s41586-022-05135-9, by the Ding–Dean team: single-molecule structure profiling distinguishes heterogeneous COOLAIR conformations and cold-associated changes; structural changes were linked to FLC expression and flowering. Its contribution is moving beyond a population-average RNA structure. It does not already resolve the proposed cellular localisation question. Reading: complete original abstract and metadata, not full Methods, supplementary data or independent replication. Yang et al. 2022 single-molecule COOLAIR structural diversity

Duncan, Johansson and Ding (2023): Quantitative Measurement

Duncan, Johansson and Ding, Journal of Experimental Botany 2023, DOI 10.1093/jxb/erac521: quantitative comparison of reference RNAs, cell-size relationships and fluorescence/background measurements supports calibrated imaging. This is directly relevant to judging apparent spatial differences. The cell and tissue context limits automatic transfer to every COOLAIR isoform or winter state. Reading: published original HTML, selected quantitative Methods, Results and Discussion; supplementary material was not read. Its December 2022 online date and April 2023 issue describe the same paper. Duncan Johansson Ding 2023 quantitative RNA imaging reference genes

Nielsen and Colleagues (2024): Parallel Regulation

Nielsen et al., PNAS 2024, DOI 10.1073/pnas.2311474121, from the Dean–Howard team: genetic and chromatin comparisons, combined with modelling, support a faster COOLAIR-linked route alongside a slower PRC2-based silencing mechanism. This prevents an overly simple account in which one RNA localisation event explains the entire winter memory. Reading: complete institutional original abstract and bibliographic verification, not the full main text or supplementary material. Nielsen et al. 2024 COOLAIR and PRC2 parallel FLC silencing

These papers establish complementary structure, measurement and regulation foundations. They do not collectively prove the new spatial hypothesis or its crop translation. The assessment covers the three originals at the different abstract and selected-passage reading depths stated above. The advertisement establishes the complementary expertise, but not meeting frequency, an imaging-support allocation, a first-year milestone or a guaranteed publication count. Those questions matter more than extrapolating supervision quality from publication venues. Exact NRPDTP COOLAIR 2027 project NRPDTP bioimaging and research facilities

Funding, Dates and Living Costs

The current NRPDTP funding page explicitly offers eligible international candidates fully funded studentships: four-year tuition, a UKRI-minimum living stipend and £5,000 per year RTSG. International appointments are capped at 30% of the annual programme intake, not a personal selection probability or 30% of this project's places. £21,805 is the 2026/27 reference stipend, approximately £1,817.08 per month if divided by twelve; the 2027/28 rate and payment schedule need the award letter. RTSG is research support, not another £5,000 of annual personal spending money. NRPDTP current four-year international funding

For October 2027 entrants, the same current page promises a contribution of up to £3,500 toward the student's own visa and immigration health surcharge costs, paid against appropriate evidence after enrolment and registration. Dependants are excluded. This is neither an upfront waiver nor unlimited reimbursement. The project introduction's “shortlisted for funding” and “awarded” descriptions should therefore be read alongside the central rule: a successful eligible candidate receives the award; the advert is not an individual offer. NRPDTP current four-year international funding

For a dated housing reference, UEA's 2026/27 price list gives Village en-suite accommodation at £178.50 per week and Crome at £209.50, with listed 41-week totals of £7,318.50 and £8,589.50. Doctoral living costs run through the year. Merely extending those unchanged weekly prices to 52 weeks gives £9,282–£10,894 for rent alone; that is an illustrative calculation, not a 2027 quote, a room guarantee or a full budget. Food, travel, deposits and summer arrangements remain additional. UEA official 2026/27 accommodation prices

Current government rates are £558 for the Student visa application and £776 per year for student IHS; visa validity and part-year rules affect the actual upfront bill. The outside-London maintenance figure is £1,171 per month for up to nine months, a visa-evidence measure rather than a full-year Norwich budget. China is on the differential-evidence list, but evidence can still be requested and the underlying financial requirement remains. The NRPDTP reimbursement does not remove the need to plan initial cash and any excess. Student visa route and application fee Student visa financial evidence China Student immigration healthcare surcharge

The current central timetable confirms 30 November 2026, interview dates 2–4 February 2027, shortlist notifications from the week of 18 January and outcomes from the week of 22 February. Start is 1 October 2027. No cutoff hour or time zone is published. NRPDTP current 2027 key dates

Applicant Fit and Application

The exact project requires a relevant first-class or upper-second-equivalent Honours degree, obtained or expected, in biology, biochemistry, molecular biology, plant science, genetics or a related discipline. A Master's is not a universal project requirement. NRPDTP also considers lower-second applicants with a relevant School-acceptable Master's or significant relevant research/non-academic experience; that exception retains the lower-second-degree premise. Exact NRPDTP COOLAIR 2027 project NRPDTP eligibility foreign degrees and internationals

There is a positive in-principle route for a Chinese applicant: NRPDTP recognises equivalent qualifications obtained outside the UK and accepts Overseas candidates into its fully funded competition. The examined official material does not establish a China-specific PhD percentage or institution-list threshold, so the applicant's actual degree and transcript need UEA assessment. The programme's specific criteria govern this route alongside the university's broader “2:1 or Master's or equivalent” guidance. NRPDTP eligibility foreign degrees and internationals UEA actual expanded general PGR admissions guide

Science PGR English currently lists IELTS 6.5 overall, every component 6.0, or PTE 61 overall/every component 60. TOEFL iBT is 88 with R20/W19/L19/S21; the iBT26 column is 4.5 overall with R3.5/W3.5/L3.5/S4, including the Special Home Edition. These tests are valid for two years from course start. Listed nationality/degree-country exemptions do not include China; an English-medium Chinese degree is not an automatic waiver. NRPDTP permits English evidence to be an offer condition rather than already achieved at application. UEA retains final acceptance discretion. UEA current Science doctoral English equivalencies NRPDTP application guidance

Apply through UEA using both mandatory NRPDTP Personal and Research Statement proformas, not a free-form substitute. Up to three projects are allowed, each with a separate application. Supply the requested qualifications/transcripts and translations, qualifications beyond the Bachelor's if studied, a 1–2-page CV, two referees including at least one academic, and applicable passport/immigration evidence. Proposed primary or secondary project supervisors, friends and relatives cannot act as referees. The current page still links proforma filenames marked 2026; confirm the correct linked versions for 2027 before submission. NRPDTP application guidance

Partner institutions state that selection is without regard to gender, marital or civil-partnership status, disability, race, nationality, ethnic origin, religion or belief, sexual orientation, age or social background. NRPDTP introduced bespoke statement templates to improve access and help under-represented groups provide relevant examples and evidence. The saved advert does not specify individual adjustments following disability disclosure; ask NRPDTP or UEA about arrangements.

Relevant experience might demonstrate careful microscopy interpretation, plant molecular biology, quantitative analysis or reproducible handling of biological data. These are preparation priorities inferred from the work, not a requirement to arrive already trained in every advertised technique. Interview preparation should explain one prior research contribution, one measurement limitation and how alternative explanations would change interpretation. The practical transferable skills are quantitative imaging, data analysis and communicating biological uncertainty, with PIPS broadening exposure beyond academia; no project-specific employment or salary outcome is published. Duncan Johansson Ding 2023 quantitative RNA imaging reference genes NRPDTP individual and cohort training NRPDTP four-year project and professional internship

Next Actions and Questions

Before applying, contact Yiliang.Ding@jic.ac.uk to clarify the first-year scope, availability of imaging training and the balance between molecular work and quantitative analysis. Ask admissions to assess the actual overseas qualification, confirm the current proformas and the deadline hour. During interview, ask how Duncan's daily support and Ding/Dean input are organised, which image-analysis resources are available, and what would count as a rigorous outcome if the expected localisation effect is absent. Exact NRPDTP COOLAIR 2027 project Susan Duncan JIC senior scientist

Before accepting, obtain the written four-year award, full Overseas tuition treatment, 2027 stipend/payment dates, RTSG arrangements and £3,500 reimbursement procedure. Confirm the UEA registration unit, progression requirements, PIPS timing and costs, and accommodation over a full year. Check the offer's subject/CAH details for any ATAS requirement: the official scheme is conditional on subject and applicant circumstances; the project’s ATAS classification remains unresolved. It is not evidence of a blanket nationality exclusion. NRPDTP current four-year international funding NBI Graduate School and UEA registration ATAS official conditional subject scope

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