EASTBIO: Stress-responsive RNA–protein interactions and transcript isoform regulation in cardiomyocytes

EASTBIO: Stress-responsive RNA–protein interactions and transcript isoform regulation in cardiomyocytes

Research Question and Applicant Fit

This Edinburgh EASTBIO project asks whether heart muscle cells change which proteins bind RNA during stress and recovery, and whether those changes alter transcript isoforms. Its distinctive training combines cardiac cell biology, quantitative proteomics and RNA analysis, with explicit separation of association from causation. International students can compete for four-year support including Edinburgh’s overseas tuition-fee difference. The deadline is 16 November 2026, with no published clock or time zone in the project description. The formal four-year registration route and individual 2027 stipend remain to be confirmed; neither an award nor a clinical outcome is guaranteed.

Research Problem and Doctoral Work

What is actually being tested

A stress-associated RNA-binding signal can change because a protein becomes more abundant, because its RNA association changes, or because the RNA population itself changes. The project proposes matched RNA-bound and total proteomes to distinguish the first two explanations, then short-read expression/splicing analysis and long-read transcript reconstruction to investigate isoforms. This is a stronger question than compiling a list of differentially expressed genes: the challenge is to connect reproducible changes across measurement layers without treating a correlated protein as the cause of an RNA change.

The advertised work begins with reproducible in-vitro stress and recovery states, initially hypoxia–reoxygenation, followed by oxidative and proteotoxic/endoplasmic-reticulum stress. Cell-state, viability and recovery criteria are to be established before molecular profiling. OOPS and quantitative mass spectrometry profile RNA-associated proteins; total-proteome measurements provide an abundance reference. Short reads support expression and differential-splicing comparisons, whereas long reads resolve full-length transcript structures and combinations that short fragments can leave ambiguous.

Integration then selects two or three candidates against predefined criteria. Perturbation/rescue, targeted splicing assessment and direct RNA-binding mapping are proposed validation categories, rather than evidence that the mechanisms already work. Human three-dimensional cardiac tissue is a final stage where feasible. A vertebrate in-vivo extension is explicitly outside the core funded project and needs separate funding and approvals. The January 2027 BSc Honours project is intended to develop initial models and assays; its future data are not assumed in the PhD proposal and January is not the advertised doctoral start date.

Useful doctoral outputs could include a reproducible stress-response data resource, a carefully validated RNA-regulatory mechanism, or an analysis showing that apparently shared responses are model- or stress-specific. These are plausible outcomes, not promised publications. Model maturity, recovery heterogeneity, proteomic missingness and isoform quantification are likely to determine how much causal work is achievable. The supervisors’ cardiac RNA and RNA-biochemistry backgrounds support the combination; their wider research programmes do not establish this new project’s results.

School, Programme and Field Context

The University of Edinburgh is the advertised host and intended degree-awarding institution. Beqqali belongs to the School of Neurological and Cardiovascular Sciences, within the College of Medicine and Veterinary Medicine, while Granneman holds a Chair in RNA Biochemistry in the School of Biological Sciences. This is cross-school supervision within one university, not evidence of a joint or double degree.

The 2027 Cardiovascular Science PhD, course 208, matches the advertised school, Centre for Cardiovascular Science and administrative contact Lynn Meikle. However, its ordinary full-time PhD option is three years, whereas this project is a four-year EASTBIO opportunity. The actual award title, application code and registration arrangement must therefore be confirmed rather than assigning the project automatically to the ordinary three-year option or Biological Sciences with Internship. The course and centre describe at least two academic advisors, a thesis committee, seminars and research-in-progress discussion. Their older BHF four-year MScR/PhD rotation scheme is a separate scheme, not this project’s curriculum. 2027 course, centre training.

EASTBIO’s training framework puts core training in years one and two, with research emphasis in years three and four. It includes cohort and professional development. Ordinary funded students undertake a 12-week non-academic PIPS before the end of year three, with host agreement and programme approval; this project is not identified as CASE and has no promised industrial placement host. A PIPS is professional experience outside the PhD project, not an additional degree or a guaranteed job. Training, PIPS.

Edinburgh is 35th overall in QS World University Rankings 2027. That is an institutional comparison, not a ranking of this RNA laboratory. More relevant subject evidence is the combination of cardiovascular training and a quantitative RNA group with original measurement and analysis publications. This offers useful breadth, but daily mentoring across locations and access to each platform still need agreement. QS.

Supervisor and Lab Assessment

Appie (Abdelaziz) Beqqali is described in his institutional profile as a Chancellor’s Fellow, which notes that he accepts PhD students. His institutional profile focuses on cardiac RNA-binding proteins, splicing and heart failure. A 2024 staff page calling him Research Fellow is an older description. Sander Granneman has held the Chair in RNA Biochemistry since 2024; his CV records doctoral-programme leadership and RNA technology expertise. His laboratory’s established systems-RNA and computational work is substantially in microbial models, so transfer to cardiomyocytes is part of the scientific challenge. Beqqali lab, Granneman lab, CV.

Three recent original papers provide complementary evidence, not three completed tests of this PhD:

• Cordiner et al., 2023, Nature Communications 14:696: Granneman is a coauthor; Torben Heick Jensen is the corresponding author. Temporal-iCLIP showed that several RNA-processing factors initially encounter nascent RNA before developing different binding profiles linked to processing. The useful lesson is that timing changes interpretation of an RNA-binding measurement. It does not establish a cardiomyocyte stress response. Reading covered the complete original abstract and substantive indexed introduction/results, not all methods or supplements. Paper.
• Winterbourne et al., 2025, Nucleic Acids Research, gkaf204: Granneman is a coauthor; Atlanta Cook is corresponding author. Structural and solution-based evidence supports RNA-dependent rearrangement and coating by NF45–NF90 complexes. It explains why binding architecture can matter beyond total protein abundance. A structural model does not by itself demonstrate a particular cardiac isoform effect. Reading covered the complete original abstract and indexed introduction/discussion portions, not a full paper or supplement review. Paper.
• Monteiro et al., 2025, Cardiovascular Research 121:988–991: this original research letter includes Beqqali as coauthor, not corresponding author. Mouse cardiac morphology/function and single-nucleus RNA evidence connect MIR503HG loss to ventricular developmental abnormalities; altered Notch activity is a proposed explanation. This supports cardiac RNA research experience, not human stress-recovery validation or a therapy. Reading covered the complete structured abstract and selected original introduction/results narrative, not all methods or underlying data. Paper.

None of these three papers lists both project supervisors. Their combined expertise is a reason to investigate the opportunity, while the division of supervision, technical support for proteomics/long reads and availability of three-dimensional cardiac tissue remain practical questions. No published meeting frequency or personal instrument allocation has been verified for this studentship.

Funding, Application, and Living Cost

The project explicitly offers a four-year EASTBIO competition covering stipend and Home tuition, with Edinburgh covering the international tuition difference for successful appointees. EASTBIO guidance cited here confirms international eligibility and a waiver for successful international candidates. The 30% international cap is across annual network intake, not this project’s number of overseas places or an individual success probability. The project’s positive funding route is established; a candidate need not already possess an award before applying. Individual 2027 stipend, payment dates and detailed award conditions are still unknown. Funding FAQ.

Apply for one EASTBIO project across the partnership. For this project, email the EASTBIO application form and PDF transcripts to Lynn.Meikle@ed.ac.uk by 16 November 2026. The project asks referees to send template references to the same address by that deadline. EASTBIO network guidance specifies two academic or professional references, excluding project supervisors, plus the anonymous EDI survey response ID on the form. No late applications are accepted. This is not the separate Biology Euclid route, and no midday cutoff or two-week reference grace period is established here. Network selection guidance normally starts studentships on 1 October; confirm that this project follows 1 October 2027 and obtain the local cutoff clock/time zone. Application, selection.

For budgeting, UKRI’s £21,805 minimum is for 2026/27, not a verified 2027/28 personal rate. Edinburgh estimates £18,504 a year / £1,542 a month for a single postgraduate in 2026/27, including accommodation/utilities averaging £978 monthly. Comparing those dated references leaves about £3,301 annually / £275 monthly, before costs outside that living budget; this is an illustration, not forecast savings. Research support is not disposable income. EASTBIO excludes visa and immigration-health costs. The cited Student visa fee reference is £558, with the student IHS rate £776 per visa year; visa length and part-year charging can exceed simple four-year multiplication. Flights, deposits, inflation and dependants require separate planning. UKRI, Edinburgh budget, visa, IHS.

Applicant Fit and Preparation

The advert does not list a separate exhaustive skills prerequisite. EASTBIO generally requires an upper-second-class degree or international equivalent and does not universally require a master’s. The 2027 CVS course reference likewise lists UK 2:1 equivalent. RNA/cell biology, quantitative proteomics or sequencing/data analysis experience would each provide a credible starting point; no evidence says applicants must already master every advertised method. A strong preparation example would explain how biological state, protein abundance and measurement uncertainty were handled in a prior project, rather than simply listing software or assays.

Chinese applicants have a positive route through international EASTBIO eligibility, the Edinburgh fee waiver and the university’s explicit recognised-Chinese-university qualification assessment. The China page’s 80–85% tables apply to taught postgraduate courses and two named MScR programmes, not a universal PhD cutoff. It says a master’s may be needed where the chosen PhD’s Qualifications section specifies one. The individual Chinese PGR equivalence and actual registered course should therefore be assessed; do not infer either automatic exclusion or a compulsory master’s from unrelated courses. China guidance.

The 2027 CVS course reference requires IELTS Academic 6.5, each 6.0; TOEFL before 21 January 2026 is 92, each 23, and from that date 4.5, each 4.5. IELTS One Skill Retake and TOEFL MyBest are not accepted. Relevant tests must be within two years on the first day of the starting month; English-taught degree exemptions have approved-country/institution and, where applicable, five-year recency restrictions. Confirm these against the actual four-year registration. EASTBIO permits applying before holding an English certificate, but it may be needed before a formal offer. ATAS rules do not generally exempt Chinese nationality: whether clearance applies depends on the offered subject classification and research statement, not nationality alone. Course, ATAS rules.

Career and Transferable Skills

The transferable value lies in reproducible multi-omics integration, RNA measurement and experimental–computational communication, supporting research, platform-science and bioinformatics pathways. Professional bioscience career resources show these directions, but no verified salary, vacancy count or placement outcome is available for this lab. Careers.

Next Actions and Questions to Verify

Before applying, confirm the vacancy remains available, the local deadline clock, exact four-year award/code, Chinese qualification equivalence and applicable English conditions with Lynn Meikle. Contact A.Beqqali@ed.ac.uk for scientific discussion; Granneman’s published professional contact is Sander.Granneman@ed.ac.uk. Prepare the single-project form, EDI response, transcripts and timely template references rather than substituting a general online enquiry.

At interview, ask how stress/recovery acceptance criteria and candidate selection will be agreed; who provides daily cardiac-model, proteomic and computational guidance; and which long-read and three-dimensional tissue resources are committed. Clarify what happens if the January Honours work or conditional tissue validation is not ready. Before accepting, establish the personal stipend/payment period, fee-waiver documentation, registration duration, PIPS arrangements and upfront immigration budget.

Evidence and Sources

Project scope and the stated 16 November 2026 deadline follow the advertisement dated 17 October 2026; no deadline time or timezone is given, and current recruitment status is unconfirmed. Programme and training conditions apply to their named sources and do not establish this project’s final registration. The three paper discussions are bounded by the specified original abstracts and selected or indexed sections; none is a complete full-text, supplementary-material or raw-data audit. Fee and living-cost figures retain the dates shown by their cited sources and are not a forecast of personal 2027 disposable income.

Project, supervisors and original research

• Beqqali current profile
• Granneman current profile
• Temporal-iCLIP, 2023
• NF45–NF90 structural study, 2025
• MIR503HG cardiac study, 2025
• Granneman lab
• Beqqali lab
• Granneman CV

Programme, funding and application

• 2027 Cardiovascular Science course
• CVS doctoral training
• EASTBIO funding and eligibility FAQ
• EASTBIO application
• EASTBIO selection
• EASTBIO training
• PIPS requirements
• China qualifications

Costs, institutional context and careers

• Edinburgh living budget
• UKRI stipend reference
• QS2027 Edinburgh
• Student visa
• Immigration healthcare charge
• ATAS rules
• Bioscience careers