PhD fellow in Molecular biology, Biotechnology and Genomics

IIT; Genova; Hybrid; EUR 16,000 - 20,000; Full time

Benefits offered by this job

International PhD program

Collaboration with Open University

Doctorate in Health, Sustainable and H

Job summary

Istituto Italiano di Tecnologia in Genoa invites excellent candidates to apply to its ARC PhD program in collaboration with the Open University. The program confers Doctorates in Health, Sustainable and Human Technologies.

One PhD fellow position will be available from 1st January 2027 in the Non-coding Genomics research Line led by Stefano Gustincich. Background: SINEUPs and antisense lncRNAs enable translational enhancement and are studied across mammalian systems.

Qualifications

• Masters-level degree is required, broadly corresponding to MSc/MChem/Meng-style, or a postgraduate Masters in the British system, or a second level Italian degree.
• Grade: upper second class (2.1) or 100/110; lower grades may be considered if accompanied by publications or relevant expertise.
• If English is not the first language, a valid IELTS with overall 6.5 and minimum 6.0 in each band is required.

Responsibilities

• Carry out computational cataloguing of lncRNAs with embedded inverted repeats across human, mouse, and other mammals.
• Perform PARIS analysis to identify lncRNA/mRNA pairs and candidate SINEUPs.
• Conduct functional validation in HEK293 and neuronal cells, measuring protein over mRNA ratios.

Skills

Molecular biology

Biochemistry

Cell culture

Cell biology

Education

Masters-level degree

Upper second class / 2:1 or 100/110 Italian system

Job description

PhD fellow in Molecular biology, Biotechnology and Genomics

Italy

IIT invites excellent candidates to apply to its PhD program organized in collaboration with the Open University; this international PhD program confers Doctorates in Health, Sustainable and Human Technologies.

In order to be admitted into the ARC program, the minimum requirements are

• a Masters-level degree, which broadly corresponds to a 4/5-year undergraduate MSc/MChem/Meng-style degree or to a postgraduate Masters in the British system, or to a second level University degree in Italy;
• a grade corresponding to an upper second class (2.1) or a merit in the UK system or 100/110 in the Italian system. Candidates with lower grades but redeeming features (publications, specific expertise) are requested to contact the potential supervisors before applying;
• where English is not the applicant’s first language, a valid IELTS (International English Language Testing System) certificate. The minimum acceptable score is an overall 6.5, with no less than 6.0 in any of the four categories

One PhD fellow position will be available from 1st of January 2027 in the Non-coding Genomics research Line led by Stefano Gustincich.

Title of the project: The SINEUPOME.

Background: SINEUPs are a class of natural and synthetic antisense long non-coding RNAs that selectively increase the translation of a target mRNA without altering its transcription or stability. They were discovered through the mouse antisense Uchl1 transcript (Carrieri et al., Nature 2012), whose activity depends on an embedded inverted SINEB2 repeat, the origin of the name.

SINEUPs have a modular architecture. A binding domain, antisense to the 5′ region of the target mRNA (typically overlapping the start codon), confers specificity. An effector domain, containing the inverted SINEB2 element or minimal functional fragments of it, drives translational enhancement. Swapping the binding domain lets SINEUPs be designed against virtually any gene of interest.

Their effect is moderate (about 1.5- to 3-fold protein increase) and stays within physiological ranges. This makes them attractive for haploinsufficiency disorders and other conditions caused by insufficient protein dosage. They are also useful for biotechnological protein production. They can be delivered as plasmids, viral vectors such as AAV, or synthetic RNA.

Description:

• Rationale. Only a handful of natural SINEUPs are known, yet inverted SINE elements are abundant in antisense transcripts across mammals. A systematic analysis would reveal how widespread translational enhancement by antisense lncRNAs really is.
• Aim 1 – Computational catalogue. Mine CAGE (FANTOM5/6), total RNA-seq and nanopore long-read datasets from human, mouse and non-model mammals to annotate lncRNAs with an embedded inverted SINE (SINEB2, MIR, Alu, FLAM).
• Aim 2 – PARIS analysis. Identify lncRNA/mRNA pairs in PARIS data from a diverse array of dataset. List which candidate SINEUPs from Aim 1 are part of the duplex.
• Aim 3 – Functional validation. Test 50–100 top SINEUP candidates in HEK293 and neuronal cells, measuring protein over mRNA ratio of the targets by western blot, qRT-PCR and polysome profiling.
• Impact. A validated atlas of natural SINEUPs and their targets, plus rules linking sequence architecture to activity, would provide both a new layer of post-transcriptional gene regulation and design principles for synthetic SINEUP therapeutics.

References

• D'Agostino S, Tettey-Matey A, Volpe M, Pierattini B, D'Agostino M, Smělá D, Ansaloni F, Broglia L, Lau P, Peruzzo O, Braccia C, Armirotti A, Scarpato M, Damiani D, Ros G, Di Carlo V, Maniscalco F, Bechara E, Tartaglia GG, Carninci P, Santoro C, Persichetti F, Pandolfini L, Simonetti A, Espinoza S, Zucchelli S, Sanges R, Bon C, Gustincich S. (2025). Internal ribosome entry sites enhance translation in trans in antisense non-coding SINEUP and circular RNAs. Nucleic Acids Res. 53(15):gkaf788.
• Carrieri C*, Cimatti L*, Biagioli M, Beugnet A, Zucchelli S, Fedele S, Pesce E, Ferrer I, Collavin L, Santoro C, Forrest AR, Carninci P, Biffo S, Stupka E, Gustincich S. (2012). Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature 491(7424):454-7.

Main Supervisor: Stefano Gustincich (Non-coding Genomics)

Additional Supervisor: Remo Sanges ( Non-coding Genomics)

Essential expertise:[essential expertise]

• Molecular biology
• Biochemistry
• Cell culture
• Cell biology

Desirable expertise:

• GenomicS
• Transcriptomics
• Knowledge of lncRNAs
• Knowledge of repetitive elements

Istituto Italiano di Tecnologia, with its headquarters in Genoa, Italy, is a non-profit institution with the primary goal of creating and disseminating scientific knowledge and strengthening Italy's technological competitiveness. IIT's research endeavour focuses on high-tech and innovation, representing the forefront of technology with possible application from medicine to industry, computer science, robotics, life sciences and nanobiotechnologies.

Istituto Italiano di Tecnologia is an Equal Opportunity Employer that actively seeks diversity in the workforce.

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