Project description
xAI helps decipher the regulatory code of context-specific gene expression in plants
Plants coordinate the activity of thousands of genes during growth, development and response to environmental cues. Deciphering the regulatory code is critical to engineering greater resilience in plants. The ERC-funded multiCODE project will address this using single-cell genomics, ‘explainable artificial intelligence’ (xAI) and synthetic promoter engineering. Unlike AI’s black box, xAI provides explanations for how an AI model reaches a conclusion. Single-cell gene expression profiling in plants will inform xAI models. The models will predict gene expression under certain conditions while identifying the underlying regulatory DNA sequences. The code will then be experimentally verified in plants via a synthetic promoter containing it, enabling precise control of plant gene expression.
Objective
Multicellular plants control the fine-grained expression of thousands of genes during growth, development, and in response to external stimuli. While gene expression varies strongly between different organs and tissues, how this specificity is encoded in the genome is largely unknown. Although various regulatory DNA sequences and sequence-specific transcription factors controlling diverse transcriptional responses have been described, the combinatorial nature of the regulatory code makes the application of rational approaches to learn and predict context-specific gene expression challenging. This is a major obstacle towards engineering plant promoters with predictable and tuneable expression.
multiCODE’s aim is uniting single-cell genomics, explainable artificial intelligence (xAI), and synthetic promoter engineering, to efficiently learn and validate regulatory sequences controlling gene expression in plants. Based on high-resolution single-cell gene expression profiling in the model Arabidopsis and the crop Brassica rapa, xAI models will be built to predict gene expression in leaves under control and stress conditions while at the same time identifying the underlying regulatory DNA sequences and syntax. The power of these predictive models will be validated by exploiting inter- and intra-species sequence variation, revealing the evolutionary conservation of the regulatory code. Furthermore, a novel multi-tier synthetic promoter engineering approach will be used to experimentally validate, directly in plants, the learned regulatory code in a high-throughput manner.
By combining the power of advanced computational and experimental methods, I will identify novel regulatory sequences and design novel synthetic promoters controlling gene expression in complex cellular contexts. This represents a crucial step towards a comprehensive understanding of gene regulation and will significantly contribute to developing stress-resilient crops.
Fields of science (EuroSciVoc)
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
This project's classification has been human-validated.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
This project's classification has been human-validated.
Keywords
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Programme(s)
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
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HORIZON.1.1 - European Research Council (ERC)
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Topic(s)
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Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Funding Scheme
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Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
HORIZON-ERC - HORIZON ERC Grants
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Call for proposal
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Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
(opens in new window) ERC-2024-ADG
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Net EU financial contribution. The sum of money that the participant receives, deducted by the EU contribution to its linked third party. It considers the distribution of the EU financial contribution between direct beneficiaries of the project and other types of participants, like third-party participants.
9052 ZWIJNAARDE - GENT
Belgium
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