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Decoding tissue-specific enhancers in plants using massively parallel assays and deep learning.

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Researchers identified thousands of active fruit enhancer sequences in tomato using massively parallel reporter assays (MPRAs). These enhancers can drive fruit-specific gene expression, enabling the design of new synthetic enhancers for targeted plant gene regulation.

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Area of Science:

  • Plant Biology
  • Molecular Biology
  • Genetics

Background:

  • Enhancers are crucial regulatory elements controlling gene expression in plants.
  • Understanding tissue-specific enhancers is key to dissecting plant development and responses.
  • The regulatory codes governing plant enhancers, particularly for fruit-specific expression, are largely unknown.

Purpose of the Study:

  • To identify and characterize functional enhancer sequences in tomato fruit.
  • To explore the sequence determinants underlying fruit-specific enhancer activity.
  • To enable the de novo design of synthetic enhancers for targeted gene expression in plants.

Main Methods:

  • Massively parallel reporter assays (MPRAs) were employed to test enhancer activity of 11,180 tomato fruit-specific gene promoter fragments.
  • Deep learning models were utilized to dissect sequence determinants of fruit enhancers.
  • Synthetic enhancers were designed based on learned regulatory rules and experimentally validated for tomato fruit specificity.

Main Results:

  • Discovered 2,436 active fruit enhancer sequences in tomato.
  • Identified a subset of enhancers exhibiting differential activity between fruit and leaves, indicating fruit-specific potential.
  • Successfully designed and validated synthetic enhancers capable of specific targeting in tomato fruit.

Conclusions:

  • A comprehensive landscape of functional enhancers in tomato fruit has been established.
  • The study provides insights into the sequence-based regulatory codes of fruit enhancers.
  • This work facilitates the rational design of synthetic enhancers for precise gene expression control in plants.