The evolution, evolvability and engineering of gene regulatory DNA

• Published in: Nature (London) Vol. 603; no. 7901; pp. 455 - 463
• Main Authors: Vaishnav, Eeshit Dhaval, de Boer, Carl G., Molinet, Jennifer, Yassour, Moran, Fan, Lin, Adiconis, Xian, Thompson, Dawn A., Levin, Joshua Z., Cubillos, Francisco A., Regev, Aviv
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 17.03.2022; Nature Publishing Group
• Subjects: 38; 45; 45/22; 45/70; 45/77; 631/114/1305; 631/114/2397; 631/181/735; 631/208/212; 631/553/552; Artificial neural networks; Biological Evolution; Deoxyribonucleic acid; Design; Divergence; DNA; Engineering; Epistasis; Evolution; Evolution, Molecular; Fitness; Gene expression; Gene Expression Regulation; Gene sequencing; Genetic algorithms; Genetic Drift; Genotype & phenotype; Humanities and Social Sciences; Modelling; Models, Genetic; multidisciplinary; Mutation; Mutation - genetics; Neural networks; Nucleotide sequence; Phenotype; Phenotypes; Regulatory sequences; Reproductive fitness; Robustness; Saccharomyces cerevisiae - genetics; Science; Science (multidisciplinary); Transcription factors; Yeast
• ISSN: 0028-0836; 1476-4687; 1476-4687
• DOI: 10.1038/s41586-022-04506-6

Mutations in non-coding regulatory DNA sequences can alter gene expression, organismal phenotype and fitness 1 – 3 . Constructing complete fitness landscapes, in which DNA sequences are mapped to fitness, is a long-standing goal in biology, but has remained elusive because it is challenging to generalize reliably to vast sequence spaces 4 – 6 . Here we build sequence-to-expression models that capture fitness landscapes and use them to decipher principles of regulatory evolution. Using millions of randomly sampled promoter DNA sequences and their measured expression levels in the yeast Saccharomyces cerevisiae , we learn deep neural network models that generalize with excellent prediction performance, and enable sequence design for expression engineering. Using our models, we study expression divergence under genetic drift and strong-selection weak-mutation regimes to find that regulatory evolution is rapid and subject to diminishing returns epistasis; that conflicting expression objectives in different environments constrain expression adaptation; and that stabilizing selection on gene expression leads to the moderation of regulatory complexity. We present an approach for using such models to detect signatures of selection on expression from natural variation in regulatory sequences and use it to discover an instance of convergent regulatory evolution. We assess mutational robustness, finding that regulatory mutation effect sizes follow a power law, characterize regulatory evolvability, visualize promoter fitness landscapes, discover evolvability archetypes and illustrate the mutational robustness of natural regulatory sequence populations. Our work provides a general framework for designing regulatory sequences and addressing fundamental questions in regulatory evolution. A framework for studying and engineering gene regulatory DNA sequences, based on deep neural sequence-to-expression models trained on large-scale libraries of random DNA, provides insight into the evolution, evolvability and fitness landscapes of regulatory DNA.