Biology subjects

Lupo, O.

Publications and source records attributed to Lupo, O..

3 recordsLinked to original sources

bioRxiv2025

Protein massively parallel binding assay reveals transcription factor binding determinants

Transcription factors select their genomic binding sites in genomes depending on their DNA binding domain (DBD) but also on regions outside the DBD (nonDBD). However, it remains challenging to define these determinants within nonDBDs and reveal their mechanism of action. Towards this, we introduce here an in-vivo method for parallel analysis of thousands of designed peptides for binding a DNA sequence of interest (Protein Massively Parallel Binding Assay, pMPBA). We apply it to scan the full sequence space of budding yeast TFs and generate a detailed map of DNA localizing determinants. Within the set of predicted DBDs, we reveal a large variation in DNA binding affinities, depending on the family and on different sequence characteristics, including charge. Strong signals were not confined to predicted DBDs but included a considerable fraction of nonDBD peptides, most of which were predicted as intrinsically disordered. pMPBA opens new possibilities for high-throughput analysis of peptide-DNA binding within cells.

genomics↗

bioRxiv2020

Mapping the architecture of regulatory variation provides insights into the evolution of complex traits

BackgroundOrganisms evolve complex traits by recruiting existing programs to new contexts, referred as co-option. Within a species, single upstream regulators can trigger full differentiation programs. Distinguishing whether co-option of differentiation programs results from variation in single regulator, or in multiple genes, is key for understanding how complex traits evolve. As an experimentally accessible model for studying this question we turned to budding yeast, where a differentiation program (filamentous) is activated in S. cerevisiae only upon starvation, but used by the related species S. paradoxus also in rich conditions. ResultsTo define expression variations associated with species-specific activation of the filamentous program, we profiled the transcriptome of S. cerevisiae, S. paradoxus and their hybrid along two cell cycles at 5-minutes resolution. As expected in cases of co-option, expression of oscillating genes varies between the species in synchrony with their growth phenotypes and was dominated by upstream trans-variations. Focusing on regulators of filamentous growth, we identified gene-linked variations (cis) in multiple genes across regulatory layers, which propagated to affect expression of target genes, as well as binding specificities of downstream transcription factor. Unexpectedly, variations in regulators essential for S. cerevisiae filamentation were individually too weak to explain activation of this program in S. paradoxus. ConclusionsOur study reveals the complex architecture of regulatory variation associated with species-specific use of a differentiation program. Based on these results, we suggest a new model in which evolutionary co-option of complex traits is stabilized in a distributed manner through multiple weak-effect variations accumulating throughout the regulatory network.

evolutionary biology↗

bioRxiv2020

Independent evolution of transcript abundance and gene regulatory dynamics

Changes in gene expression drive novel phenotypes, raising interest in how gene expression evolves. In contrast to the static genome, cells regulate gene expression to accommodate changing conditions. Previous comparative studies focused on specific conditions, describing inter-species variation in expression levels, but providing limited information about variations in gene regulation. To close this gap, we profiled gene expression of related yeast species in hundreds of conditions, and used co-expression analysis to distinguish variations in transcription regulation from variations in expression levels or environmental perception. The majority of genes whose expression varied between the species maintained a conserved transcriptional regulation. Profiling the interspecific hybrid provided insights into the basis of variations, showed that trans-varying alleles interact dominantly, and revealed complementation of cis-variations by variations in trans. Our data suggests that gene expression diverges primarily through changes in promoter strength that do not alter gene positioning within the transcription network.

systems biology↗