Additional insights into the organization of transcriptional regulatory modules based on a 3D model of the Saccharomyces cerevisiae genome

Abstract

Objectives Transcriptional regulatory modules are usually modelled via a network, in which nodes correspond to genes and edges correspond to regulatory associations between them. In the model yeast Saccharomyces cerevisiae, the topological properties of such a network are well-described (distribution of degrees, hierarchical levels, organization in network motifs, etc.). To go further on this, our aim was to search for additional information resulting from the new combination of classical representations of transcriptional regulatory networks with more realistic models of the spatial organization of S. cerevisiae genome in the nucleus. Results Taking advantage of independent studies with high-quality datasets, i.e. lists of target genes for specific transcription factors and chromosome positions in a three dimensional space representing the nucleus, particular spatial co-localizations of genes that shared common regulatory mechanisms were searched. All transcriptional modules of S. cerevisiae, as described in the latest release of the YEASTRACT database were analyzed and significant biases toward co-localization for a few sets of target genes were observed. To help other researchers to reproduce such analysis with any list of genes of their interest, an interactive web tool called 3D-Scere (https://3d-scere.ijm.fr/) is provided.

Data integration and analysis for circadian medicine

“…Compared to other types of data, individual types of omics data are relatively well standardized with formats such as FASTQ being able to represent a wide range of molecular measurements 35 and projects such as Ensembl providing systems and ontologies of stable identifiers for genes, transcripts, proteins, and exons. 36 However, there is a lack of standards for multi-omics data. 37 In regard to tooling, a wide variety of solutions for multi-omics integration, analysis, or visualization have been developed and made available to the community.…”

Visual integration of omics data to improve 3D models of fungal chromosomes

“…In this study, we are specifically interested in seeing the spatial organization of fungal chromosomes. Our laboratory has long-standing expertise in functional genomics projects in yeasts (Denecker et al 2020; Poinsignon et al 2022; Sénécaut et al 2022) or filamentous fungi (Grognet et al 2019; Carlier et al 2021; Lelandais et al 2022), and spatial genome organization in fungi has already been investigated, for model species like Saccharomyces cerevisiae (Duan et al 2010; Tokuda et al 2012), Schizosaccharomyces pombe (Grand et al 2014; Tanizawa et al 2010; Gallardo et al 2019; Noma 2017) and Neurospora crassa (Galazka et al 2016; Rodriguez et al 2022). Notably, the nuclear architecture of N. crassa , a multicellular fungus that grows as a mycelium with a network of hyphae (Galagan et al 2003), has structural homology (thanks to the existence of heterochromatin and euchromatin) with the human genome (Rodriguez et al 2022).…”