Zambada-Moreno, O. | Search bioRxiv

bioRxiv2023

Dynamic co-expression modular network analysis of bHLH transcription factors regulation in the potato spindle tuber viroid-tomato pathosystem

Viroids, minimalist plant pathogens, present significant threats to crops by causing severe diseases. The use of high-throughput sequencing technologies for analyzing the transcriptomes of viroid-infected host plants has yielded informative information on gene regulation by these pathogens, however a complete understanding of the transcriptome data suffers from the inclusion of numerous genes of unknown function. Co-expression analysis addresses this by clustering genes into modules based on global gene expression levels. Our previous study emphasized basic helix-loop-helix protein (bHLH) transcriptional reprogramming in tomato in response to different potato spindle tuber viroid (PSTVd) strains. In the current research, we delve into tissue-specific gene modules, particularly in root and leaf tissues, governed by bHLH transcription factors during PSTVd infections. Utilizing public datasets that span Control (C; (mock-inoculated), PSTVd-mild (M), and PSTVd-severe (S23) strains in time-course infections, we uncovered differentially expressed gene modules. These modules were functionally characterized, identifying essential hub genes. We identified the roles of bHLH transcription factors (TFs) in managing processes like photosynthesis and rapid membrane repair in infected roots. In leaves, external layer alterations influenced photosynthesis, linking bHLH TFs to distinct metabolic functions. Expanding on these findings, we explored bipartite networks, discerning both common and unique bHLH TF regulatory roles, notably highlighting the bifan motifs significance in these interactions. Through this holistic approach, we deepen our understanding of viroid-host interactions and the intricate regulatory mechanisms underpinning them.

systems biology↗

bioRxiv2022

Deciphering the tissue-specific regulatory role of intronless genes across cancers

Intronless genes (IGs) or single-exon genes lacking an intron are found across most Eukaryotes. Notably, IGs display a higher transcriptional fidelity as they are not regulated through alternative splicing, suggesting better predictability biomarkers and easier regulation as targets for therapy. Cancer is a complex disease that relies on progressive uncontrolled cell division linked with multiple dysfunctional biological processes. Tumor heterogeneity remains the most challenging feature in cancer diagnosis and treatment. Given the clinical relevance of IGs, we aim to identify their unique expression profiles and interactome, that may act as functional signatures across eight different cancers. We identified 940 protein-coding IGs in the human genome, of which about 35% were differentially expressed across the analyzed cancer datasets. Specifically, [~]78% of differentially expressed IGs were undergoing transcriptional reprogramming with elevated expression in tumor cells. Remarkably, in all the studied tumors, a highly conserved induction of a group of deacetylase-histones located in a region of chromosome 6 enriched in nucleosome and chromatin condensation processes. This study highlights that differentially expressed human intronless genes across cancer types are prevalent in epigenetic regulatory roles participating in specific PPI networks for ESCA, GBM, and LUAD tumors. We determine that IGs play a key role in the tumor phenotype at transcriptional and post-transcriptional levels, with important mechanisms such as interactomics rewiring.

genomics↗