Biology subjects

Clavell-Revelles, P.

Publications and source records attributed to Clavell-Revelles, P..

2 recordsLinked to original sources

bioRxiv2025

Spalt-related is an integrated stress response-activated inhibitor of mTORC1-mediated growth

Anabolic and catabolic processes are coordinated by a conserved regulatory network, which includes the nutrient sensing protein kinase mTOR complex 1 (mTORC1) and the insulin- and stress-responsive transcription factor FoxO. In physiological setting these regulators align growth, storage, reproduction, and aging with nutrient availability. Here, we identify transcription factor Spalt-related (Salr), previously implicated in organogenesis, as a negative regulator of growth and lipid storage. In the Drosophila fat body Salr activates catabolic gene expression and restricts mTORC1-mediated cell growth. The genomic binding of Salr overlaps extensively with that of FoxO and similar convergence is observed between their mammalian homologs SALL1 and FOXO1. Both Salr and FoxO are activated upon fasting but respond to distinct cues: while FoxO displays transient activation and is responsive to AKT inhibition, Salr is activated in a slow and sustained manner through the integrated stress response. Once activated, Salr counters nuclear localization of FoxO. Together, Salr and FoxO are converging transcriptional activators of catabolism during nutrient stress.

cell biology↗

bioRxiv2025

Long-read transcriptomics of a diverse human cohort reveals widespread ancestry bias in gene annotation

Accurate gene annotations are fundamental for interpreting genetic variation, cellular function, and disease mechanisms. However, current human gene annotations are largely derived from transcriptomic data of individuals with European ancestry, introducing potential biases that remain uncharacterized. Here, we generate over 800 million full-length reads with long-read RNA-seq in 43 lymphoblastoid cell line samples from eight genetically-diverse human populations and build a cross-ancestry gene annotation. We show that transcripts from non-European samples are underrepresented in reference gene annotations, leading to systematic biases in allele-specific transcript usage analyses. Furthermore, we show that personal genome assemblies enhance transcript discovery compared to the generic GRCh38 reference assembly, even though genomic regions unique to each individual are heavily depleted of genes. These findings underscore the urgent need for a more inclusive gene annotation framework that accurately represents global transcriptome diversity.

genomics↗