Biology subjects

Marchi, F.

Publications and source records attributed to Marchi, F..

3 recordsLinked to original sources

bioRxiv2024

Structural and evolutionary features of red algal UV sex chromosomes

BackgroundSex chromosomes in red algae have remained relatively understudied, despite their fundamental role in understanding the evolution of sex determination across eukaryotes. In this study, we investigate the structure, gene composition, and evolutionary history of the U and V sex chromosomes in four Gracilaria species, which diverged approximately 100 million years ago (MYA). ResultsOur findings reveal that UV sex chromosomes, previously identified in green and brown algae as well as bryophytes, have also evolved in red algae, contributing to the diversity of sex determination systems across eukaryotes. The shared orthology of conserved sex-determining region (SDR) genes between Gracilaria and distantly related red algae suggests that this system may have originated approximately 390 MYA, making it one of the oldest known sex chromosome systems. The SDR in Gracilaria is relatively small but contains conserved gametologs and V-specific genes involved in transcriptional regulation and signaling, suggesting their essential role in sexual differentiation. Unlike the conserved V-specific genes, U-specific genes appear absent, pointing to a dominant role of the V chromosome in sex determination. The evolution of Gracilaria sex chromosomes involved recombination suppression, gene relocations, duplications, and potential gene loss. Despite their ancient origin, the sex chromosomes show low levels of degeneration, likely due to haploid purifying selection during the gametophytic phase of the life cycle. ConclusionThis study provides the first detailed characterization of the U and V sex chromosomes in red algae, preparing the ground for future studies on reproductive life cycles and speciation in this understudied group of eukaryotes.

evolutionary biology↗

bioRxiv2023

THE RHODOEXPLORER PLATFORM FOR RED ALGAL GENOMICS AND WHOLE GENOME ASSEMBLIES FOR SEVERAL GRACILARIA SPECIES

Macroalgal (seaweed) genomic resources are generally lacking as compared to other eukaryotic taxa, and this is particularly true in the red algae (Rhodophyta). Understanding red algal genomes is critical to understanding eukaryotic evolution given that red algal genes are spread across eukaryotic lineages from secondary endosymbiosis and red algae diverged early in the Archaeplastids. The Gracilariales are highly diverse and widely distributed order whose species can serve as ecosystem engineers in intertidal habitats, including several notorious introduced species. The genus Gracilaria is cultivated worldwide, in part for its production of agar and other bioactive compounds with downstream pharmaceutical and industrial applications. This genus is also emerging as a model for algal evolutionary ecology. Here, we report new whole genome assemblies for two species (G. chilensis and G. gracilis), a draft genome assembly of G. caudata, and genome annotation of the previously published G. vermiculophylla genome. To facilitate accessibility and comparative analysis, we integrated these data in a newly created web-based portal dedicated to red algal genomics (https://rhodoexplorer.sb-roscoff.fr). These genomes will provide a resource for understanding algal biology and, more broadly, eukaryotic evolution.

genomics↗

bioRxiv2020

Myeloid lncRNA LOUP Mediates Opposing Regulatory Effects of RUNX1 and RUNX1-ETO in t(8;21) AML

The mechanism underlying cell type-specific gene induction conferred by ubiquitous transcription factors as well as disruptions caused by their chimeric derivatives in leukemia is not well understood. Here we investigate whether RNAs coordinate with transcription factors to drive myeloid gene transcription. In an integrated genome-wide approach surveying for gene loci exhibiting concurrent RNA- and DNA-interactions with the broadly expressed transcription factor RUNX1, we identified the long noncoding RNA LOUP. This myeloid-specific and polyadenylated lncRNA induces myeloid differentiation and inhibits cell growth, acting as a transcriptional inducer of the myeloid master regulator PU.1. Mechanistically, LOUP recruits RUNX1 to both the PU.1 enhancer and the promoter, leading to the formation of an active chromatin loop. In t(8;21) acute myeloid leukemia, wherein RUNX1 is fused to ETO, the resulting oncogenic fusion protein RUNX1-ETO limits chromatin accessibility at the LOUP locus, causing inhibition of LOUP and PU.1 expression. These findings highlight the important role of the interplay between cell type-specific RNAs and transcription factors as well as their oncogenic derivatives in modulating lineage-gene activation and raise the possibility that RNA regulators of transcription factors represent alternative targets for therapeutic development. KEY POINTSO_LIlncRNA LOUP coordinates with RUNX1 to induces PU.1 long-range transcription, conferring myeloid differentiation and inhibiting cell growth. C_LIO_LIRUNX1-ETO limits chromatin accessibility at the LOUP locus, causing inhibition of LOUP and PU.1 expression in t(8;21) AML. C_LI

cancer biology↗