Biology subjects

Santos-Pereira, J. M.

Publications and source records attributed to Santos-Pereira, J. M..

7 recordsLinked to original sources

bioRxiv2026

KAT3 Shuttling Between Neuronal Identity and Activity-Dependent Plasticity Programs Drives Large-Scale Chromatin Remodeling

Activity-dependent transcription is a central feature of neuronal plasticity. Here, we show that neuronal activation triggers genome-wide redistribution of CBP and p300 in hippocampal neurons. Upon stimulation, KAT3 cofactors relocate from super-enhancers supporting neuronal identity to enhancers associated with activity-regulated genes, accompanied by transient changes in H3K27ac, chromatin accessibility, and three-dimensional genome architecture. Mechanistically, distinct TF families control KAT3 shuttling: proneural bHLH factors such as NeuroD2 maintain cofactor occupancy at identity-associated regulatory elements, whereas AP-1 binds de novo at plasticity-associated loci. This dynamic redistribution reshapes enhancer landscapes and chromatin interactions, enabling robust activation of plasticity genes while transiently attenuating neuronal identity programs. Remarkably, FOS overexpression is sufficient to reproduce the repression of neuronal identity genes observed during stimulation. Together, our findings reveal a reversible competition between transcriptional networks governing neuronal identity and plasticity and identify KAT3 redistribution as a key mechanism coupling neuronal activity to large-scale chromatin remodeling.

neuroscience↗

bioRxiv2024

Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes

Despite the growing abundance of sequenced animal genomes, we only have detailed knowledge of regulatory organization for a handful of lineages, particularly flies and vertebrates. These two groups of taxa show contrasting trends in the molecular mechanisms of 3D chromatin organization and long-term evolutionary dynamics of cis-regulatory element (CREs) conservation. To help us identify shared versus derived features that could be responsible for the evolution of these different regulatory architectures in animals, we studied the evolution and organization of the regulatory genome of echinoderms, a lineage whose phylogenetic position and relatively slow molecular evolution has proven particularly useful for evolutionary studies. First, using PacBio and HiC data, we generated new reference genome assemblies for two species belonging to two different echinoderm classes: the purple sea urchin Strongylocentrotus purpuratus and the bat sea star Patiria miniata. Second, we characterized their 3D chromatin architecture, identifying TAD-like domains in echinoderms that, like in flies, do not seem to be associated with CTCF motif orientation. Third, we systematically profiled CREs during sea star and sea urchin development using ATAC-seq, comparing their regulatory logic and dynamics over multiple developmental stages. Finally, we investigated sea urchin and sea star CRE evolution across multiple evolutionary distances and timescales, from closely related species to other echinoderm classes and deuterostome lineages. This showed the presence of several thousand elements conserved for hundreds of millions of years, revealing a vertebrate-like pattern of CRE evolution that probably constitutes an ancestral property of the regulatory evolution of animals.

evolutionary biology↗

bioRxiv2024

Single-cell multi-omics, spatial transcriptomics and systematic perturbation decode circuitry of neural crest fate decisions

The cranial neural crest (NC) is a migratory embryonic population ideal for studying cell plasticity, motility, and fate establishment. Although NC migration has been linked to changes in cell adhesion, polarity, and signaling, the gene regulatory circuitry governing these processes remained obscure. Using time-resolved single-cell multi-omics, spatial transcriptomics, and gene regulatory network reconstruction, we identified ten programs underlying 23 NC cell states and three spatial trajectories. Using in silico perturbation and systematic CRISPR/Cas9-mediated Perturb-seq, we uncovered novel lineage drivers and an endothelial-like program controlling NC migration, distinct from the epithelial-to-mesenchymal transition (EMT) program. We show that endothelial-like regulons (fli1a, elk3) drive migration through direct or tiered activation via the "FOX:ETS-Ebf3a-targets" axis, while ETS suppressors (erf, erfl3) maintain cell plasticity. Using the newly developed SyncReg tool, we identify functional redundancy among ETS regulons, which has thus far obscured their critical roles in NC migration, and we quantify their synergy with retinoic acid receptors, also essential for this process. Our GRN model, combined with novel velocity-embedded simulations, accurately predicted the functions of all major regulons, which were confirmed by in vivo functional perturbations. This study provides a comprehensive, validated cranial NC regulatory landscape, resolving heterogeneous regulatory circuits underlying NC cell motility and plasticity.

developmental biology↗

bioRxiv2024

CRISPR-RfxCas13d screening uncovers Bckdk as a post-translational regulator of the maternal-to-zygotic transition in teleosts

The Maternal-to-Zygotic transition (MZT) is a reprograming process encompassing zygotic genome activation (ZGA) and the clearance of maternally-provided mRNAs. While some factors regulating MZT have been identified, there are thousands of maternal RNAs whose function has not been ascribed yet. Here, we have performed a proof-of-principle CRISPR-RfxCas13d maternal screening targeting mRNAs encoding protein kinases and phosphatases in zebrafish and identified Bckdk as a novel post-translational regulator of MZT. Bckdk mRNA knockdown caused epiboly defects, ZGA deregulation, H3K27ac reduction and a partial impairment of miR-430 processing. Phospho-proteomic analysis revealed that Phf10/Baf45a, a chromatin remodeling factor, is less phosphorylated upon Bckdk depletion. Further, phf10 mRNA knockdown also altered ZGA and Phf10 constitutively phosphorylated rescued the developmental defects observed after bckdk mRNA depletion. Altogether, our results demonstrate the competence of CRISPR-RfxCas13d screenings to uncover new regulators of early vertebrate development and shed light on the post-translational control of MZT mediated by protein phosphorylation.

developmental biology↗

bioRxiv2023

Essential role of PLD2 in hypoxia-induced stemness and therapy resistance in ovarian tumors

Hypoxia in solid tumors is a source of chemoresistance that determines poor patient prognosis and relies on the presence of cancer stem cells (CSCs). Here we use ovarian cancer (OC) as a model and a combination of 2D and 3D cell cultures, xenograft models, patient samples, transcriptional databases, iPSCs and ATAC-seq, to address the mechanisms leading to hypoxia-induced CSC generation and chemoresistance. We show that hypoxia activates the expression of the PLD2 gene encoding phospholipase D2. PLD2 overexpression leads to increased CSC-like features, similar to hypoxia, while PLD2 depletion in hypoxia partially suppresses these effects, indicating a role of PLD2 in hypoxia-induced CSC generation in OC. Finally, PLD2 overexpression provokes chemoresistance that is suppressed by combination treatment with PLD2 inhibition. Altogether, our work highlights the HIF-1D-PLD2 axis in hypoxia-induced CSC generation and chemoresistance in OC and proposes an alternative treatment for patients with high PLD2 expression. Statement of SignificanceHypoxia in solid tumors is a major source of chemoresistance and cancer stem cells. We show that hypoxia-induced stemness is mediated by phospholipase D2 in ovarian tumors, generating therapy resistance that is overcome by phospholipase D inhibition. Therefore, we propose an alternative treatment for patients with high PLD2 expression.

cancer biology↗

bioRxiv2023

Rewiring of the epigenome and chromatin architecture by retinoic acid signaling during zebrafish embryonic development

BackgroundRetinoic acid (RA) functions as a ligand for the nuclear RA receptors (RARs), which regulate the expression of target genes by binding to RA response elements. RA signaling is required for multiple processes during chordate embryonic development, such as body axis extension, hindbrain antero-posterior patterning and forelimb bud initiation. Although some RA target genes have been identified, little is known about the genome-wide effects of RA signaling during in vivo embryonic development. ResultsHere we stimulate the RA pathway during development by treating zebrafish embryos with all-trans-RA (atRA), the most abundant form of RA, and use a combination of RNA-seq, ATAC-seq, ChIP-seq and HiChIP to gain insight into the molecular mechanisms by which RA signaling control target gene expression. We find that RA signaling is involved in anterior/posterior patterning and development of the central nervous system, participating in the transition from pluripotency to differentiation. atRA treatment also induces alterations in chromatin accessibility during early development and promotes chromatin binding of RARa and the RA targets Hoxb1b, Meis2b and Sox3, which cooperate in central nervous system development. Finally, we show that RA induces a rewiring of chromatin architecture, with alterations in chromatin 3D interactions that are consistent with target gene expression. This is illustrated by the specific induction of anterior HoxB genes by RARs, among other examples. ConclusionsAltogether, our findings identify genome-wide targets of RA signaling during embryonic development and provide a molecular mechanism by which developmental signaling pathways regulate the expression of target genes by altering chromatin topology.

developmental biology↗

bioRxiv2020

CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression

CTCF is an 11-zinc-finger DNA-binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding1-5. CTCF mediates long-range chromatin looping and is enriched at the boundaries of topologically associating domains, which are sub-megabase chromatin structures that are believed to facilitate enhancer-promoter interactions within regulatory landscapes 6-12. Although CTCF is essential for cycling cells and developing embryos13,14, its in vitro removal has only modest effects over gene expression5,15, challenging the concept that CTCF-mediated chromatin interactions and topologically associated domains are a fundamental requirement for gene regulation16-18. Here we link the loss of chromatin structure and gene regulation in an in vivo model and during animal development. We generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes, including many developmental genes. In addition, chromatin accessibility, both at CTCF binding sites and cis-regulatory elements, is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution, we further demonstrate that promoters fail to fully establish long-range contacts with their associated regulatory landscapes, leading to altered gene expression patterns and disruption of developmental programs. Our results demonstrate that CTCF and topologically associating domains are essential to regulate gene expression during embryonic development, providing the structural basis for the establishment of developmental gene regulatory landscapes.

developmental biology↗