Biology subjects

Manosalva, I.

Publications and source records attributed to Manosalva, I..

3 recordsLinked to original sources

bioRxiv2026

Epromoter 3D interaction-associated regulation in T-acute Lymphoblastic Leukemia

Background: Promoters have been traditionally seen as contiguous gene-adjacent cis-regulatory elements. Yet, substantial studies corroborate that Epromoters (promoters with enhancer activity) engage in distal forms of gene regulation. Although in the three-dimensional (3D) space enhancer-promoter networks have been well studied, the contribution of the circuits of promoter-promoter (P-P) interactions is poorly understood. Furthermore, whether the regulatory aspects of P-P interactions in cancer may be controlled by physical 3D-mediated Epromoter interactions remains elusive. Results: We show that Epromoter-mediated 3D interactions regulate target genes and participate in cluster co-regulation, playing a critical role in T-cell acute Lymphoblastic Leukemia (T-ALL). To achieve this, we first leveraged survival CRISPR screenings in T-ALL model cells (Jurkat) to identify potential Epromoters. By integrating these findings with an H3K27ac HiChIP dataset from T-ALL cells, we characterized a set of Epromoters that establish 3D genome interactions with other promoters. We observed that promoters organize into dense, promoter-rich genomic clusters, and that among them, the clusters enriched with Epromoters actively regulate complex gene expression networks. To investigate gene coregulation, we integrated transcriptomic data from T-ALL patients and found that promoter-promoter (P-P) pairs exhibit positive correlation at multiple levels, and that several Jurkat Epromoter candidate clusters are significantly co-regulated in the patient cohort. To experimentally validate these candidates, we utilized CRISPRi to inhibit Epromoters, which revealed direct transcriptional regulation of multiple target genes within each hub. Finally, we performed cell competition assays to confirm that these Epromoters are vital for T-ALL cell survival. Conclusions: Our analysis provides support for the role of Epromoters in the regulation of 3D P-P interactions and co-regulation of promoter hubs, and how these interactions play a critical part in T-ALL cell survival.

cancer biology↗

bioRxiv2025

Exonic enhancers are a widespread class of dual-function regulatory elements

Exonic enhancers (EEs) occupy an under-appreciated niche in gene regulation. By integrating transcription factor binding, chromatin accessibility, and high-throughput enhancer-reporter assays, we demonstrate that many protein-coding exons possess enhancer activity across species. These EEs exhibit characteristic epigenomic signatures, form long-range interactions with gene promoters, and can be altered by both nonsynonymous and synonymous variants. CRISPR-mediated inactivation demonstrated the involvement of EEs in the cis-regulation of host and distal gene expression. Through large-scale cancer genome analyses, we reveal that EE mutations correlate with dysregulated target-gene expression and clinical outcomes, highlighting their potential relevance in disease. Evolutionary comparisons show that EEs exhibit both strong sequence constraint and lineage-specific plasticity, suggesting that they serve ancient regulatory functions while also contributing to species divergence. Our findings redefine the landscape of functional elements by establishing EEs as a component of gene regulation, while revealing how coding regions can simultaneously fulfil both protein-coding and cis-regulatory roles.

genomics↗

bioRxiv2024

Unraveling a novel dual-function regulatory element showing epistatic interaction with a variant that escapes genome-wide association studies.

Regulation of gene expression has recently been complexified by the identification of Epromoters, a subset of promoters with enhancer function. Here, we uncovered the first dual cis-regulatory element, "ESpromoter," exhibiting both enhancer and silencer function, as a regulator of the nearby genes ATP2B4 and LAX1 in single human T cells. Through integrative approach, we pinpointed functional rs11240391, a severe malaria risk variant that escapes detection in genome-wide association studies, challenging conventional strategies for identifying causal variants. CRISPR-modified cells demonstrated the regulatory effect of ESpromoter and rs11240391 on LAX1 expression and T cell activation. Furthermore, our findings revealed an epistatic interaction between ESpromoter SNPs and rs11240391, impacting severe malaria susceptibility by further reducing LAX1 expression. This groundbreaking discovery challenges the conventional enhancer-silencer dichotomy. It highlights the sophistication of transcriptional regulation and argues for an integrated approach combining genetics, epigenetics, and genomics to identify new therapeutic targets for complex diseases. HIGHLIGHTSO_LINovel dual enhancer-silencer element (ESpromoter) in a single human cell type C_LIO_LIFunctional SNP for severe malaria risk that escapes genome-wide association studies C_LIO_LIGenome editing at the SNP demonstrates a regulatory effect on LAX1 and T cell activation C_LIO_LIEpistatic interaction between SNPs increases the risk of severe malaria C_LI In briefEpistatic interaction between common variants within a novel dual enhancer-silencer regulatory element and the LAX1 promoter variant is responsible for severe malaria susceptibility through T-cell activation.

genomics↗