Biology subjects

Rebelo, A. R.

Publications and source records attributed to Rebelo, A. R..

4 recordsLinked to original sources

bioRxiv2026

A Mediator-dependent hypertranscriptional program governs neural stem cell fate decisions in vivo

Hypertranscription, a global increase in transcriptional output, is a defining feature of stem cells, but its biological relevance and regulation in vivo remain unclear. Using Drosophila neural stem cells (neuroblasts), we investigate the function and regulation of hypertranscription. Neuroblasts exhibit higher transcriptional activity than their differentiated progeny, establishing them as a model of hypertranscriptional stem cells. We identify the Mediator complex as a key regulator of this elevated transcriptional state. Mediator is broadly enriched across neuroblast chromatin, and its depletion causes a substantial, selective reduction in transcription in neuroblasts, with only mild effects in differentiated cells. Functionally, Mediator depletion impairs lineage progression, causing an accumulation of undifferentiated, stem-like cells, highlighting the necessity of hypertranscription for proper stem cell fate and differentiation. Finally, we show that Drosophila brain tumor neuroblasts exhibit an exaggerated, Mediator-dependent hypertranscriptional program. These findings establish Mediator as a central regulator of hypertranscription in both normal and tumorigenic neural stem cells, crucial for neural differentiation and stem cell fate progression.

developmental biology↗

bioRxiv2021

Sequencing Micronuclei Reveals the Landscape of Chromosomal Instability

Genome instability (GIN) is a main contributing factor to congenital and somatic diseases, but its sporadic occurrence in individual cell cycles makes it difficult to study mechanistically. One profound manifestation of GIN is the formation of micronuclei (MN), the engulfment of chromosomes or chromosome fragments in their own nuclear structures separate from the main nucleus. Here, we developed MN-seq, an approach for sequencing the DNA contained within micronuclei. We applied MN-seq to mice with mutations in Mcm4 and Rad9a, which disrupt DNA replication, repair, and damage responses. Data analysis and simulations show that centromere presence, fragment length, and a heterogenous landscape of chromosomal fragility all contribute to the patterns of DNA present within MN. In particular, we show that long genes, but also gene-poor regions, are associated with chromosome breaks that lead to the enrichment of particular genomic sequences in MN, in a genetic background-specific manner. Finally, we introduce single-cell micronucleus sequencing (scMN-seq), an approach to sequence the DNA present in MN of individual cells. Together, sequencing micronuclei provides a systematic approach for studying GIN and reveals novel molecular associations with chromosome breakage and segregation.

genomics↗

bioRxiv2021

Comprehensive analysis of DNA replication timing in genetic diseases and gene knockouts identifies MCM10 as a novel regulator of the replication program

Cellular proliferation depends on the accurate and timely replication of the genome. Several genetic diseases are caused by mutations in key DNA replication genes; however, it remains unclear whether these genes influence the normal program of DNA replication timing. Similarly, the factors that regulate DNA replication dynamics are poorly understood. To systematically identify trans-acting modulators of replication timing, we profiled replication in 184 cell lines from three cell types, encompassing 60 different gene knockouts or genetic diseases. Through a rigorous approach that considers the background variability of replication timing, we concluded that most samples displayed normal replication timing. However, mutations in two genes showed consistently abnormal replication timing. The first gene was RIF1, a known modulator of replication timing. The second was MCM10, a highly conserved member of the pre-replication complex. MCM10 mutant cells demonstrated replication timing variability comprising 46% of the genome and at different locations than RIF1 knockouts. Replication timing alterations in MCM10-mutant cells was predominantly comprised of replication initiation defects. Taken together, this study demonstrates the remarkable robustness of the human replication timing program and reveals MCM10 as a novel modulator of DNA replication timing.

genetics↗

bioRxiv2017

ALUMINUM RESISTANCE TRANSCRIPTION FACTOR 1 (ART1) underlies a major Al resistance QTL and interacts with natural variation in the genetic background to quantitatively regulate Al resistance in rice.

Transcription factors (TFs) mediate stress resistance indirectly via physiological mechanisms driven by the genes they regulate. When studying TF-mediated stress resistance, it is important to understand how TFs interact with different genetic backgrounds. Here, we fine-mapped the aluminum (Al) resistance QTL Alt12.1 to a 44 Kb region containing six gene models. Among them is ART1, which encodes a C2H2-type zinc finger TF required for Al resistance in rice. The parents of the mapping population, Al-resistant Azucena (tropical japonica) and Al-sensitive IR64 (indica), showed similar ART1 expression levels but extensive sequence polymorphism within the ART1 coding region. Using reciprocal near-isogenic lines (NILs) in the Azucena and IR64 genetic backgrounds, we examined how allele-swapping Alt12.1 would affect plant responses to Al. Analysis of global transcriptional responses to Al stress in roots of the NILs alongside their recurrent parents demonstrated that the ART1 from Al-resistant Azucena led to greater changes in gene expression in response to Al when compared to the ART1 from IR64 in both genetic backgrounds. The presence of the ART1 allele from the opposite parent affected the expression of several genes not previously implicated in rice Al tolerance. We highlight examples where putatively functional variation in cis-regulatory regions of ART1-regulated genes interacts with ART1 to determine gene expression in response to Al. This ART1-promoter interaction may be associated with transgressive variation for Al resistance in the Azucena x IR64 population. These results illustrate how ART1 interacts with the genetic background to contribute to quantitative phenotypic variation in rice Al resistance.

plant biology↗