Biology subjects

Vivori, C.

Publications and source records attributed to Vivori, C..

6 recordsLinked to original sources

bioRxiv2026

Co-option of a mouse-specific retrotransposon rewires Ash2l isoform usage to prime developmental promoters

How pluripotent stem cells pre-configure the chromatin landscape to enable timely activation of developmental gene programs remains a central question in developmental biology. Here we demonstrate that the core chromatin regulator ASH2L undergoes a developmentally regulated transcription start site (TSS) switch that generates two protein isoforms with distinct developmental functions: a full-length ASH2L containing an N-terminal intrinsically disordered region (IDR), and a conserved, truncated protein isoform lacking this region. In mouse pluripotent stem cells, a lineage-specific ERV-K retrotransposon drives the upstream TSS, which suppresses the downstream TSS through transcription-coupled SETD2-mediated histone H3 lysine 36 methylation. The resulting stem cell-specific truncated ASH2L assembles into COMPASS complexes and enhances histone H3 lysine 4 trimethylation at promoters governing early development. Despite being restricted to pluripotent stem cells, truncated ASH2L is required for proper axial patterning in gastruloids and for the transition of neural progenitors to motor neurons. This temporal decoupling, wherein a chromatin state established during pluripotency executes its function only after the establishing isoform disappears, defines an epigenetic priming mechanism for developmental timing. Thus, lineage-specific retrotransposon co-option reveals how a dedicated protein isoform configures the pluripotent epigenome for developmental transitions after its own expression has ceased.

molecular biology↗

bioRxiv2025

Mapping and quantifying nascent transcript start sites using TT-TSS-seq

Transcription initiation is a highly dynamic and tightly regulated process involving the coordinated action of transcription factors, chromatin remodelers, and RNA polymerase which determine where and when transcription begins. Accurately mapping and quantifying transcription start sites (TSSs) from nascently transcribed RNAs remains a key area of interest, as it provides critical insights into transcription dynamics. Here, we combined transient transcriptome sequencing with transcription start site sequencing (TT-TSS-seq) to accurately map and quantify transcription initiation sites from nascent transcripts. Since transient metabolic labelling yields low-input RNA, we optimized the TSS-seq protocol to enhance sensitivity and accuracy. Specifically, we refined enzymatic reactions for decapping and RNA ligation and incorporated 5 oligonucleotides containing unique molecular identifiers (UMIs) and barcodes to enable accurate quantification and sample multiplexing. The TT-TSS-seq approach detected transcription initiation of unstable transcripts, such as enhancer RNAs. Moreover, we identified that a large fraction of genes use multiple transcription initiation sites, yet often produce only a single stable transcript. Overall, TT-TSS-seq provides precise mapping and quantification of transcription initiation sites, offering new insights into transcriptional dynamics and expanding the toolkit for studying gene regulation.

molecular biology↗

bioRxiv2025

DNA supercoiling impacts alternative transcription start site selection in yeast

Most genes are transcribed from multiple transcription start sites (TSSs), defined as alternative TSSs, which are highly regulated and can lead to various gene regulatory outcomes including changes in translation efficiency and protein isoform expression. Transcription factors and chromatin regulators control alternative TSS selection. DNA supercoiling affects multiple aspects of transcription including transcription initiation; however, its regulatory effect on genes with multiple TSSs is not known. Here, we investigated how DNA supercoiling impacts alternative TSS usage in Saccharomyces cerevisiae. We depleted topoisomerases during early meiosis, where alternative TSS usage is prevalent, and applied an improved TSS sequencing protocol. We show that supercoiling affects alternative TSS usage at almost 600 genes. Increased alternative and aberrant TSS usage was observed near and within open reading frames, likely resulting from transcription-induced supercoiling originating from upstream alternative TSSs. DNA supercoiling had the greatest impact on genes with a dominant alternative TSS, significant spacing between alternative TSSs, and greater overall gene length. Our results establish that DNA supercoiling release during transcription is critical for correct TSS selection.

molecular biology↗

bioRxiv2021

RSC-mediated nucleosome positioning and GRFs form barriers in promoters to limit divergent noncoding transcription

The directionality of gene promoters - the ratio of protein-coding over divergent noncoding transcription - is highly variable and regulated. How promoter directionality is controlled remains poorly understood. Here, we show that the chromatin remodelling complex RSC and general regulatory factors (GRFs) dictate promoter directionality by attenuating divergent transcription. At gene promoters that are highly directional, depletion of RSC leads to a relative increase in divergent noncoding transcription and thus a decrease in promoter directionality. We find that RSC facilitates nucleosome positioning upstream in promoters at the sites of divergent transcription. These highly directional promoters are also enriched for the binding of GRFs such as Reb1 and Abf1. Ectopic targeting of divergent transcription initiation sites with GRFs or the dCas9 protein suppresses divergent transcription. Our data suggest that RSC and GRFs play a pervasive role in limiting divergent transcription. We propose that any DNA binding factor, when stably associated with cryptic transcription start sites, form barriers for repressing divergent transcription. Our study provides an explanation as to why certain promoters are more directional than others.

molecular biology↗

bioRxiv2020

Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1 and TIA1

In contrast to the extensively studied rewiring of epigenetic and transcriptional programs required for cell reprogramming, the dynamics of post-transcriptional changes and their associated regulatory mechanisms remain poorly understood. Here we have studied the dynamics of alternative splicing (AS) changes occurring during efficient reprogramming of mouse B cells into induced pluripotent stem (iPS) cells. These changes, generally uncoupled from transcriptional regulation, significantly overlapped with splicing programs reported during reprogramming of mouse embryonic fibroblasts (MEFs). Correlation between gene expression of potential regulators and specific clusters of AS changes enabled the identification and subsequent validation of CPSF3 and hnRNP UL1 as facilitators, and TIA1 as repressor of MEFs reprogramming. These RNA-binding proteins control partially overlapping programs of splicing regulation affecting genes involved in developmental and morphogenetic processes. Our results reveal common programs of splicing regulation during reprogramming of different cell types and identify three novel regulators of this process.

molecular biology↗

bioRxiv2020

Hnrnpul1 loss of function affects skeletal and limb development

Mutations in RNA binding proteins can lead to pleiotropic phenotypes including craniofacial, skeletal, limb and neurological symptoms. Heterogeneous Nuclear Ribonucleoproteins (hnRNPs) are involved in nucleic acid binding, transcription and splicing through direct binding to DNA and RNA, or through interaction with other proteins in the spliceosome. We show a developmental role for Hnrnpul1 in zebrafish, resulting in reduced craniofacial tendon length, severe adult-onset scoliosis and reduced fin size. We demonstrate a role of Hnrnpul1 in alternative splicing and transcriptional regulation using RNA sequencing. Given its cross-species conservation and role in splicing it would not be surprising if it had a role in human development but the developmental role of this gene in humans has not been explored. Whole exome sequencing detected a frameshift variant in HNRNPUL1 in two siblings with congenital limb malformations which remain variants of unknown significance. Zebrafish Hnrnpul1 mutants suggest an important developmental role of hnRNPUL1 and provide motivation for exploring potential conservation of ancient regulatory circuits involving hnRNPUL1 in human development.

developmental biology↗