Biology subjects

Planells, J.

Publications and source records attributed to Planells, J..

8 recordsLinked to original sources

bioRxiv2026

Afadin Loss Uncovers an Ectopic Neurogenic Niche and Reorganizes the Adult Ventricular-Subventricular Zone

Stem cells are generally thought to depend on specialized niches that provide signals for their long-term maintenance. Whether stem-cell competence is intrinsically constrained by anatomical organization remains unclear. Here, we show that neural stem cells can establish and sustain functional persistent stem-cell populations outside their normal anatomical context. Using developmental deletion of the cell-adhesion regulator Afadin as a tool to disrupt cortical tissue organization, we find that neural progenitors are displaced from the ventricular surface and establish an ectopic germinal zone (EGZ) into advanced adulthood. EGZ stem-cell populations retain self-renewal and multilineage differentiation capacity throughout this period. In parallel, the ventricular-subventricular zone (V-SVZ) undergoes persistent reorganization of tissue architecture, cellular composition, molecular state, and stem-cell activity. Together, these findings reveal unexpected plasticity in the relationship between stem cells and their tissue environment, suggesting that canonical niche anatomy may constrain where stem cells normally reside without defining the limits of functional stem-cell competence.

neuroscience↗

bioRxiv2026

RNA degradation by DIS3 is a necessary step in the resolution of backtracked transcription complexes

The RNA exosome is known to participate in transcription, but the contribution of its ribonuclease activities to this process remains unclear. Here we investigated the role of DIS3, one of the exosome ribonucleases, in transcription by RNA polymerase II (RNAPII). Rapid depletion of DIS3 reduced RNA synthesis and induced RNAPII elongation defects that were exacerbated by UV irradiation, a treatment that generates transcription-blocking DNA lesions and promotes RNAPII backtracking. Notably, DIS3 itself was redistributed following UV irradiation in a manner that closely paralleled RNAPII dynamics, which suggested that DIS3 acts in concert with the transcription machinery. We also investigated whether RNA degradation by DIS3 was required for transcription elongation and found that the 3-5 exoribonucleolytic activity of DIS3, but not its endonucleolytic activity, is essential for efficient transcription elongation. More specifically, DIS3 degrades the 3 ends of backtracked RNA, as shown by sequencing of RNA fragments released by TFIIS-induced transcript cleavage in vitro. This DIS3-dependent degradation of backtracked RNA is critical for resolving stalled RNAPII complexes and enabling productive transcription elongation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=169 SRC="FIGDIR/small/703186v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@c080dorg.highwire.dtl.DTLVardef@1e4b375org.highwire.dtl.DTLVardef@1c1f575org.highwire.dtl.DTLVardef@d9d640_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDIS3 depletion leads to severely reduced rates of RNA synthesis in human cells. C_LIO_LITranscription-blocking lesions reveal a critical role for DIS3 in RNA polymerase II elongation. C_LIO_LIThe 3 to 5 exoribonuclease activity of DIS3 is necessary for transcription elongation. C_LIO_LIDIS3-mediated degradation of backtracked RNA is required for the resolution of stalled transcription complexes. C_LI

molecular biology↗

bioRxiv2025

TET2-dependent differential 5hmC deposition balances adult neural stem cell activation and differentiation

Ten-eleven translocation (TET) enzymes are key regulators of active DNA demethylation, converting 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and thereby shaping the epigenetic landscape and cellular identity. While their roles have been characterized in pluripotent and some multipotent stem cells, their function in adult neural stem cells (NSCs) of the subventricular zone (SVZ) remains poorly understood. Here, we show that TET2 is critical for the maintenance and differentiation of adult NSCs, orchestrating locus-specific 5hmC deposition across promoters, gene bodies, and enhancers. Importantly, 5hmC remodeling segregates into two functionally distinct programs: promoter-associated gains of 5hmC are strongly TET2-dependent and drive transcription of genes controlling neural differentiation and calcium signaling, whereas gene body- and enhancer-associated 5hmC gains partially depend on TET2 and sustain proliferative and metabolic pathways, thereby maintaining stemness. Loss of TET2 disrupts these 5hmC programs, downregulates key differentiation- and calcium-related genes, and impairs the normal differentiation-associated increase in intracellular calcium, revealing a functional consequence of altered epigenetic regulation. Together, our findings uncover a pivotal role for TET2 in coordinating complementary epigenetic and transcriptional programs that balance stemness and differentiation in adult NSCs.

neuroscience↗

bioRxiv2025

eIF5A coordinates the transcription and translation of its target genes

Maintaining balanced cellular protein levels requires precise control of gene expression and effective coordination between the various stages of the process, from transcription to translation. In recent years, several components of the translation apparatus have been found in the nuclei of various eukaryotes, where they regulate transcription, mRNA processing or export, thereby integrating different stages of gene expression. eIF5A is an essential and evolutionarily conserved translation elongation factor that is involved in viral infection and in the development of diseases such as cancer and neurodevelopmental disorders. eIF5A promotes translation elongation by binding to ribosomes that stall at codons encoding problematic amino acids for peptide bond formation, such as consecutive prolines, also known as polyproline motifs. Although eIF5A shuttles between the nucleus and cytoplasm, its specific nuclear roles remain poorly defined. Here, we demonstrate that nuclear yeast eIF5A binds to chromatin and represses gene transcription by preventing the binding of RNA polymerase II. Importantly, chromatin binding and transcriptional repression by eIF5A have a higher impact on genes encoding its own translational targets. The presence of polyproline motifs in genes imposes both translation and transcriptional control by eIF5A. Furthermore, eIF5As active engagement in cytoplasmic translation is necessary for its role in repressing transcription. Our results suggest that eIF5A coordinates gene expression by promoting the cytoplasmic translation of specific genes while repressing their transcription in the nucleus, thus ensuring efficient final protein synthesis. Significance StatementOur study provides genome-wide and gene-specific evidence supporting the role of the translation elongation factor eIF5A in transcription. eIF5A is essential in eukaryotes, facilitating the translation of mRNAs encoding stretches of problematic amino acids, such as consecutive prolines. Through its role in the synthesis of specific proteins, eIF5A has been linked to development and different diseases, including cancer and diabetes. We have now discovered that eIF5A also controls the transcription of its translation target genes and this effect is driven by the presence of eIF5A-dependent motifs at their sequences. In the nucleus, eIF5A binds to specific genes and attenuates the binding of RNA polymerase II. By negatively regulating transcription and positively regulating translation, eIF5A coordinates gene expression, fine-tuning protein levels.

molecular biology↗

bioRxiv2025

TET3 protects the Dlk1-Dio3 Imprinted Locus from DNA hypomethylation during adult NSC Reprogramming

Genomic imprinting is an epigenetic mechanism that drives monoallelic gene expression depending on parental origin. Loss of imprinting (LOI) is associated with human imprinting disorders, fetal development, and cancer progression. Imprinted genes, organized in clusters, are regulated by methylation at imprint control regions (ICRs), differentially methylated regions (DMRs) between parental chromosomes. Somatic cell reprogramming into induced pluripotent stem cells (iPSCs) is a valuable tool for studying pluripotency and holds promise for patient-specific therapies. Discerning whether genomic imprinting changes during reprogramming represent epigenetic abnormalities or essential adaptations linked to pluripotency is crucial. Here, we perform RNA-seq and MeDIP-seq analysis on mouse iPSCs derived from neural stem cells (NSCs). Our findings reveal that ICRs undergo DNA hypomethylation, confirming widespread LOI in pluripotent cells. However, the IG-DMR within the Dlk1-Dio3 imprinted cluster resists hypomethylation, a hallmark of successful pluripotency acquisition. We also identify a non-canonical role of TET3 in IG-DMR methylation protection through transcriptional regulation of Oct4 and Trim28. These findings highlight genomic imprinting as a key mechanism of gene dosage control in pluripotency acquisition and maintenance.

cell biology↗

bioRxiv2024

Alterations of genomic imprinting appear during the reprogramming of adult neural stem cells

Genomic imprinting is an epigenetic mechanism that causes monoallelic expression of genes depending on their parental origin. Loss of imprinting (LOI) is associated with cancer progression and human imprinting disorders (IDs), impacting foetal development, metabolism and cognition. Imprinted genes, organized in clusters, rely on methylation at imprint control regions (ICRs), which are differentially methylated regions (DMRs) on both parental chromosomes. Somatic cell reprogramming into induced pluripotent stem cells (iPSCs) is a valuable tool to understand the mechanisms associated with pluripotency and holds promise for generating patient-specific stem cells for therapeutical applications to treat different pathologies such as IDs. Here, we conduct genome-wide RNA-seq and MeDIP-seq analysis on mouse iPSCs derived from adult neural stem cells (NSCs). Our findings reveal a comprehensive alteration in iPSCs transcriptome profile, aligning with DNA hypomethylation. This correlation is pivotal in discerning which modifications in genomic imprinting during the reprogramming process represent undesirable epigenetic abnormalities that could compromiise the quality of iPSCs. Simultaneously, it helps identify genuine epigenetic modifications that are inherently linked to pluripotency, thus ensuring a clearer understanding of the factors influencing iPSC quality and pluripotent potential.

cell biology↗

bioRxiv2023

Genetic inactivation of essential HSF1 reveals an isolated transcriptional stress response selectively induced by protein misfolding

Heat Shock Factor 1 (Hsf1) in yeast drives the basal transcription of key proteostasis factors and its activity is induced as part of the core heat shock response. Exploring Hsf1 specific functions has been challenging due to the essential nature of the HSF1 gene and the extensive overlap of target promoters with environmental stress response (ESR) transcription factors Msn2 and Msn4 (Msn2/4). In this study, we constructed a viable hsf1{Delta} strain by replacing the HSF1 open reading frame with genes that constitutively express Hsp40, Hsp70 and Hsp90 from Hsf1-independent promoters. Phenotypic analysis showed that the hsf1{Delta} strain grow slowly, is sensitive to heat as well as protein misfolding and accumulates protein aggregates. Transcriptome analysis revealed that the transcriptional response to protein misfolding induced by azetidine-2-carboxylic acid is fully dependent of Hsf1. In contrast, the hsf1{Delta} strain responded to heat shock through the ESR. Following HS, Hsf1 and Msn2/4 showed functional compensatory induction with stronger activation of the remaining stress pathway when the other branch was inactivated. Thus, we provide a long overdue genetic test of the function of Hsf1 in yeast using the novel hsf1{Delta} construct. Our data highlight that the accumulation of misfolded proteins is uniquely sensed by Hsf1-Hsp70 chaperone titration inducing a highly selective transcriptional stress response.

molecular biology↗

bioRxiv2023

The exosome degrades chromatin-associated RNAs genome-wide and maintains chromatin homeostasis

Chromatin-associated RNAs (caRNAs) modulate chromatin organization and function. The RNA exosome degrades different types of nuclear transcripts, but its role in chromatin has not been addressed. Here we have used Drosophila melanogaster S2 cells as a model system to identify the repertoire of caRNAs and establish the role of the exosome in their regulation. We have analyzed both unique and repetitive sequences, and combining RNA-seq and ATAC-seq we show that the simultaneous depletion of the exosome catalytic subunits RRP6 and DIS3 not only affects caRNA levels but also changes the local chromatin accessibility at specific loci. We have identified a group of exosome-sensitive genes that are involved in developmental regulation and are characterized by a balanced chromatin state in which Polycomb and Trithorax factors coexist. Our results reveal that RNA degradation by the exosome is an important mechanism for the homeostasis of such balanced chromatin states. Given that eukaryotic genomes are repetitive to a large extent, we have also analyzed repetitive caRNAs (rep-caRNAs) and we show that the exosome is needed to control repcaRNA levels and to maintain the degree of chromatin packaging in repetitive genomic regions. This role is particularly relevant in the pericentromeric regions where the exosome is required to silence LTR elements and maintain centromere organization.

genomics↗