Biology subjects

Goni, E.

Publications and source records attributed to Goni, E..

4 recordsLinked to original sources

bioRxiv2024

YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response.

Cells have evolved a robust and highly regulated DNA damage response to preserve their genomic integrity. Although increasing evidence highlights the relevance of RNA regulation, our understanding of its impact on a fully efficient DNA damage response remains limited. Here, through a targeted CRISPR-knockout screen, we identified RNA binding proteins and modifiers that participate in mediating the p53 response. Among the top hits, m6A reader YTHDC1 was identified as a master regulator of p53 expression. YTHDC1 binds to the transcription start sites of TP53 and other genes involved in DNA damage response, promoting their transcriptional elongation. YTHDC1 deficiency leads to reduced TP53 expression, and also retention of introns leading to aberrant protein production of key DNA damage factors. While intron retention is dependent on m6A, YTHDC1 favors TP53 transcriptional pause-release independently of m6A. Depletion of YTHDC1 causes genomic instability and aberrant cancer cell proliferation mediated by genes regulated by YTHDC1. Our results uncover YTHDC1 as an orchestrator of the DNA damage response through distinct mechanisms of co-transcriptional mRNA regulation.

cancer biology↗

bioRxiv2024

Uncovering functional lncRNAs by scRNA-seq with ELATUS

Long non-coding RNAs (lncRNAs) play fundamental roles in cellular processes and pathologies, regulating gene expression at multiple levels. Despite being highly cell type-specific, their study at single-cell (sc) level has been challenging due to their less accurate annotation and low expression compared to protein-coding genes. To identify the important, albeit widely overlooked, specific lncRNAs from scRNA-seq data, here, we develop a computational framework, ELATUS, based on the pseudoaligner Kallisto that enhances the detection of functional lncRNAs previously undetected and exhibits higher concordance with the ATAC-seq profiles in single-cell multiome data. Importantly, we then independently confirmed the expression patterns of cell type-specific lncRNAs exclusively detected with ELATUS and unveiled biologically important lncRNAs, such as AL121895.1, a previously undocumented cis-repressor lncRNA, whose role in breast cancer progression was unnoticed by traditional methodologies. Our results emphasize the necessity for an alternative scRNA-seq workflow tailored to lncRNAs that sheds light on the multifaceted roles of lncRNAs.

bioinformatics↗

bioRxiv2024

A senescence-specific lncRNA controls metabolic rewiring of senescent cells

Despite the classical view of senescence as passive growth arrest, senescent cells remain metabolically active to be able to cope with the energetic demand of the senescence program. However, the mechanisms underlying this metabolic reprogramming remain poorly understood. We have identified sin-lncRNA, a previously uncharacterized lncRNA, that plays a pivotal role in this response. Sin-lncRNA is only expressed by senescent cells, induced by the senescence master regulator C/EBP{beta}. While strongly activated in senescence, sin-lncRNA loss reinforces the senescence program by altering oxidative phosphorylation and rewiring mitochondrial metabolism. By interacting with the TCA enzyme dihydrolipoamide S-succinyltransferase (DLST) it facilitates its localization to the mitochondria. On the other hand, sin-lncRNA depletion results in DLST nuclear translocation linked to DLST-dependent transcriptional alteration of OXPHOS genes. While in highly proliferative cancer cells, sin-lncRNA expression remains undetected, it is strongly induced upon cisplatin-induced senescence. Depletion of sin-lncRNA in ovarian cancer cells results in deficient oxygen consumption and increased extracellular acidification, sensitizing the cells to cisplatin treatment. Altogether, these results indicate that sin-lncRNA is specifically induced in cellular senescence to maintain metabolic homeostasis. Our findings reveal a new regulatory mechanism in which a lncRNA contributes to the adaptive metabolic changes in senescent cells, unveiling the existence of an RNA-dependent metabolic rewiring specific to senescent cells.

cell biology↗

bioRxiv2023

ORC1 binds to cis-transcribed RNAs for efficient activation of replication origins

Cells must coordinate the activation of thousands of replication origins dispersed throughout their genome. Active transcription is known to favor the formation of mammalian origins, although the role that RNA plays in this process remains unclear. We show that the ORC1 subunit of the human Origin Recognition Complex interacts with RNAs transcribed from genes with origins in their transcription start sites (TSSs), displaying a positive correlation between RNA binding and origin activity. RNA depletion, or the use of ORC1 RNA-binding mutant, result in inefficient activation of proximal origins, linked to impaired ORC1 chromatin release. ORC1 RNA binding activity resides in its intrinsically disordered region, involved in intra- and inter-molecular interactions, regulation by phosphorylation, and phase-separation. We show that RNA binding favors ORC1 chromatin release, by regulating its phosphorylation and subsequent degradation. We propose that fluctuating concentrations of RNA during the cell cycle may play a sequential role in controlling origins through interaction with this flexible region of ORC1. Our results unveil a novel non-coding function of RNA as a dynamic component of the chromatin, orchestrating the activation of replication origins. One sentence summaryThe human origin recognition complex subunit 1 ORC1, binds to RNAs transcribed from genes with origins of replication at the TSS, which is required for optimal origin activation.

molecular biology↗