Biology subjects

Peris, G.

Publications and source records attributed to Peris, G..

6 recordsLinked to original sources

bioRxiv2026

Identification of cellular double-stranded RNAs in mammalian embryonic stem cells

Antiviral defence mechanisms are typically activated upon sensing virus-derived nucleic acids. During replication, viruses generate double-stranded RNA (dsRNA) intermediates that the innate immune system can sense, triggering several defence pathways. Conversely, mammalian cells avoid accumulating their own endogenous dsRNA to prevent activating these defence mechanisms. However, we demonstrate that mammalian embryonic stem cells (ESCs) accumulate endogenous dsRNA without activating these responses, as they lack all classical dsRNA-mediated antiviral pathways. To identify these endogenous dsRNAs, we have developed a method that includes an antibody-based purification coupled to RNase I treatment to enrich bona fide dsRNAs. The RNase I treatment results in an enrichment on sense/antisense and A-to-I edited transcripts, suggesting that they are true dsRNA in cells. Our refined protocol reveals that transposable elements (TEs), primarily the young elements from the LINE and LTR classes, are the predominant sources of dsRNA in ESCs. This approach will be useful for investigating the role of dsRNA in disease settings, such as autoimmunity or cancer, where endogenous dsRNA accumulation has also been observed.

molecular biology↗

bioRxiv2025

DICER1 syndrome mutations lead to a gain of 3p-miRNA function, HERVH activity and increased metastatic potential

The DICER1 gene is mutated in cancer, including DICER1 syndrome, a rare tumour predisposition syndrome. Cancer-associated hotspot mutations have been reported in both catalytic domains of DICER1 and are predicted to disrupt miRNA biogenesis. To understand how these hotspot mutations contribute to cancer development, we have generated cell lines harbouring single amino acid substitutions within the catalytic RNase IIIa (S1344L) or RNase IIIb (D1709N) domains of the endogenous DICER1 gene. We show that both mutations result in a widespread loss of 5p miRNAs, and, unexpectedly, an increase in 3p passenger strands loading into AGO2. The shared similarities between both mutants can be attributed to the structural proximity of the S1344 residue to the RNase IIIb catalytic centre. Functionally, we found that changes in the repertoire of miRNAs loaded into AGO2 result in altered gene expression, impacting critical pathways for cancer development, including metastatic potential. Additionally, our results indicate that inactivating the processing activity of DICER1 does not result in genomic instability. Instead, mutations cause specific upregulation of human endogenous retrovirus H (HERVH) through miRNA-independent mechanisms, suggesting that both canonical and non-canonical DICER1 functions are important to understand DICER1 syndrome.

molecular biology↗

bioRxiv2025

Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8

The type I interferon (IFN) response is the main innate immune pathway against viruses in mammals. This pathway must be tightly regulated to prevent viral spread while avoiding excessive immune responses. Here, we show that inactivation of the double-stranded RNA (dsRNA)-binding protein DGCR8 unleashes the IFN response in human cells. We demonstrate that DGCR8 restricts the accumulation of endogenous dsRNA originating from protein-coding mRNAs that harbour transposable elements (TEs), primarily Alu. We propose that DGCR8 binding to TE-rich mRNAs is essential to resolve dsRNA structures, and in its absence, accumulated dsRNA signals through the RIG-I-like signalling pathway triggering the IFN response. This mechanism is relevant to conditions where DGCR8 expression levels are altered, including the 22q11.2 deletion syndrome (22qDS). Supporting this, we show that 22qDS-derived cells exhibit an exacerbated type I IFN response which inversely correlated with DGCR8 levels. All these together demonstrate the importance of suppressing endogenous TE-dsRNA accumulation to prevent unwanted immune activation and associated disease pathogenesis.

molecular biology↗

bioRxiv2024

BMAL1 represses transposable elements independently of CLOCK in pluripotent cells

Circadian oscillations of gene transcripts rely on a negative feedback loop executed by the activating BMAL1-CLOCK heterodimer and its negative regulators PER and CRY. Although circadian rhythms and CLOCK protein are mostly absent during embryogenesis, the lack of BMAL1 during prenatal development causes an early aging phenotype during adulthood, suggesting that BMAL1 carries out an unknown non-circadian function during organism development that is fundamental for healthy adult life. Here, we show that BMAL1 interacts with TRIM28 and represses transcription of totipotency-associated MERVL retrotransposons in mouse pluripotent cells. Deletion of Bmal1 leads to genome-wide upregulation of MERVLs, changes in the three-dimensional organization of the genome, and acquisition of totipotency-associated features. Overall, we demonstrate that in pluripotent cells BMAL1 is redeployed as a transcriptional repressor of transposable elements (TEs) in a CLOCK-independent way. We propose that BMAL1-TRIM28 activity during prenatal life is essential for optimal health and life span in mammals.

molecular biology↗

bioRxiv2024

DGCR8 haploinsufficiency leads to primate-specific RNA dysregulation and pluripotency defects

The 22q11.2 deletion syndrome (22qDS) is caused by a microdeletion in chromosome 22, including DGCR8, an essential gene for miRNA production. The contribution of human DGCR8 hemizygosity to the disease is still unclear. In this study, we generated two human pluripotent cell models containing a single functional DGCR8 allele to elucidate its role on 22qDS. DGCR8+/-cells show increased apoptosis as well as self-renewal and differentiation defects in both the naive and primed states. The expression of primate-specific miRNAs was largely affected, due to impaired miRNA processing and chromatin accessibility. DGCR8+/- cells also displayed a pronounced reduction in human endogenous retrovirus class H (HERVH) expression, a primate-specific retroelement essential for pluripotency maintenance. Importantly, the reintroduction of primate-specific miRNAs as well as the miR-371-3 cluster rescued the cellular and molecular phenotypes of DGCR8+/-cells. Our results suggest that DGCR8 is haploinsufficient in humans and that miRNAs and transposable elements may have co-evolved in primates as part of an essential regulatory network to maintain stem cell identity.

molecular biology↗

bioRxiv2020

The tumor suppressor microRNA let-7 inhibits human LINE-1 retrotransposition

Nearly half of the human genome is made of transposable elements (TEs) whose activity continues to impact its structure and function. Among them, Long INterspersed Element class 1 (LINE-1 or L1) elements are the only autonomously active TEs in humans. L1s are expressed and mobilized in different cancers, generating mutagenic insertions that could affect malignancy. Tumor suppressor microRNAs are [~]22nt RNAs that post-transcriptionally regulate oncogene expression and are frequently downregulated in cancer. Here we explore whether they also influence L1 mobilization. We found that downregulation of let-7 correlates with accumulation of L1 insertions in human lung cancer. Furthermore, we demonstrate that let-7 binds to the L1 mRNA and impairs the translation of the second L1-encoded protein, ORF2p, reducing its mobilization. Overall, our data uncover a new role for let-7, one of the most relevant microRNAs, which is to maintain somatic genome integrity by restricting L1 retrotransposition.

molecular biology↗