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Vourekas, A.

Publications and source records attributed to Vourekas, A..

7 recordsLinked to original sources

An ancestral tRNA maturation enzyme repurposed for cytoplasmic non-coding RNA processing

Ribonuclease Z enzymes remove 3' trailers from precursor tRNAs. In human cells, ELAC2/RNase ZL matures nuclear and mitochondrial pre-tRNAs, whereas the cytosolic short paralog ELAC1/RNase ZS repairs ANKZF1-cleaved tRNAs, but its broader substrate repertoire remains unclear. We investigated ELAC1 function using transcriptome profiling, small RNA sequencing, CLIP-seq, and biochemical reconstitution. ELAC1 was dispensable for canonical tRNA processing but associated with structured RNA polymerase III transcripts, prominently Y RNAs and vault RNAs (vtRNAs). Purified ELAC1 cleaved all four human vtRNAs near their 3' ends, with high-resolution mapping identifying a conserved cleavage position within the 3' extension. Efficient cleavage required structural features of the vtRNA terminal region. In contrast, ELAC2 showed little or no vtRNA cleavage under the conditions tested and displayed stricter substrate and cleavage-site selection on pre-tRNA. Loss and re-expression of ELAC1 altered structured ncRNA abundance and small-RNA end profiles. These findings identify vtRNAs as direct ELAC1 substrates and support functional specialization of human ELAC paralogs, with ELAC2 favoring precise pre-tRNA maturation and ELAC1 exhibiting broader RNA substrate specificity.

molecular biology↗

Human mascRNA interacts with SUMO E1 and reshapes nuclear SUMOylation

Human mascRNA is a tRNA-like 58-nucleotide non-coding RNA processed from the 3' end of the MALAT1 transcript. Although mascRNA has been implicated in diverse cellular processes, its molecular mechanism has remained unclear. Here, we reveal a direct functional link between mascRNA and the SUMOylation pathway. Structural probing and SEC-SAXS confirm the compact, tRNA-like architecture of mascRNA in solution, while biochemical assays demonstrate its direct interaction with the SUMO E1 activating enzyme in vitro. Proteomic analyses show that mascRNA engages nuclear protein networks enriched for SUMOylated factors, including chromatin remodelers and nucleolar components. Transfection of synthetic mascRNA alters SAE2 and SUMO1 nuclear organization and broadly reduces nuclear SUMOylation, accompanied by decreased ProMyeLocytic (PML) body abundance and SUMO colocalization. SUMO1 immunoprecipitation and mass spectrometry reveal widespread decreases in SUMO conjugation, particularly among proteins involved in RNA metabolism and rRNA biogenesis with nuclear body localization. We further validate reduced SUMOylation of nucleolar factors such as BEND3 and ZNF106. These findings position mascRNA as a structured RNA ligand that modulates SUMO-dependent nuclear architecture and protein homeostasis, uncovering an unexpected intersection between RNA biology and post-translational modification networks. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/700226v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@e94a88org.highwire.dtl.DTLVardef@1c62aforg.highwire.dtl.DTLVardef@192cf37org.highwire.dtl.DTLVardef@1624896_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

Establishment and functional characterization of bovine endometrial epithelial organoids

Pre-implantation embryonic loss constitutes a major barrier to reproductive efficiency in livestock, yet the extrinsic determinants of embryonic survival remain poorly defined. Intra-organoid fluid (IOF) faithfully recapitulates native tissue secretions across multiple organ systems. We hypothesized that bovine endometrial epithelial organoids (BEEO) would produce IOF that mirrored in vivo uterine luminal fluid composition and extend embryo culture duration in vitro. We pursued three objectives: (a) establish and morphologically characterize BEEO, (b) define BEEO transcriptomic and secretory responses to estradiol (E2), medroxyprogesterone acetate (MPA), and interferon-tau (IFN{tau}), and (c) determine whether BEEO-derived IOF can support in vitro embryonic development beyond Day 8 (hatched blastocyst stage) under conventional culture conditions. BEEO were established from primary endometrial tissue (n=4) and maintained a stable epithelial phenotype through multiple passages. Transcriptomic profiling revealed robust responses to stimulation, with E2, MPA, and IFN{tau} inducing distinct gene expression programs consistent with in vivo effects. IOF metabolomic analysis confirmed hormone-dependent regulation of IOF secretory output, with E2+MPA (diestrus mimic) enhancing the production of metabolites implicated in conceptus development. Remarkably, IOF from diestrus mimic-stimulated BEEO, despite being diluted approximately seven-fold in PBS, maintained embryo survival rates comparable to optimized commercial medium, and exceeded PBS-only controls. These findings position BEEO as a physiologically relevant model for dissecting maternal-embryo interactions in vitro and identifying targets to improve fertility in cattle and other livestock.

cell biology↗

Oviduct fluid metabolic regulation of embryonic genome methylation

Adverse maternal health and lifestyle during pregnancy can program offspring susceptibility to noncommunicable diseases in adulthood. Oviduct fluid facilitates key preimplantation milestones, including embryonic genome activation. However, the regulatory mechanisms governing oviduct fluid composition, and the developmental consequences of its disruption, remain unclear. Capitalizing on conserved dynamics between human and bovine embryonic genome activation, we first established and characterized bovine oviduct epithelial organoids as a model system. Organoids were then exposed to {Delta}-tetrahydrocannabinol (THC) and cannabidiol (CBD) to test the hypothesis that exocannabinoids alter intra-organoid fluid composition. Treatment altered the organoid transcriptome and intra-organoid fluid metabolome, notably elevating 5'-deoxyadenosine levels. Subsequent embryo culture with 5'-deoxyadenosine during embryonic genome activation resulted in aberrant DNA methylation patterning - independently of direct THC and CBD exposure. These findings identify a novel, indirect, mechanism by which maternal exposures disrupt embryonic development through changes in oviductal metabolite secretions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/659599v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@19ac750org.highwire.dtl.DTLVardef@935709org.highwire.dtl.DTLVardef@13723a8org.highwire.dtl.DTLVardef@105f473_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

cell biology↗

DDX3X acts as a selective dual switch regulator of mRNA translation in acute ER stress

In eukaryotes, regulation of mRNA translation initiation greatly impacts gene expression, and is critical for cellular stress responses. DDX3X is a ubiquitous DEAD-box RNA helicase whose precise role in 5 UTR scanning and start codon decoding in non-stressed and stressed cells is still elusive. Here we show that DDX3X engages with thousands of mRNAs as part of the eIF4F-mediated 48S scanning complex, simultaneously acting to promote or suppress translation of select mRNAs in non-stressed conditions, and switches this regulation in opposite directions in acute ER stress. We find distinct DDX3X binding patterns of differentially regulated mRNAs, which lead us to identify N4-acetylation of cytidines surrounding the start codon as an accompanying feature of mRNAs subject to DDX3X-mediated selective dual regulation. Our findings illuminate the role of DDX3X in stress response and highlight a novel connection between an RNA helicase and a post-transcriptional modification in regulating mRNA translation.

molecular biology↗

All ribosomal RNAs and 45S spacers from humans to worms are packed with organism-specific motifs whose other copies are found predominantly in numerous nervous system genes including many associated with human disorders

The nucleotide sequences of ribosomal RNAs (rRNAs) and the spacers of 45S are tuned to fulfill optimally their respective roles during ribosome biosynthesis and function. We report that these sequences satisfy additional genome-wide constraints in humans, mice, fruit flies, and worms. In all four organisms, the rRNAs and 45S spacers are densely packed with organism-specific nucleotide motifs with many additional identical copies throughout the genome. The human rRNAs and 45S spacers contain 1,723 motifs whose sequences are unique to the rRNAs/spacers of primates. These motifs have numerous additional exact intronic and exonic copies whose genomic placement is also unique to primates. Specific combinations of the motifs appear exclusively in 3,430 human nervous system and developmental genes, including 1,046 risk genes for autism, schizophrenia, and bipolar disorder. RNA/RNA crosslinking experiments show that the rRNA/spacer motifs are contact points for rRNA-mRNA and mRNA-mRNA heteroduplexes. RNA binding protein (RBP) assays show that these motifs are also in the binding sites of 113 RBPs. RNA sequencing reveals that rRNAs and spacers produce endogenous small non-coding RNAs (sncRNAs) that carry the same primate-specific motifs. Lastly, the motifs intergenic and intronic copies overlap 131 GWAS polymorphisms associated with neuropathologies (p-val<3.9e-12). The findings suggest that the motifs facilitate RNA/RNA and RBP/RNA interactions that are affected by polymorphisms and modulated by rRNA- and spacer-derived sncRNAs carrying the same motifs. Our study also genetically links for the first time rRNAs and 45S spacers to autism and other typically human neurological disorders. Mutation panels based on these motifs can lead to new molecular diagnostics for these disorders, whereas snRNAs carrying these motifs can serve as drugs or potential therapeutic targets. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/627812v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@146feadorg.highwire.dtl.DTLVardef@1fa501corg.highwire.dtl.DTLVardef@a17f14org.highwire.dtl.DTLVardef@9e2053_HPS_FORMAT_FIGEXP M_FIG C_FIG The human ribosomal RNAs and the 45S spacers share primate-specific motifs with thousands of nervous system genes, including risk genes for autism and other neurological disorders. Similar links between rRNAs/spacers and nervous system genes exist in mice, fruit flies, and worms but are achieved through motifs that are unique to each organism. In humans, the motifs are at the contact points of endogenous gene-gene and rRNA-gene heteroduplexes, as well as the binding sites of RNA binding proteins (RBPs) in genes and rRNAs/spacers. Endogenous small RNAs carrying these shared motifs modulate these endogenous interactions and are disrupted by mutations at the motifs genomic copies. Mutation panels based on these motifs can lead to new diagnostics for autism and other disorders, while the small RNAs carrying the motifs can serve as drugs or potential therapeutic targets.

neuroscience↗

The MOV10 RNA helicase is a dosage-dependent host restriction factor for LINE1 retrotransposition in mice

Transposable elements constitute nearly half of the mammalian genome and play important roles in genome evolution. While a multitude of both transcriptional and post-transcriptional mechanisms exist to silence transposable elements, control of transposition in vivo remains poorly understood. MOV10, an RNA helicase, is a potent inhibitor of mobilization of retrotransposons and retroviruses in cell culture assays. Here we report that MOV10 restricts LINE1 retrotransposition in mice. Although MOV10 is broadly expressed, its loss causes only incomplete penetrance of embryonic lethality, and the surviving MOV10-deficient mice are healthy and fertile. Biochemically, MOV10 forms a complex with UPF1, a key component of the nonsense-mediated mRNA decay pathway, and primarily binds to the 3UTR of somatically expressed transcripts in testis. Consequently, loss of MOV10 results in an altered transcriptome and a modest upregulation of two LINE1 families in testis. Analyses using a LINE1 reporter transgene reveal that loss of MOV10 leads to increased LINE1 retrotransposition in somatic and reproductive tissues from both embryos and adult mice. Moreover, the degree of LINE1 retrotransposition inhibition is dependent on the Mov10 gene dosage. Furthermore, MOV10 deficiency reduces reproductive fitness over successive generations. Our findings demonstrate that MOV10 attenuates LINE1 retrotransposition in a dosage-dependent manner in mice. Author summaryTransposable elements (TEs), including L1 and SINEs, are abundant in the genome and play important roles in evolution, development, and diseases. While TEs propagate in individuals and across generations, the host organism needs to suppress them, resulting in an ongoing arms race between TEs and the host genome. L1, a retrotransposon, accounts for about 17% of the mammalian genome. L1 encodes two proteins, which bind to the L1 transcript to form L1 ribonucleoprotein particles. L1 proliferates in the genome via retrotransposition. A multitude of transcriptional and post-transcriptional mechanisms exist to suppress TEs, however, retrotransposition of TEs remains poorly understood. L1 ribonucleoprotein particles are associated with a large number of host proteins, one of which is the MOV10 RNA helicase. MOV10 exhibits anti-viral activities against retroviruses such as HIV-1. In cultured cells, MOV10 is a potent inhibitor of retrotransposition of L1, SINEs, and IAP. Although MOV10 is expressed in a broad range of tissues, loss of MOV10 causes only incomplete penetrance of embryonic lethality. The viable MOV10-deficient mice are grossly normal and fertile. Importantly, analyses using a L1 transgene reporter reveal that MOV10 inhibits L1 retrotransposition in both somatic tissues and reproductive tissues in a gene dosage-dependent manner. Therefore, MOV10 functions as a host restriction factor for L1 and possibly other transposable elements in vivo.

developmental biology↗