Diagenode

D-Plex small RNA-seq

36 publications found.

Pervasive translation of Xrn1-sensitive unstable long non-coding RNAs in yeast
Published: March, 2024

Abstract: Despite being predicted to lack coding potential, cytoplasmic long non-coding (lnc)RNAs can associate with ribosomes. However, the landscape and biological relevance of lncRNAs translation remains poorly studied. In yeast, cytoplasmic Xrn1-sensiti...
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Aseptic loosening around total joint replacement in humans is regulated by miR-1246 and miR-6089 via the Wnt signalling pathway
Published: January, 2024

Abstract: Background: Total joint replacement for osteoarthritis is one of the most successful surgical procedures in modern medicine. However, aseptic loosening continues to be a leading cause of revision arthroplasty. The diagnosis of aseptic looseni...
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An inappropriate decline in ribosome levels drives a diverse set of neurodevelopmental disorders
Published: January, 2024

Abstract: Many neurodevelopmental defects are linked to perturbations in genes involved in housekeeping functions, such as those encoding ribosome biogenesis factors. However, how reductions in ribosome biogenesis can result in tissue and developmental spec...
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Challenges in characterization of transcriptomes of extracellular vesicles and non-vesicular extracellular RNA carriers
Published: December, 2023

Abstract: Since its original discovery over a decade ago, extracellular RNA (exRNA) has been found in all biological fluids. Furthermore, extracellular microRNA has been shown to be involved in communication between various cell types. Importantly, the exRN...
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Guidelines for Performing Ribosome Profiling in Plants Including Structural Analysis of rRNA Fragments
Published: November, 2023

Abstract: Ribosome profiling (or Ribo-seq) is a technique that provides genome-wide information on the translational landscape (translatome). Across different plant studies, variable methodological setups have been described which raises questions about the...
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Integrated multiplexed assays of variant effect reveal cis-regulatory determinants of catechol-O-methyltransferase gene expression
Published: November, 2023

Abstract: Multiplexed assays of variant effect are powerful methods to profile the consequences of rare variants on gene expression and organismal fitness. Yet, few studies have integrated several multiplexed assays to map variant effects on gene expression...
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The Ribosome Assembly Factor Reh1 is Released from the Polypeptide Exit Tunnel in the Pioneer Round of Translation
Published: October, 2023

Abstract: Assembly of functional ribosomal subunits and successfully delivering them to the translating pool is a prerequisite for protein synthesis and cell growth. In S. cerevisiae, the ribosome assembly factor Reh1 binds to pre-60S subunits at ...
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Knockout of the longevity gene Klotho perturbs aging- and Alzheimer’s disease-linked brain microRNAs and tRNA fragments
Published: September, 2023

Abstract: Overexpression of the longevity gene Klotho prolongs, while its knockout shortens lifespan and impairs cognition via altered fibroblast growth factor signaling that perturbs myelination and synapse formation; however, comprehensive analysis of Klo...
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Single-cell quantification of ribosome occupancy in early mouse development
Published: June, 2023

Abstract: Translation regulation is critical for early mammalian embryonic development1. However, previous studies had been restricted to bulk measurements2, precluding precise determination of translation regulation including allele-specific analyses. Here...
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DIS3 ribonuclease prevents the cytoplasmic accumulation of lncRNAs carrying non-canonical ORFs, which represent a source of cancer immunopeptides.
Published: June, 2023

Abstract: Around 12% of multiple myeloma (MM) cases harbour mutations in DIS3, which encodes an RNA decay enzyme that controls the turnover of some long noncoding RNAs (lncRNAs). Although lncRNAs, by definition, do not encode proteins, some can be a so...
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Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADPribosylation dependent manner to induce translational stalling.
Published: May, 2023

Abstract: In light of the numerous studies identifying post-transcriptional regulators on the surface of the endoplasmic reticulum (ER), we asked whether there are factors that regulate compartment specific mRNA translation in human cells. Using a proteomic...
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Towards a human brain EV atlas: Characteristics of EVs from different brain regions, including small RNA and protein profiles.
Published: May, 2023

Abstract: Extracellular vesicles (EVs) are released from different cell types in the central nervous system (CNS) and play roles in regulating physiological and pathological functions. Although brain-derived EVs (bdEVs) have been successfully collected from...
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RNA landscapes of brain tissue and brain tissue-derived extracellularvesicles in simian immunodeficiency virus (SIV) infection andSIV-related central nervous system pathology.
Published: April, 2023

Abstract: Antiretroviral treatment regimens can effectively control HIV replication and some aspects of disease progression. However, molecular events in end-organ diseases such as central nervous system (CNS) disease are not yet fully understood, and routi...
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Immunoregulatory Biomarkers of the Remission Phase in Type 1 Diabetes: miR-30d-5p Modulates PD-1 Expression and Regulatory T Cell Expansion
Published: February, 2023

Abstract: The partial remission (PR) phase of type 1 diabetes (T1D) is an underexplored period characterized by endogenous insulin production and downmodulated autoimmunity. To comprehend the mechanisms behind this transitory phase and develop precision med...
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Ageing-associated small RNA cargo of extracellular vesicles.
Published: January, 2023

Abstract: Previous work on murine models and humans demonstrated global as well as tissue-specific molecular ageing trajectories of RNAs. Extracellular vesicles (EVs) are membrane vesicles mediating the horizontal transfer of genetic information between dif...
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The piRNA-pathway factor FKBP6 is essential for spermatogenesis butdispensable for control of meiotic LINE-1 expression in humans.
Published: October, 2022

Abstract: Infertility affects around 7\% of the male population and can be due to severe spermatogenic failure (SPGF), resulting in no or very few sperm in the ejaculate. We initially identified a homozygous frameshift variant in FKBP6 in a man with extreme...
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The seminal plasma microbiome of men with testicular germ cell tumours described by small RNA sequencing
Published: September, 2022

Abstract: Background: It has been estimated that microorganisms are involved in the pathogenesis of approximately 20% of all cancers. Testicular germ cell tumours (TGCTs) are the most common type of malignancy in young men and arise from the precursor ...
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Neutral sphingomyelinase 2 inhibition attenuates extracellular vesiclerelease and improves neurobehavioral deficits in murine HIV.
Published: July, 2022

Abstract: People living with HIV (PLH) have significantly higher rates of cognitive impairment (CI) and major depressive disorder (MDD) versus the general population. The enzyme neutral sphingomyelinase 2 (nSMase2) is involved in the biogenesis of ceramide ...
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A novel, essential trans-splicing protein connects the nematode SL1snRNP to the CBC-ARS2 complex.
Published: July, 2022

Abstract: Spliced leader trans-splicing is essential for gene expression in many eukaryotes. To elucidate the molecular mechanism of this process, we characterise the molecules associated with the Caenorhabditis elegans major spliced leader snRNP (SL1 snRNP...
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Interspecies effectors of a transgenerational memory of bacterial infection in Caenorhabditis elegans.
Published: July, 2022

Abstract: The inheritance of memory is an adaptive trait. Microbes challenge the immunity of organisms and trigger behavioral adaptations that can be inherited, but how bacteria produce inheritance of a trait is unknown. We use and its bacteria to study the...
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Diverse Monogenic Subforms of Human Spermatogenic Failure
Published: July, 2022

Abstract: Non-obstructive azoospermia (NOA) is the most severe form of male infertility and typically incurable with current medicine. Due to the biological complexity of sperm production, defining the genetic basis of NOA has proven challenging, and to dat...
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Ultrasensitive Ribo-seq reveals translational landscapes during mammalian oocyte-to-embryo transition and pre-implantation development.
Published: June, 2022

Abstract: In mammals, translational control plays critical roles during oocyte-to-embryo transition (OET) when transcription ceases. However, the underlying regulatory mechanisms remain challenging to study. Here, using low-input Ribo-seq (Ribo-lite), we in...
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Translation is a key determinant controlling the fate of cytoplasmic long non-coding RNAs
Published: May, 2022

Abstract: Despite predicted to lack coding potential, cytoplasmic long non-coding (lnc)RNAs can associate with ribosomes, resulting in some cases into the production of functional peptides. However, the biological and mechanistic relevance of this pervasive...
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MGcount: a total RNA-seq quantification tool to address multi-mappingand multi-overlapping alignments ambiguity in non-coding transcripts
Published: January, 2022

Abstract: Background Total-RNA sequencing (total-RNA-seq) allows the simultaneous study of both the coding and the non-coding transcriptome. Yet, computational pipelines have traditionally focused on particular biotypes, making assumptions that are not full...
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Single cell quantification of ribosome occupancy in early mouse development
Published: December, 2021

Abstract: Technological limitations precluded transcriptome-wide analyses of translation at single cell resolution. To solve this challenge, we developed a novel microfluidic isotachophoresis approach, named RIBOsome profiling via IsoTachoPhoresis (Ribo-ITP...
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Single cell quantification of ribosome occupancy in early mousedevelopment
Published: December, 2021

Abstract: Technological limitations precluded transcriptome-wide analyses of translation at single cell resolution. To solve this challenge, we developed a novel microfluidic isotachophoresis approach, named RIBOsome profiling via IsoTachoPhoresis (Ribo-ITP...
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Functional microRNA targetome undergoes degeneration-induced shift in the retina
Published: August, 2021

Abstract: Background: MicroRNA (miRNA) play a significant role in the pathogenesis of complex neurodegenerative diseases including age-related macular degeneration (AMD), acting as post-transcriptional gene suppressors through their association with ...
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Functional microRNA targetome undergoes degeneration-induced shift inthe retina.
Published: August, 2021

Abstract: BACKGROUND: MicroRNA (miRNA) play a significant role in the pathogenesis of complex neurodegenerative diseases including age-related macular degeneration (AMD), acting as post-transcriptional gene suppressors through their association with argonau...
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Single-cell microRNA sequencing method comparison and application tocell lines and circulating lung tumor cells
Published: July, 2021

Abstract: Molecular single cell analyses provide insights into physiological and pathological processes. Here, in a stepwise approach, we first evaluate 19 protocols for single cell small RNA sequencing on MCF7 cells spiked with 1 pg of 1,006 miRNAs....
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Small RNAs in Seminal Plasma as Novel Biomarkers for Germ Cell Tumors
Published: May, 2021

Abstract: Circulating miRNAs secreted by testicular germ cell tumors (TGCT) show great potential as novel non-invasive biomarkers for diagnosis of TGCT. Seminal plasma (SP) represents a biofluid closer to the primary site. Here, we investigate whether small...
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Small RNAs in Seminal Plasma as Novel Biomarkers for GermCell Tumors.
Published: May, 2021

Abstract: Circulating miRNAs secreted by testicular germ cell tumors (TGCT) show great potential as novel non-invasive biomarkers for diagnosis of TGCT. Seminal plasma (SP) represents a biofluid closer to the primary site. Here, we investigate whether small...
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Bacterial small RNAs and host epigenetic effectors of atransgenerational memory of pathogens in C. elegans
Published: March, 2021

Abstract: The inheritance of memories is adaptive for survival. Microbes interact with all organisms challenging their immunity and triggering behavioral adaptations. Some of these behaviors induced by bacteria can be inherited although the mechanisms of ac...
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Interspecies RNA Interactome of Pathogen and Host in aHeritable Defensive Strategy.
Published: January, 2021

Abstract: Communication with bacteria deeply impacts the life history traits of their hosts. Through specific molecules and metabolites, bacteria can promote short- and long-term phenotypic and behavioral changes in the nematode . The chronic exposure of to...
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Distinct Extracellular RNA Profiles in Different PlasmaComponents.
Published: January, 2021

Abstract: Circulating extracellular RNAs (exRNAs) have great potential to serve as biomarkers for a wide range of diagnostic, therapeutic, and prognostic applications. So far, knowledge of the difference among different sources of exRNAs is limited. To addr...
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Genes with 5′ terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 NSP1 protein
Published: September, 2020

Abstract: Viruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms to co-opt host translation for their survival. SARS-CoV-2 relies on a non-structural protein, NSP1, for shutting dow...
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The ribosomal protein S1-dependent standby site in tisB mRNA consists of a single-stranded region and a 5′ structure element
Published: July, 2019

Abstract: In bacteria, stable RNA structures that sequester ribosome-binding sites (RBS) impair translation initiation, and thus protein output. In some cases, ribosome standby can overcome inhibition by structure: 30S subunits bind sequence-nonspecifically...
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