23 papers · ranked by Valyu relevance
Paulina Bolc, Marta Puchta-Jasińska, Adrian Motor, Marcin Maździarz + 2 more
Drought is a leading constraint on plant productivity and will intensify with climate change. Plant acclimation emerges from a multilayered regulatory system that integrates signaling, transcriptional reprogramming, RNA-based control, and chromatin dynamics. Within this hierarchy, non-coding RNAs (ncRNAs) provide a…
Yongji Yang, Yi Hu, Tao Li, Qi You + 1 more
In organisms, non-coding RNAs (ncRNAs) are key regulatory elements that modulate, the expression of genes involved in diverse biological traits. Among them, micro RNAs (miRNAs), small interfering RNAs (siRNAs), and long non-coding RNAs (lncRNAs) have become major research focuses. Wheat, the world’s most widely grown…
Nair Sreejith, Singh Deepshikha, Saha Aditi, Datta Bhaskar + 1 more
Long non-coding RNAs (lncRNAs) account for a major proportion of the transcriptional output in complex organismal genomes. Their emergence as auxiliary regulators of gene expression as well as their roles in metastasis and cancer progression has put them in the limelight. LncRNAs perform multitudes of functions and…
Javier Avalos, Adrián Perera-Bonaño, M. Carmen Limón, André P. Gerber
Long noncoding RNAs (lncRNAs) are transcripts generated by polymerase II, therefore subject to 5′ capping and 3′ polyadenylation, categorized as such when they are at least 200 nt in size and lack coding function. The lncRNAs were initially interpreted as spurious transcription products, but over the last two decades…
Riccardo Aguti, Mattia Bernetti, Andrea Cavalli, Matteo Masetti
Long non-coding RNAs (lncRNAs) are increasingly recognized as druggable targets due to their conserved secondary/tertiary structures and regulatory roles in disease. A prototypical example is the MALAT1 triple helix, whose stability supports transcript persistence and is implicated in oncogenesis. Here, we evaluate the…
Jaeyoon Lee, Madhav Mantri, Kavita Murthy, Luise A. Seeker + 4 more
The biological significance of non-coding RNAs has been increasingly appreciated as their roles in various cellular processes are uncovered. However, single-cell transcriptomic profiling of human samples has focused primarily on protein-coding genes by targeting polyadenylated RNA transcripts, leaving the expression…
Samuel Z. Desind, Samira K. Bell, Carol S. Lutz
Noncoding RNAs (ncRNAs) are a diverse and abundant class of molecules that play essential roles in gene regulation across eukaryotic organisms, including roles in human homeostasis and disease. Historically regarded as transcriptional artifacts or byproducts, ncRNAs are now recognized as essential regulators of…
Zhihua Jiang, Michee van Rooyen, Jennifer J. Michal, Isyana Khaerunnisa + 4 more
Despite decades of genome sequencing and annotation, a fundamental paradox remains unresolved: how organisms with finite and relatively stable gene numbers generate extraordinary phenotypic diversity. In this review, we propose that regulated RNA variant diversity provides a critical level of resolution for…
Shafaque Zahra, Rashmi Gangwar, Sneha Tiwari, Dipul Kumar Biswas + 2 more
Transfer RNA-derived non-coding RNAs (tncRNAs) are potential regulators of gene expression in plants, and it’s crucial to understand their diversity and functional roles in modulating plant stress responses. Here, we have investigated abiotic stress-responsive tncRNAs in two important crops, rice and chickpea, under…
Yu-Li He, Loh, Youshin
The emerging field of epigenetics has recently unveiled a dynamic landscape in which gene expression is not determined solely by genetic sequences but also by intricate regulatory mechanisms. This review examines the interactions between these regulatory mechanisms, including DNA methylation and non-coding RNAs…
Giuseppe Scafuro, Myriam Karam, Ayesha Khan, Chiara Tammaro + 8 more
Title: Simple Summary Non-coding RNAs, particularly microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are key regulators of gene expression that interact within complex networks and play a central role in cancer. Their cross-regulation influences major cellular processes such as proliferation…
Janki Insan, Manoj B Menon, Sonam Dhamija
Conventional gene annotation pipelines classify eukaryotic genes into protein-coding and non-coding. Alternative splicing may generate non-coding transcript variants from protein-coding genes, that are expressed in tissue- or disease-specific manner. We and others have described the genes which transcribe both coding…
Eric Malekos, Valeriy Smaliy, Susan Carpenter
Ribosome profiling has revealed thousands of noncanonical translation events across mammalian genomes, yet functional characterization has overwhelmingly focused on proliferative fitness in cancer cell lines. Here, we present a comprehensive survey of noncanonical translation in the mouse immune system and its…
Ning Lu, Xin Gao, Michael C. Lanz, Marianna E. Estrada + 3 more
Genome size varies widely across eukaryotes, largely because of differences in non-coding DNA, but the physiological consequences of this variation remain unclear. To directly test how non-coding DNA abundance influences cellular physiology, we engineered a scalable genome-expansion system in the budding yeast S.…
Angela Yao
RNA's diverse biological functions stem from its structural versatility, yet accurately predicting and designing RNA sequences given a 3D conformation (inverse folding) remains a challenge. Here, I introduce a deep learning framework that integrates Geometric Vector Perceptron (GVP) layers with a Transformer…
Selitskiy, Stanislav
Large Artificial Neural Network (ANN) models have demonstrated success in various domains, including general text and image generation, drug discovery, and protein-RNA (ribonucleic acid) binding tasks. However, these models typically demand substantial computational resources, time, and data for effective training.…
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Nuclear magnetic resonance (NMR) spectroscopy is a powerful analytical tool that can be used to determine the structures of both small organic molecules and large biomacromolecules. Many undergraduate students are exposed to NMR spectral analysis during organic chemistry courses, but few students have the opportunity…
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RNA droplets assembled from co-transcriptionally folded nanostructures have recently emerged as a promising platform for constructing protocells and minimal synthetic cell models. In these systems, a custom-designed DNA template encodes an RNA nanostar, which is produced by transcription and self-assembles into…
Guillaume Hummel, David Pflieger, Alexandre Berr, Laurence Drouard
Transfer RNAs (tRNAs) are universal adaptors of the genetic code, yet their evolutionary dynamics across photosynthetic eukaryotes remain underexplored. Here, we present the largest comparative re-analysis integrating the PlantRNA database with published data to explore tRNA gene evolution. We find that tRNA gene…
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RNA molecules fold into complex three-dimensional structures that determine their function. A wide range of mathematical frameworks, such as chord diagrams, fatgraphs, and context-free grammars, have been used to represent these structures; however, these models have largely been developed from mathematical motivations…
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RNA–RNA interactions drive the formation of biomolecular condensates via liquid–liquid phase separation (LLPS), but the molecular mechanisms governing this phenomenon remain poorly understood. Here, we employ Martini 3 coarse-grained simulations to investigate phase transitions of G4C2 RNA repeats—sequences implicated…
Li, Siyuan, Yu, Kai + 16 more
Modeling genomic sequences faces two unsolved challenges: the information density varies widely across different regions, while there is no clearly defined minimum vocabulary unit. Relying on either four primitive bases or independently designed DNA tokenizers, existing approaches with naive masked language modeling…
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mRNA-based technology has emerged as a new class of medicines with a wide range of applications, including viral vaccines, cancer vaccines, and therapeutics for the treatment of metabolic diseases and cardiovascular conditions. Impurities, including double-stranded RNA (dsRNA), mRNA fragments, and mRNA multimers…