28 papers · ranked by Valyu relevance
Jorge Ruiz‐Orera, Xavier Messeguer, Juan A. Subirana, M. Mar Albà
1 Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB) - Hospital del Mar Research Institute (IMIM) - Universitat Pompeu Fabra (UPF), Barcelona, Spain. 2 Universitat Politècnica de Catalunya (UPC), Barcelona. 3 Real Academia de Ciències i Arts de Barcelona (RACAB). 4 Catalan Institution for…
Victoria E. Villegas, Peter G. Zaphiropoulos, Martin Pichler
Antisense transcription, considered until recently as transcriptional noise, is a very common phenomenon in human and eukaryotic transcriptomes, operating in two ways based on whether the antisense RNA acts in cis or in trans. This process can generate long non-coding RNAs (lncRNAs), one of the most diverse classes of…
Elena López-Jiménez, Eduardo Andrés-León, Michael Janitz
The mammalian genome comprehends a small minority of genes that encode for proteins (barely 2% of the total genome in humans) and an immense majority of genes that are transcribed into RNA but not encoded for proteins (ncRNAs). These non-coding genes are intimately related to the expression regulation of protein-coding…
Roman Beňačka, Daniela Szabóová, Zuzana Guľašová, Zdenka Hertelyová + 3 more
Non-coding RNAs (ncRNAs) are abundant single-stranded RNA molecules in human cells, involved in various cellular processes ranging from DNA replication and mRNA translation regulation to genome stability defense. MicroRNAs are multifunctional ncRNA molecules of 18-24 nt in length, involved in gene silencing through…
William A. Haseltine, Roberto Patarca, Alfonso Baldi
Human genome projects in the 1990s identified about 20,000 protein-coding sequences. We are now in the RNA revolution, propelled by the realization that genes determine phenotype beyond the foundational central molecular biology dogma, stating that inherited linear pieces of DNA are transcribed to RNAs and translated…
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…
Éva Márton, Alexandra Varga, Dóra Domoszlai, Gergely Buglyó + 9 more
'Anita Balázs' 'András Penyige' 'István Balogh' 'Bálint Nagy' 'Melinda Szilágyi' 'Charles H. Lawrie' 'Margarete Odenthal' 'Sanjay Premi' 'Jyoti Srivastava'] Title: Simple Summary The field of non-coding RNAs has growing interest in cancer research since these molecules play a prominent role in the regulation of cancer…
Daniel Frías-Lasserre
The origin of genes is one of the most enigmatic events in the origin of life. It has been suggested that noncoding (nc) RNA was probably a precursor in the formation of the first polypeptide, and also at the origin of the first manifestation of life and genes. ncRNAs are also becoming central for understanding gene…
David da Costa Correia, Francisco M. Couto, Hugo Martiniano
Non-coding RNAs (ncRNAs) represent the majority of human gene products, and are involved in various important biological processes, being considered relevant disease biomarkers and therapeutic agents. However, information about these biomolecules remains sparsely distributed, mostly in the form of scientific research…
Amil Shah, Vincenzo Zappavigna
The discovery of oncogenes and tumor suppressor genes provided important insights into the molecular pathogenesis of cancer but also revealed some contradictions in the prevailing somatic mutation theory. The evidence that noncoding RNAs (ncRNAs) form an elaborate network that regulates the flow of genetic information…
Jill Ashey, Javier A. Rodriguez-Casariego, Kathleen M. Durkin, Zachary Bengtsson + 6 more
Non-coding RNAs (ncRNAs) play critical regulatory roles in gene expression regulation that influences diverse biological processes in response to environmental change. Yet their characterization in non-model organisms, particularly sessile, benthic ecosystem engineers such as reef-building corals that are sensitive to…
Sarangdhar Nayak, Pawan K. Dhar
The dark genome comprising of non-expressing, non-translating, and extinct DNA sequences has remained a largely unexplored genomic space. Using computational and experimental approaches, novel insights into the dark matter genome have recently been gained, revealing the presence of a vast and unexplored resource.…
Lauren Michelle Lui, Torben Nielsen
Functional annotation of microbial genomes is often biased toward protein-coding genes, leaving a vast, unexplored landscape of non-coding RNAs (ncRNAs) that are critical for regulating bacterial and archaeal physiology, stress response and metabolism. Identifying ncRNAs directly from genomic sequence is a paramount…
Emanuele Cavalleri, Alberto Cabri, Mauricio Soto, Sara Bonfitto + 8 more
'Paolo Perlasca' 'Jessica Gliozzo' 'Tiffany J Callahan' 'Justin Reese' 'Peter N. Robinson' 'Elena Casiraghi' 'Giorgio Valentini' 'Marco Mesiti'] The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs…
Sophie R Atkinson, Samuel Marguerat, Danny A Bitton, Maria Rodríguez-López + 7 more
Transcriptomes feature pervasive, but poorly defined long non-coding RNAs (lncRNAs). We identify 5775 novel lncRNAs in Schizosaccharomyces pombe, nearly 4-times the previously annotated lncRNAs. Most lncRNAs become derepressed under genetic and physiological perturbations, especially during late meiosis. These lncRNAs…
Muhammad Nabeel Asima, Muhammad Imran Malik, Andreas Dengela, Sheraz Ahmed
'Sheraz Ahmed'] Functional or non-coding RNAs are attracting more attention as they are now potentially considered valuable resources in the development of new drugs intended to cure several human diseases. The identification of drugs targeting the regulatory circuits of functional RNAs depends on knowing its family, a…
Paulo Amaral, Sílvia Carbonell Sala, Francisco M. De La Vega, Tiago Faial + 17 more
'Tiago Faial' 'Adam Frankish' 'T Gingeras' 'Roderic Guigó' 'Jennifer Harrow' 'Artemis G. Hatzigeorgiou' 'Rory Johnson' 'Terence D. Murphy' 'Mihaela Pertea' 'Kim D. Pruitt' 'Shashikant Pujar' 'Hazuki Takahashi' 'Igor Ulitsky' 'Ales Varabyou' 'Christine A. Wells' 'Mark Yandell' 'Piero Carninci' 'Steven L. Salzberg']…
Neha Periwal, Priya Sharma, Pooja Arora, Saurabh Pandey + 2 more
Classification among coding (CDS) and non-coding RNA (ncRNA) sequences is a challenge and several machine learning models have been developed for the same. Since the frequency of curated coding sequences is many-folds as compared to that of the ncRNAs, we devised a novel approach to work with the complete datasets from…
Janet Sasso, Barbara Ambrose, Rumiana Tenchov, Ruchira Datta + 3 more
In the last decade, there has been a shift in research, clinical development, and commercial activity to exploit the many roles of RNA in physiology for use in medicine. With the rapid success in the development of lipid-RNA nanoparticles for mRNA vaccines against COVID-19 and with several approved RNA-based drugs, RNA…
Ken Nishikawa, Akira R. Kinjo
The epigenome, i.e. the whole of chromatin modifications, is transferred from mother to daughter cells during cell differentiation. When de novo chromatin modifications (establishment or erasure of, respectively, new or pre-existing DNA methylations and/or histone modifications) are made in a daughter cell, however, it…
Thaís A. R. Ramos, Nilbson R. O. Galindo, Raúl Arias-Carrasco, Cecília F. da Silva + 2 more
Non-coding RNAs (ncRNAs) are important players in the cellular regulation of organisms from different kingdoms. One of the key steps in ncRNAs research is the ability to distinguish coding/non-coding sequences. We applied 7 machine learning algorithms (Naive Bayes, SVM, KNN, Random Forest, XGBoost, ANN and DL) through…
Dan Graur
Noncoding RNA (ncRNA) and long noncoding RNA (lncRNA) are scientifically invalid terms because they define molecular entities according to properties they do not possess and functions they do not perform. Here, I suggest retiring these two terms. Instead, I suggest using an evolutionary classification of genomic…
Marc P. Hoeppner, Lars Barquist, Paul P. Gardner
We present an introduction to RNA databases. The history and technology behind RNA databases is briefly discussed. We examine differing methods of data collection and curation, and discuss their impact on both the scope and accuracy of the resulting databases. Finally, we demonstrate these principals through detailed…
Authors not listed
Antisense oligonucleotides (ASOs) are a promising class of therapeutics designed to modulate gene expression. Both key mechanisms of action for ASOs operate in the nucleus: splice-switching ASOs modify pre-mRNA, processed in the nucleus, and mRNA-degrading ASOs require RNase H, an enzyme predominantly active in the…
Hirotake Udono, Minzhi Fan, Yoko Saito, Hirohisa Ohno + 4 more
Programmable droplets, artificial liquid-like condensates of nucleic acids, are intelligent out-of-equilibrium systems that allow the critical aspects of their biological counterparts to be harnessed programmably, such as molecular sensing and phase-state change. While DNA has been central to the previous efforts, less…
Authors not listed
One aim of the international Human Proteome Organization (HUPO) Human Proteome Project (HPP) is to obtain high-confidence translation evidence for every human protein-coding gene established in its target list of 19433 entries based on the protein-coding genes from Ensembl-GENCODE. However, 76 are annotated in…
Authors not listed
A chemical method suitable for the synthesis of RNAs containing modifications such as N4-acetylcytidine (ac4C) that are unstable under the basic and nucleophilic conditions used by standard RNA synthesis methods is described. The method uses the 4-((t-butyldimethylsilyl)oxy)-2-methoxybutanoyl (SoM) group for the…
Authors not listed
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…