26 papers · ranked by Valyu relevance
Victor E. Nava, Pin-Yu Perera, Nirbhay Kumar, Maneesh Jain + 3 more
'Ramar Thangam' 'Ramasamy Paulmurugan' 'Heemin Kang'] Noncoding RNAs (ncRNAs) defy the central dogma by representing a family of RNA molecules that are not translated into protein but can convey information encoded in their DNA. Elucidating the exact function of ncRNA has been a focus of discovery in the last decade…
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…
Saakshi Jalali, Deeksha Bhartiya, Mukesh Kumar Lalwani, Sridhar Sivasubbu + 1 more
'Sridhar Sivasubbu' 'Vinod Scaria'] Long noncoding RNAs (lncRNAs) are a recently discovered class of non-protein coding RNAs which have now increasingly been shown to be involved in a wide variety of biological processes as regulatory molecules. The functional role of many of the members of this class has been an…
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…
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…
Joseph L. Tsenum, Maria Poptsova
Long non-coding RNAs (lncRNAs) can perform their regulatory roles by forming triple helices through RNA-DNA interaction. Although this has been verified by few in vivo and in vitro methods, in silico approaches that seek to predict the potentials of lncRNAs and DNA sites becoming a triplex forming structure is…
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…
Brian McClannahan, Cuncong Zhong, Guanghui Wang
—In the last decade, the discovery of noncoding RNA (ncRNA) has exploded. Classifying these ncRNA is critical to determining their function. This thesis proposes a new method employing deep convolutional neural networks (CNNs) to classify ncRNA sequences. To this end, this paper first proposes an efficient approach to…
Patrizio Arrigo, Alessandra Pulliero
In the last decade the role of noncoding RNAs (ncRNAs) emerges not only as key elements of posttranscriptional gene silencing, but also as important players of epigenetic regulation. New kind and new functions of ncRNAs are continuously discovered and one of their most important roles is the mediation of environmental…
Ira W. Deveson, Marion E. Brunck, James Blackburn, Elizabeth Tseng + 8 more
The human genome encodes an unknown diversity of genes and isoforms. RNA Sequencing (RNA-Seq) suffers from an expression-dependent bias that impedes discovery of low-abundance transcripts and has prevented a complete census of human gene expression. Here we performed targeted single-molecule and short-read RNA-Seq 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.…
Qili Shi, Haochen Li, Junjiao Song, Hao Wu + 5 more
Pre-messenger RNA transcribed from canonical protein-coding genes is frequently alternatively spliced into diverse mature mRNA isoforms, thus translating into various protein products. However, it remains unknown whether human mRNA from a protein-coding gene harbors noncoding splice isoforms in the genome. Herein, we…
Stinus Lindgreen, Sinan U. Umu, Alicia Sook-Wei Lai, Hisham Eldai + 8 more
'Wenting Liu' 'Stephanie McGimpsey' 'Nicole E. Wheeler' 'Patrick J. Biggs' 'Nick Thomson' 'Lars Barquist' 'Anthony M. Poole' 'Paul P. Gardner'] Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While…
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…
Gali Housman, Igor Ulitsky
Long noncoding RNAs (lncRNAs) are a diverse class of RNAs with increasingly appreciated functions in vertebrates, yet much of their biology remains poorly understood. In particular, it is unclear to what extent the current catalog of over 10,000 distinct annotated lncRNAs is indeed devoid of genes coding for proteins.…
Javad Noorbakhsh, Alex Lang, Pankaj Mehta
MicroRNAs are small noncoding RNAs that regulate genes post-transciptionally by binding and degrading target eukaryotic mRNAs. We use a quantitative model to study gene regulation by inhibitory microRNAs and compare it to gene regulation by prokaryotic small non-coding RNAs (sRNAs). Our model uses a combination of…
Andrew CK Wu, Harshil Patel, Minghao Chia, Fabien Moretto + 3 more
Many active eukaryotic gene promoters exhibit divergent noncoding transcription, but the mechanisms restricting expression of these transcripts are not well understood. Here we demonstrate how a sequence-specific transcription factor represses divergent noncoding transcription at highly expressed genes in yeast. We…
Valentina Agoni
Many efforts have been done in order to explain the role of junk DNA, but its function remain to be elucidated. In addition the GC-content variations among species still represent an enigma. Both these two mysteries can have a common explanation: we hypothesize that the role of junk DNA is to preserve the mutations…
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
Targeting RNA with small molecules represents a promising yet relatively unexplored avenue for the design of new drugs. Nevertheless, challenges arise from the lack of computational models and techniques able to accurately model RNA systems, and predict their binding affinities to small molecules. Here, we tackle these…
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…
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
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…
Anna Knörlein, Chris Sarnowski, Tebbe de Vries, Moritz Stoltz + 5 more
Understanding structure-function relationships of RNA-binding proteins requires knowledge of how they bind RNAs in vivo. RNA-protein interactions are studied using light-induced cross-linking at “zero-distance”, yielding nucleotide/amino-acid adducts for mass-spectrometry (MS)-based characterization. However…