26 papers · ranked by Valyu relevance
Jasdeep Kaur Dhanoa, Ram Saran Sethi, Ramneek Verma, Jaspreet Singh Arora + 1 more
The central dogma of gene expression propounds that DNA is transcribed to mRNA and finally gets translated into protein. Only 2-3% of the genomic DNA is transcribed to protein-coding mRNA. Interestingly, only a further minuscule part of genomic DNA encodes for long non-coding RNAs (lncRNAs) which are characteristically…
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…
Marina R. Hadjicharalambous, Mark A. Lindsay
Innate immunity provides the initial defence against infection and it is now clear that long non-coding RNAs (lncRNAs) are important regulators of this response. Following activation of the innate response, we commonly see rapid induction of these lncRNAs and this is often mediated via the pro-inflammatory…
Beata Smolarz, Anna Zadrożna-Nowak, Hanna Romanowicz, Peter Hamar
Long noncoding RNAs (lncRNAs) are the largest groups of ribonucleic acids, but, despite the increasing amount of literature data, the least understood. Given the involvement of lncRNA in basic cellular processes, especially in the regulation of transcription, the role of these noncoding molecules seems to be of great…
John S. Mattick
Transcriptomic studies have demonstrated that the vast majority of the genomes of mammals and other complex organisms is expressed in highly dynamic and cell-specific patterns to produce large numbers of intergenic, antisense and intronic long non-protein-coding RNAs (lncRNAs). Despite well characterized examples…
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…
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…
Joseph L. Tsenum
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…
Romana Butova, Petra Vychytilova-Faltejskova, Adela Souckova, Sabina Sevcikova + 1 more
'Sabina Sevcikova' 'Roman Hajek'] Multiple myeloma (MM) is the second most common hematooncological disease of malignant plasma cells in the bone marrow. While new treatment brought unprecedented increase of survival of patients, MM pathogenesis is yet to be clarified. Increasing evidence of expression of long…
Andoni Garitano-Trojaola, Xabier Agirre, Felipe Prósper, Puri Fortes
Long non-coding RNAs (lncRNAs) are functional RNAs longer than 200 nucleotides in length. LncRNAs are as diverse as mRNAs and they normally share the same biosynthetic machinery based on RNA polymerase II, splicing and polyadenylation. However, lncRNAs have low coding potential. Compared to mRNAs, lncRNAs are…
Qais Ahmad Naseer, Abdul Malik, Fengyuan Zhang, Shengxia Chen
Long noncoding RNAs (lncRNAs), which are more than 200 nucleotides in length and do not encode proteins, play crucial roles in governing gene expression at both the transcriptional and posttranscriptional levels. These molecules demonstrate specific expression patterns in various tissues and developmental stages…
Yagoub A. I. Adam, Evandro Eduardo Seron Ruiz, Alessandra Alaniz Macedo
Long non-coding RNAs (lncRNAs) play crucial roles in diverse biological processes. For example, they help to regulate gene expression and to shape the 3D organization of the cellular nucleus. However, their functions in these processes are not well known. Most of the ongoing research efforts regarding lncRNAs have…
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…
Shiv Kumar Meena, Michel Heidecker, Susanne Engelmann, Ammar Jaber + 5 more
Natural antisense long noncoding RNAs (lncNATs) are involved in the regulation of gene expression in plants, modulating different relevant developmental processes and responses to various stimuli. We identified and characterized two lncNATs (NAT1_UGT73C6_ and NAT2_UGT73C6_, collectively NATs_UGT73C6_) in Arabidopsis…
Isaac Adeyemi Babarinde, Andrew Paul Hutchins
Investigating the functions and activities of genes requires proper annotation of the transcribed units. However, transcript assembly efforts have produced a surprisingly large variation in the number of transcripts, and especially so for noncoding transcripts. The heterogeneity of the assembled transcript sets might…
Anyou Wang
The mechanisms underlying lifespan evolution in organisms have long been mysterious. However, recent studies have demonstrated that organisms evolutionarily gain noncoding RNAs (ncRNAs) that carry endogenous profound functions in higher organisms1,2, including lifespan3 . This study unveils ncRNAs as crucial drivers…
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']…
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…
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…
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…
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…
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…
Matthew Disney, Amirhossein Taghavi, Jared Baisden, Jessica Childs-Disney + 1 more
RNA G4C2 and C4G2 repeat expansions in the chromosome 9 open reading frame 72 gene (C9orf72) are the most common cause of genetically defined amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), referred to as c9ALS/FTD. The gene is bidirectionally transcribed, producing G4C2 repeats, r(G4C2)exp, in…
Aarav Arora, Igor Tsigelny, Valentina Kouznetsova
Purpose Laryngeal cancer (LC) is the most common head and neck cancer, which often goes undiagnosed due to the expensiveness and inaccessible nature of current diagnosis methods. Many recent studies have shown that microRNAs (miRNAs) are crucial biomarkers for a variety of cancers. Methods In this study, we create a…
Yipeng Yin, Reed Arneson, Yinan Yuan, Shiyue Fang
The longest oligos that can be chemically synthesized using known methods are typically considered to be 200-mers. Here, we report direct synthesis of an 800-mer green fluorescent protein (GFP) gene and a 1,728-mer Φ29 DNA polymerase gene on an automated synthesizer. Key innovations that enabled the breakthrough…
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…