25 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…
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…
Jing Li, Zhenyu Xuan, Changning Liu
Long non-coding RNAs (lncRNAs) are a heterogeneous class of RNAs that are generally defined as non-protein-coding transcripts longer than 200 nucleotides. Recently, an increasing number of studies have shown that lncRNAs can be involved in various critical biological processes, such as chromatin remodeling, gene…
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…
Wenchao Li, Yang Yang Wang, Lifei Xiao, Jiangwei Ding + 3 more
'Feng Wang' 'Tao Sun'] Increasingly studies have shown that the formation mechanism of many human diseases is very complex, which is determined by environmental factors and genetic factors rather than fully following Mendel’s genetic law of inheritance. Long non-coding RNA (lncRNA) is a class of endogenous non-protein…
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…
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…
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…
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…
Apexa Modi, Gonzalo Lopez, Karina L. Conkrite, Chun Su + 17 more
Long non-coding RNAs (lncRNAs) play an important role in gene regulation and contribute to tumorigenesis. While pan-cancer studies of lncRNA expression have been performed for adult malignancies, the lncRNA landscape across pediatric cancers remains largely uncharted. Here, we curate RNA sequencing data for 1,044…
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…
Monah Abou Alezz, Ludovica Celli, Giulia Belotti, Antonella Lisa + 1 more
Long non-coding (lnc) RNAs are today recognized as a new class of regulatory molecules despite very little is known about their functions in the cell. Due to their overall low level of expression and tissue-specificity, their identification and annotation in many genomes remains challenging. In this study, we exploited…
Nicholas Jeon, Xiaoning Qian, Lamin SaidyKhan, Paul de Figueiredo + 1 more
Prediction of long non-coding RNAs Authors: ['Nicholas Jeon' 'Xiaoning Qian' 'Lamin SaidyKhan' 'Paul de Figueiredo' 'Byung-Jun Yoon'] Long non-coding RNAs (lncRNAs) serve as crucial regulators in numerous biological processes. Although they share sequence similarities with messenger RNAs (mRNAs), lncRNAs perform…
Sumukh Deshpande, James Shuttleworth, Jianhua Yang, Sandy Taramonli + 1 more
'Matthew England'] Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs which play a significant role in several biological processes. RNA-seq based transcriptome sequencing has been extensively used for identification of lncRNAs. However, accurate identification of lncRNAs in RNA-seq datasets is crucial for…
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…
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…
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…
Xiaomin Liu, Shimaa Soliman, Saeid Parast, Madhurima Das + 1 more
Latency: A Review Authors: ['Xiaomin Liu' 'Shimaa Soliman' 'Saeid Parast' 'Madhurima Das' 'Steven M. Wolinsky'] Abstract: The existence of latent cellular reservoirs is recognized as the major barrier to an HIV cure. Reactivating and eliminating "shock and kill" or permanently silencing "block and lock" the latent HIV…
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…
Selene M.C. Cannelli, Ritvik Gupta, Tan Nguyen, Arunava Poddar + 3 more
Liquid-liquid phase separation (LLPS) is a process that often occurs due to binding between oppositely charged biopolymers, and has gained increasing attention recently due to their ubiquity in biological systems and ability to direct essential cellular processes. For example, aberrant biological LLPS can lead to 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…
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…