23 papers · ranked by Valyu relevance
E Hanson, S Ingold, C Haas, J Ballantyne
The recovery of a DNA profile from the perpetrator or victim in criminal investigations can provide valuable ‘source level’ information for investigators. However, a DNA profile does not reveal the circumstances by which biological material was transferred. Some contextual information can be obtained by a determination…
Ploy N. Pratanwanich, Fei Yao, Ying Chen, Casslynn W.Q. Koh + 10 more
Differences in RNA expression can provide insights into the molecular identity of a cell, pathways involved in human diseases, and variation in RNA levels across patients associated with clinical phenotypes. RNA modifications such as m6A have been found to contribute to molecular functions of RNAs. However…
Katannya Kapeli, Gene W. Yeo
Translational control of messenger RNAs (mRNAs) is a key aspect of neurobiology, defects of which can lead to neurological diseases. In response to stimuli, local translation of mRNAs is activated at synapses to facilitate long-lasting forms of synaptic plasticity, the cellular basis for learning, and memory formation.…
Eleonora de Klerk, Johan T. den Dunnen, Peter A. C. ‘t Hoen
Technological advances in the sequencing field support in-depth characterization of the transcriptome. Here, we review genome-wide RNA sequencing methods used to investigate specific aspects of gene expression and its regulation, from transcription to RNA processing and translation. We discuss tag-based methods for…
Zhiliang Bai, Dingyao Zhang, Yan Gao, Bo Tao + 14 more
Spatial transcriptomics has emerged as a powerful tool for dissecting spatial cellular heterogeneity but as of today is largely limited to gene expression analysis. Yet, the life of RNA molecules is multifaceted and dynamic, requiring spatial profiling of different RNA species throughout the life cycle to delve into…
Audrey M Michel, Pavel V Baranov
Ribosome profiling or ribo-seq is a new technique that provides genome-wide information on protein synthesis (GWIPS) in vivo. It is based on the deep sequencing of ribosome protected mRNA fragments allowing the measurement of ribosome density along all RNA molecules present in the cell. At the same time, the high…
Eugenia G Giannopoulou, Olivier Elemento, Lionel B Ivashkiv
Studying the factors that control gene expression is of substantial importance for rheumatic diseases with poorly understood etiopathogenesis. In the past, gene expression microarrays have been used to measure transcript abundance on a genome-wide scale in a particular cell, tissue or organ. Microarray analysis has led…
Florian Thibord, Claire Perret, Maguelonne Roux, Pierre Suchon + 4 more
Next-generation sequencing is an increasingly popular and efficient approach to characterize the full set of microRNAs (miRNAs) present in human biosamples. MiRNAs’ detection and quantification still remain a challenge as they can undergo different post transcriptional modifications and might harbor genetic variations…
Wei Vivian Li, Jingyi Jessica Li
Background: Since the invention of next-generation RNA sequencing (RNA-seq) technologies, they have become a powerful tool to study the presence and quantity of RNA molecules in biological samples and have revolutionized transcriptomic studies. The analysis of RNA-seq data at four different levels (samples, genes…
Hyeongseon Jeon, Juan Xie, Yeseul Jeon, Kyeong Joo Jung + 3 more
'Arkobrato Gupta' 'Won Chang' 'Dongjun Chung'] Gene expression profiling technologies have been used in various applications such as cancer biology. The development of gene expression profiling has expanded the scope of target discovery in transcriptomic studies, and each technology produces data with distinct…
Authors not listed
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…
Qiuyi Wang, Yuanhui Mao
Ribosome profiling has revolutionized our understanding of gene expression regulation by providing a snapshot of global translation in vivo. This powerful technique enables the investigation of the dynamics of translation initiation, elongation, and termination, and has provided insights into the regulation of protein…
Jun Zhang, Jianbo Qiao, Zhiqun Zhao, Chenglin Yin + 4 more
N6-methyladenosine (m6A) is a crucial epitranscriptomic mark. While Nanopore Direct RNA Sequencing (DRS) enables transcriptome-wide detection, most existing methods neglect or lack the capacity to effectively process the intrinsically variable-length raw signals generated by DRS reads.Here, we present MultiNano, a…
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…
Ya-Hui Lin, Jennifer E. Dodd, Luisa Cutillo, Lydia M. Castelli + 14 more
Transcriptomes and translatomes measure genome-wide levels of total and ribosome-associated RNAs. A few hundred translatomes were reported over >250,000 transcriptomes highlighting the challenges of identifying translating RNAs. Here, we used a human isogenic inducible model of TDP-43-linked amyotrophic lateral…
C. Joel McManus, Gemma E. May, Pieter Spealman, Alan Shteyman
Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of posttranscriptional gene regulatory evolution are largely unknown. Here we used…
Jingyi Jessica Li, Peter J. Bickel, Mark D. Biggin
Large scale surveys in mammalian tissue culture cells suggest that the protein expressed at the median abundance is present at 8,000 - 16,000 molecules per cell and that differences in mRNA expression between genes explain only 10-40% of the differences in protein levels. We find, however, that these surveys have…
Irina V. Goldenkova-Pavlova, Olga S. Pavlenko, Orkhan N. Mustafaev, Igor V. Deyneko + 2 more
'Igor V. Deyneko' 'Ksenya V. Kabardaeva' 'Alexander A. Tyurin'] The control of translation in the course of gene expression regulation plays a crucial role in plants’ cellular events and, particularly, in responses to environmental factors. The paradox of the great variance between levels of mRNAs and their protein…
Michael Lanzillotti, Jennifer Brodbelt
Broad interest in nucleic acids – both their therapeutic capabilities and understanding the nuances of their structure and resulting function – has increased in recent years. Post-transcriptional modifications in particular have become an important analysis target, as these covalent modifications to the sugars…
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…
Harrison Lawson, Huy Nguyen, Ayesha Tupe, Mariah Arral + 4 more
Over the last two decades, the utility of metal-organic frameworks (MOFs) has expanded from catalysis and gas storage to biomedical applications such as drug delivery. At first, MOF-based delivery platforms focused on delivering small molecules, with current work focusing on nucleic acids, such as DNA, short guide RNA…
Sunit Pal, Ilja Gordijenko, Stefan Schmeing, Somarghya Biswas + 3 more
The removal of poly(A) tail from mRNA sequences reduces their stability and translational activity. The deadenylation process is mainly regulated by the CCR4-NOT complex for which potent chemical inhibitors are rare. The subunit NOT9 binds various RNA binding proteins (RBPs) which recruit mRNA in a sequence-specific…
Authors not listed
Therapeutic oligonucleotides (ONs) are short synthetic DNA or RNA strands used to modulate protein expression in disease treatment. Besides the full-length product (FLP), ON samples contain many closely related impurities that must be profiled to ensure drug quality. Separation techniques, such as ion-pairing…