24 papers · ranked by Valyu relevance
Xiaofeng Dai, Li Shen
The human history has witnessed the rapid development of technologies such as high-throughput sequencing and mass spectrometry that led to the concept of “omics” and methodological advancement in systematically interrogating a cellular system. Yet, the ever-growing types of molecules and regulatory mechanisms being…
Jingjing Zhai, Jie Song, Qian Cheng, Yunjia Tang + 1 more
The epitranscriptome, also known as chemical modifications of RNA (CMRs), is a newly discovered layer of gene regulation, the biological importance of which emerged through analysis of only a small fraction of CMRs detected by high-throughput sequencing technologies. Understanding of the epitranscriptome is hampered by…
Ghada Mubarak, Farah R. Zahir, Margaret M. DeAngelis
With the advent of genome-wide screening methods-beginning with microarray technologies and moving onto next generation sequencing methods-the era of precision and personalized medicine was born. Genomics led the way, and its contributions are well recognized. However, “other-omics” fields have rapidly emerged and are…
Ana Kvolik Pavić, Josipa Čonkaš, Ivan Mumlek, Vedran Zubčić + 2 more
Epitranscriptomics is the study of modifications of RNA molecules by small molecular residues, such as the methyl (-CH3) group. These modifications are inheritable and reversible. A specific group of enzymes called “writers” introduces the change to the RNA; “erasers” delete it, while “readers” stimulate a downstream…
Pablo Santamarina-Ojeda, Agustín F. Fernández, Mario F. Fraga, Mikael S. Lindström
'Mikael S. Lindström'] Title: Simple Summary Epitranscriptomic modifications impact RNA stability and function, influencing key biological processes. While initially behind epigenetics, the field has advanced in the last decade, linking these modifications to development and diseases like cancer. High-grade gliomas…
Michael S. Bosmeny, Adrian A. Pater, Li Zhang, Lydia Larkai + 5 more
Post-transcriptional modifications to RNA, which comprise the epitranscriptome, play important roles in RNA metabolism, gene regulation, and human disease, including viral pathogenesis. Modifications to the RNA viral genome and transcripts of human immunodeficiency virus 1 (HIV-1) have been reported and investigated in…
Francisco Ortigosa, César Lobato-Fernández, Juan Antonio Pérez-Claros, Francisco R. Cantón + 3 more
Epitranscriptomic modifications constitute a gene expression checkpoint in all living organisms. As nitrogen is an essential element for plant growth and development, a reasonable hypothesis is that changes in the epitranscriptome may regulate nitrogen acquisition and metabolism. In this study, epitranscriptomic…
Sreeram Srinivasan, Ajit Chande
Post-transcriptional chemical modifications of RNA, collectively termed the epitranscriptome, have emerged as critical regulatory layers governing viral replication, pathogenicity, and host– virus interactions. Despite the rapid accumulation of experimental data on viral RNA modifications, no dedicated, freely…
Yen-Yu Yang, Zhongwen Cao, Yinsheng Wang
Epitranscriptomics is a rapidly evolving field that explores chemical modifications in RNA and how they contribute to dynamic and reversible regulations of gene expression. These modifications, for example, N6-methyladenosine (m6A), are crucial in various RNA metabolic processes, including splicing, stability…
Ágota Tűzesi, Susannah Hallal, Laveniya Satgunaseelan, Michael E. Buckland + 2 more
'Michael E. Buckland' 'Kimberley L. Alexander' 'Dimitrios Moris'] Simple Summary Glioblastoma is a complex and aggressive primary brain tumour that is rapidly fatal. Timely and accurate diagnosis is therefore crucial. Here, we explore the newly emerging field of epitranscriptomics to understand the modifications that…
Alexander Apostle, Yipeng Yin, Komal Chillar, Adikari M. D. N. Eriyagama + 4 more
Like other viruses, SARS-CoV-2 causes different symptoms and different degrees of harmfulness to different individuals. Potential reasons include an individual's viral dose exposure, the affinity of an individual's ACE2 to the spike protein of the virus, and the ability of the individual's induced immune system to…
Maud Lemercier, Paola Arrubarrena, Salvatore Di Giorgio, Julia Brettschneider + 10 more
Detecting chemical modifications on RNA molecules remains a key challenge in epitranscriptomics. Traditional reverse transcription-based sequencing methods introduce enzymeand sequence-dependent biases and fragment RNA molecules, confounding the accurate mapping of modifications across the transcriptome. Nanopore…
Ehsan Pashay Ahi, Morgane Frapin, Mikaela Hukkanen, Craig R. Primmer
Better understanding the molecular processes contributing to variation in maturation timing is important for Atlantic salmon (Salmo salar) aquaculture, as early maturation causes considerable financial losses. The m6A RNA methylation is a highly conserved and dynamically reversible mechanism controlling gene expression…
Kevin B. Dsouza, Adam Y. Li, Vijay K. Bhargava, Maxwell W. Libbrecht
The availability of thousands of assays of epigenetic activity necessitates compressed representations of these data sets that summarize the epigenetic landscape of the genome. Until recently, most such representations were celltype specific, applying to a single tissue or cell state. Recently, neural networks have…
O.G. Akintunde, Trichina Tucker, Valerie J. Carabetta
The genetic information that dictates the structure and function of all life forms is encoded in the DNA. In 1953, Watson and Crick first presented the double helical structure of a DNA molecule. Their findings unearthed the desire to elucidate the exact composition and sequence of DNA molecules. Discoveries and the…
David Angeles-Albores, Carmie Puckett Robinson, Brian A. Williams, Paul W. Sternberg
RNA-seq is commonly used to identify genetic modules that respond to a perturbation. Although transcriptomes have been mainly used for target gene discovery, their quantitative nature makes them attractive structures with which to study genetic interactions. To understand whether whole-organism RNA-seq is suitable for…
Norberto Sánchez-Cruz, Jose L. Medina-Franco
Motivation: The identification of protein targets of small molecules is essential for drug discovery. With the increasing amount of chemogenomic data in the public domain, multiple ligand-based models for target prediction have emerged. However, these models are generally biased by the number of known ligands for…
Norberto Sánchez-Cruz, Jose L. Medina-Franco
Epigenetic targets are a significant focus for drug discovery research, as demonstrated by the eight approved epigenetic drugs for treatment of cancer and the increasing availability of chemogenomic data related to epigenetics. This data represents a large amount of structure-activity relationships that has not been…
Michael Lanzillotti, Jennifer Brodbelt
Mass spectrometry has proven to be a highly effective tool for characterization of RNA post-transcriptional modifications. For both synthetic RNAs and ones from biological sources, mass spectrometry can interrogate multiple, co-occurring covalent modifications at the nucleotide level simultaneously. To expand the…
Dylan Molho, Jiayuan Ding, Zhaoheng Li, Hongzhi Wen + 11 more
'Yixin Wang' 'Julian Venegas' 'Wei Jin' 'Renming Liu' 'Runze Su' 'Patrick Danaher' 'Robert Yang' 'Yu L. Lei' 'Yuying Xie' 'Jiliang Tang'] Single-cell technologies are revolutionizing the entire field of biology. The large volumes of data generated by single-cell technologies are high-dimensional, sparse, heterogeneous…
Sai Guna Ranjan Gurazada, H Kennedy, Richard D. Braatz, Steven J. Mehrman + 2 more
adeno-associated virus (rAAV) gene therapy manufacturing Authors: ['Sai Guna Ranjan Gurazada' 'H Kennedy' 'Richard D. Braatz' 'Steven J. Mehrman' 'Shawn W. Polson' 'Irene Rombel'] Gene therapy is poised to transition from niche to mainstream medicine, with recombinant adeno-associated virus (rAAV) as the vector of…
Jingfei Zhang, Hongyu Zhao
An expression quantitative trait locus (eQTL) is a chromosomal region where genetic variants are associated with the expression levels of certain genes that can be both nearby or distant. The identifications of eQTLs for different tissues, cell types, and contexts have led to better understanding of the dynamic…
Monique G.P. van der Wijst, Dylan H. de Vries, Hilde E. Groot, Gosia Trynka + 10 more
'Gosia Trynka' 'Chung-Chau Hon' 'Martijn C. Nawijn' 'Youssef Idaghdour' 'Pim van der Harst' 'Chun Ye' 'Joseph E. Powell' 'Fabian J. Theis' 'Ahmed Mahfouz' 'Matthias Heinig' 'Lude Franke'] 6 Program in Biology, Public Health Research Center, New York University Abu Dhabi, UAE 7 Institute for Human Genetics, Bakar…
Dhrithi Deshpande, Karishma Chhugani, Yutong Chang, Aaron Karlsberg + 12 more
'Caitlin Loeffler' 'Jinyang Zhang' 'Agata Muszyńska' 'Jeremy Rotman' 'Laura Tao' 'Brunilda Balliu' 'Elizabeth Tseng' 'Eleazar Eskin' 'Fangqing Zhao' 'Pejman Mohammadi' 'Paweł P. Łabaj' 'Serghei Mangul'] Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA 90095, USA…