Hettinger, Zachary R Confides, Amy L Vanderklish, Peter W Sidhom, Silvana Masternak, Michal M Dupont-Versteegden, Esther E
Published in
Experimental gerontology
RNA binding protein motif 3 (RBM3) is an RNA-binding and cold shock protein that protects myoblasts and promotes skeletal muscle hypertrophy by enhancing mRNA stability and translation. Muscle size is decreased during aging; however, it is typically delayed in models of extended lifespan such as the long-lived Ames Dwarf (df/df) mice and calorie re...
Deng, Lei Liu, Youzhi Shi, Yechuan Zhang, Wenhao Yang, Chun Liu, Hui
Published in
BMC Genomics
BackgroundRNA binding proteins (RBPs) play a vital role in post-transcriptional processes in all eukaryotes, such as splicing regulation, mRNA transport, and modulation of mRNA translation and decay. The identification of RBP binding sites is a crucial step in understanding the biological mechanism of post-transcriptional gene regulation. However, ...
Pan, Xiaoyong Fang, Yi Li, Xianfeng Yang, Yang Shen, Hong-Bin
Published in
BMC Genomics
BackgroundRNA-binding proteins (RBPs) play crucial roles in various biological processes. Deep learning-based methods have been demonstrated powerful on predicting RBP sites on RNAs. However, the training of deep learning models is very time-intensive and computationally intensive.ResultsHere we present a deep learning-based RBPsuite, an easy-to-us...
Okholm, Trine Line Hauge Sathe, Shashank Park, Samuel S. Kamstrup, Andreas Bjerregaard Rasmussen, Asta Mannstaedt Shankar, Archana Chua, Zong Ming Fristrup, Niels Nielsen, Morten Muhlig Vang, Søren
...
Published in
Genome Medicine
BackgroundCircular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown to bind RNA-binding proteins (RBPs); however, little is known about the prevalence and distribution of these interactions in different biological contexts.MethodsWe conduct an extensi...
Perdikari, Theodora Myrto Murthy, Anastasia C Ryan, Veronica H Watters, Scott Naik, Mandar T Fawzi, Nicolas L
Published in
The EMBO journal
Tightly packed complexes of nucleocapsid protein and genomic RNA form the core of viruses and assemble within viral factories, dynamic compartments formed within the host cells associated with human stress granules. Here, we test the possibility that the multivalent RNA-binding nucleocapsid protein (N) from severe acute respiratory syndrome coronav...
Shema Mugisha, Christian Tenneti, Kasyap Kutluay, Sebla B
Published in
Methods (San Diego, Calif.)
Viral and cellular RNA-binding proteins regulate numerous key steps in the replication of diverse virus genera. Viruses efficiently co-opt the host cell machinery for purposes such as transcription, splicing and subcellular localization of viral genomes. Though viral RNAs often need to resemble cellular RNAs to effectively utilize the cellular mach...
Esparza-Moltó, Pau B Cuezva, José M
Published in
Antioxidants & redox signaling
Significance: Cancer is a major disease imposing high personal and economic burden draining large part of National Health Care and Research budgets worldwide. In the last decade, research in cancer has underscored the reprogramming of metabolism to an enhanced aerobic glycolysis as a major trait of the cancer phenotype with great potential for targ...
Ghidini, Alice Cléry, Antoine Halloy, François Allain, Frédéric H T Hall, Jonathan
Published in
Angewandte Chemie (International ed. in English)
Defects in the functions of RNA binding proteins (RBPs) are at the origin of many diseases; however, targeting RBPs with conventional drugs has proven difficult. PROTACs are a new class of drugs that mediate selective degradation of a target protein through a cell's ubiquitination machinery. PROTACs comprise a moiety that binds the selected protein...
Ng Kwan Lim, Evelyne Sasseville, Charles Carrier, Marie-Claude Massé, Eric
Published in
Trends in genetics : TIG
RNA binding proteins (RBPs) are ubiquitously found in all kingdoms of life. They are involved in a plethora of regulatory events, ranging from direct regulation of gene expression to guiding modification of RNA molecules. As bacterial regulators, RBPs can act alone or in concert with RNA-based regulators, such as small regulatory RNAs (sRNAs), ribo...
Zbinden, Aurélie Pérez-Berlanga, Manuela De Rossi, Pierre Polymenidou, Magdalini
Published in
Developmental cell
Protein aggregation is the main hallmark of neurodegenerative diseases. Many proteins found in pathological inclusions are known to undergo liquid-liquid phase separation, a reversible process of molecular self-assembly. Emerging evidence supports the hypothesis that aberrant phase separation behavior may serve as a trigger of protein aggregation i...
