What is RNA-seq based differential gene expression’s (DGE) blind spot? RNA-seq is a powerful and widely employed tool to quantify gene expression at the RNA level. However, that there are several limitations when using RNA-seq only derived gene expression counts to predict differential gene expression (DGE) across different treatments or conditions. The primary blind spot […]
Ribosome Profiling: A Window into Translation Dynamics Ribosome profiling provides a snapshot of active translation by sequencing ribosome-protected mRNA fragments1 allowing the identification of which mRNAs are being translated, thereby offering insights into the translational control of gene expression. Ribo-seq data are instrumental in revealing the intricacies of translation initiation, elongation, and termination, as well […]
Not all codons are decoded at the same rate Not all codons are decoded at the same rate; some are translated quickly, while others may cause ribosomes to pause or move slower. These differences in decoding rates can be influenced by factors such as codon sequence, tRNA abundance and mRNA structure. Ribosome profiling (Ribo-seq) maps […]
https://eirnabio.com/wp-content/uploads/2025/08/Question-29.mp4 Introduction Ribosome profiling (Ribo-seq)’s capture of the precise location and density of ribosomes across the entire transcriptome provides a snapshot of actively translated regions. Recent research has leveraged Ribo-seq’s inherent triplet periodicity signal and mRNA positional information to predict the translation of open reading frames (ORFs) alternative to the annotated protein coding ORF (CDS)1,2. […]
https://eirnabio.com/wp-content/uploads/2025/08/Question-5.mp4 Introduction Insight into translational efficiency Polysome profiling allows monitoring of mRNA translation activity using sucrose gradient fractionation. The sequencing of the collected polysome fractions offers two key advantages over Ribo-seq: (1) it enables the quantification of the exact number of ribosomes per mRNA, and (2) the longer reads of polysome-seq allow for more accurate […]
