Ribosome Profiling (Ribo-seq) has revolutionized the study of RNA translation by providing information on ribosome positions across all translated RNAs with...
Read More »Ribotoolkit – an integrated platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution
Ribosome profiling (Ribo-seq) is a powerful technology for globally monitoring RNA translation; ranging from codon occupancy profiling, identification of actively translated open reading frames (ORFs), to the quantification of translational efficiency under...
Read More »End-enriched RNA-sequencing reveals evolutionary convergence of pathway-specific enzyme expression stoichiometry
Coexpression of proteins in response to pathway-inducing signals is the founding paradigm of gene regulation. However, it remains unexplored whether the relative abundance of co-regulated proteins...
Read More »TCP-seq – translation complex profile sequencing to study the in vivo dynamics of mRNA-ribosome interactions
Messenger RNA (mRNA) translation is a tightly controlled process that is integral to gene expression. It features intricate and dynamic interactions of the small and large subunits of the ribosome with mRNAs, aided by multiple auxiliary factors during distinct initiation, ...
Read More »Plastid – nucleotide-resolution analysis of next-generation sequencing and genomics data
Next-generation sequencing (NGS) informs many biological questions with unprecedented depth and nucleotide resolution. These assays have created a need for analytical tools that enable users to manipulate data nucleotide-by-nucleotide robustly and easily. Furthermore, because many NGS assays encode information jointly ...
Read More »RiboDiff – Detecting Changes of mRNA Translation Efficiency from Ribosome Footprints
Deep sequencing based ribosome footprint profiling can provide novel insights into the regulatory mechanisms of protein translation. However, the observed ribosome profile is fundamentally confounded by transcriptional activity. In order to decipher principles of translation regulation, tools that can reliably ...
Read More »RiboProfiling – a Bioconductor package for standard Ribo-seq pipeline processing
The ribosome profiling technique (Ribo-seq) allows the selective sequencing of translated RNA regions. Recently, the analysis of genomic sequences associated to Ribo-seq reads has been widely employed to assess their coding potential. These analyses led to the identification of differentially ...
Read More »Ribosome profiling reveals dynamic translational landscape in maize seedlings
Plant can respond to environmental changes with various mechanisms occurred at transcriptional and translational levels. Thus far, there have been relatively extensive understandings of stress responses of plants on transcriptional level, while little is known about that on translational level. ...
Read More »Researchers use parallel analysis of mRNA structure (PARS), ribosome profiling and RNA sequencing (RNA-seq) to reveal that bacterial mRNA structure functions beyond information transfer
Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and ...
Read More »A streamlined ribosome profiling protocol for the characterization of microorganisms
Ribosome profiling is a powerful tool for characterizing in vivo protein translation at the genome scale, with multiple applications ranging from detailed molecular mechanisms to systems-level predictive modeling. Though highly effective, this intricate technique has yet to become widely used ...
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