Many of the highly abundant proteins were ribosomal proteins and translation factors, which we reasoned could bind to the beads nonspecifically and rank highly due to their sheer abundance in bacteria. At the same time, RNAP-interacting proteins expressed at low levels would automatically rank low...
Our current and prior findings highlight how chemical modifications of mRNA tune the dynamics of protein synthesis at different steps of translation elongation.This is a preview of subscription content, access via your institution Access options
Aging poses a global challenge as human longevity increases and the population’s age structure changes1. Despite longer life spans, the proportion of disease-free life time has not kept pace, with 16%-20% of seniors suffering from late-life illness and organ failure2,3.The lung, with its ...
The genetic code is redundant, meaning that most amino acids can be encoded by more than one codon. Highly expressed genes tend to use optimal codons to increase the accuracy and speed of translation. Thus, codon usage biases provide a signature of the r
The essential steps in the calculations reported here are 1) defining standard states, 2) identifying model proteins for systems of interest, 3) assessing the relative abundances of model proteins in metastable equilibrium, 4) visualizing the results of the calculations on chemical diagrams and 5) ...
The fact that incoherent FFL is missing in our cancer regulation network may imply an important and specific aspect of cancer cells. While the overall working pipeline turns out to be effective in this work, some specific steps need to be discussed. For example, the prefiltration step (...
transcript. We then selected the subset of mRNAs for which ≥ 90% of the 3P-seq tags corresponded to a single dominant 3′ UTR isoform and used this dominant 3′ UTR isoform as the annotation for the corresponding gene. These steps followed the training framework previously described [51]...
Transcription, the synthesis of RNA from DNA. Genetic information flows from DNA into protein, the substance that gives an organism its form. This flow of information occurs through the sequential processes of transcription (DNA to RNA) and translation (
(Oxford Nanopore) with default parameters. Two trimming steps were employed. Adapter sequence was first trimmed by porechop (version 0.2.4) (https://github.com/rrwick/Porechop) with parameters “--check_reads 10000 --adapter_threshold 100 --end_size 100 --min_trim_size 5 --end_threshold ...
In both UK Biobank release v3 and our NewMood database, genetic variants were restricted to biallelic single-nucleotide polymorphisms (SNPs), analyzing directly genotyped and imputed variants as well. QC steps are detailed in Supplementary File S1. 2.4. Analyses Descriptive statistical analyses, as...