Lightnews — Scholar-powered news

Richard Mott @richardmott.bsky.social · 8d

We have just published a paper in Genome Biology, rdcu.be/eIMLf. We explore the information flow between genome, gene body methylation, transcriptome, translatome and proteome in Arabidopsis. This is part of a BBSRC-funded collaboration with UCL, Rothamsted Research and University of Cambridge.

Information flow between omic levels in Arabidopsis thaliana

3 11

Richard Mott @richardmott.bsky.social · Jan 16

Freddie Theodoulou gives a nice writeup of the study

Frederica Theodoulou @freddietheodoulou.bsky.social · Jan 13

Happy to start 2025 by sharing our new preprint biorxiv.org/cgi/content/... -the first paper from our BBSRC collaborative project with
@richardmott.bsky.social and Kathryn Lilley to understand what controls protein abundance in plants. 🧵 1/9

$Genomic information pathways and their numerical linkages in relation to the Central Dogma. The boxes show different omic levels in Col-0 and Can-0. Black arrows indicate the flow of information implied by the Central Dogma starting from CDS (peach) via gbM (green) to mRNA (light blue), ribosome-associated mRNA (yellow) and finally protein (pink). The strength of Pearson correlation between levels is shown both by the numbers and by the thickness of the corresponding black arrows, and represents the correlation between quantitative expression levels (except in the case of CDS where is represents the correlation derived from the multiple regression codon frequency model, i.e. the square root of the fraction of variance explained). The merged arrows connecting CDS, gbM and mRNA to protein show the result of combining information into a single model; note that their combined correlation of 0.720 is less than the sum of their individual effects. The correlation of tRNA levels (lilac) with genome-wide codon and amino acid frequencies is shown on the left. The correlations between corresponding Col-0 and Can-0 omic levels are shown next to the grey double-headed arrows.$

1 1

Richard Mott @richardmott.bsky.social · Jan 16

We've submitted a preprint to BioRXiv www.biorxiv.org/content/10.1..., from a BBSRC-funded collaboration between UCL, Rothamsted and Cambridge, UK.

We ask how well one can predict protein abundance in Arabidopsis thaliana rosettes based on the genome, epigenome and transcriptome and translatome.

Genomic information pathways and their numerical linkages in relation to the Central Dogma. The boxes show different omic levels in Col-0 and Can-0. Black arrows indicate the flow of information implied by the Central Dogma starting from CDS (peach) via gbM (green) to mRNA (light blue), ribosome-associated mRNA (yellow) and finally protein (pink). The strength of connection between levels is shown both by the numbers (Pearson correlation scale) and by the thickness of the corresponding black arrows, and represents the correlation between quantitative expression levels. The merged arrows connecting CDS, gbM and mRNA to protein show the result of combining information into a single model; note that their combined correlation of 0.720 is less than the sum of their individual effects. The correlation of tRNA levels (lilac) with genome-wide codon and amino acid frequencies is shown on the left. The correlations between corresponding Col-0 and Can-0 omic levels are shown next to the grey double-headed arrows

3