Eckford, A. | Search bioRxiv

bioRxiv2024

The GC-content at the 5'ends of human protein-coding genes is undergoing mutational decay

In vertebrates, most protein-coding genes have a peak of GC-content near their 5 transcriptional start site (TSS). This feature promotes both the efficient nuclear export and translation of mRNAs. Despite the importance of GC-content for RNA metabolism, its general features, origin, and maintenance remain mysterious. We investigated the evolutionary forces shaping GC-content at the transcriptional start site (TSS) of genes through both comparative genomic analysis of nucleotide substitution rates between different species and by examining human de novo mutations. Our data suggests that GC-peaks at TSSs were present in the last vertebrate common ancestor and are largely dictated by recombination patterns. We observe that in primates and rodents, where recombination is directed away from TSSs by PRDM9, GC-content at protein-coding gene TSSs is currently undergoing mutational decay. In canids, which lack PRDM9 and perform recombination at TSSs, GC-content at protein-coding gene TSSs is increasing. These patterns extend into the open reading frame affecting protein-coding regions, and we show that changes in GC-content due to recombination affect synonymous codon position choices at the start of the open reading frame. Our results indicate that although high GC-content in protein-coding genes may be shaped by selective pressures to enhance expression, the dynamics of GC-content in mammals are largely shaped by patterns of recombination.

genomics↗

bioRxiv2023

Comparing kinetic proofreading and kinetic segregation for T cell receptor activation

The T cell receptor (TCR) is a key component of the adaptive immune system, recognizing foreign antigens and triggering an immune response. Competing models exist to explain the high sensitivity and selectivity of the TCR in discriminating self from non-self antigens, particularly models using kinetic proofreading (KP), kinetic segregation (KS), and combinations of the two. In this paper, we consider the role and importance of KS in TCR activation, using two models: classic KP (cKP), without KS, where antigen-TCR binding is required for activation, and a combination of KP and KS (KS-KP), where only residence within a close contact is required for activation. Building on previous work, our computational model is the first to permit a head-to-head comparison of these models in silico. While we find that both models can be used to explain the probability of TCR activation across much of the parameter space, we find biologically important regions in the parameter space where significant differences in performance can be expected. Furthermore, we show that the available experimental evidence may favour the KS-KP model over cKP. Our results may be used to motivate and guide future experiments to determine highly accurate computational models for the TCR. Author summaryThe T cell receptor (TCR) is a master of reliable sensing: it detects faint signals (rare ligands derived from foreign proteins) over high noise (abundant ligands derived from the bodys own proteins) to set T cells on a course to exterminate pathogens and tumours, a process that is central to our immune response. Despite decades of studying TCR signalling, we still do not know how the TCR can be so exceptionally sensitive and accurate. It is widely believed that kinetic proofreading (KP), in which the TCR binds to an antigen and triggers a series of phosphorylation steps prior to activation, plays an important role. However, recent results suggest that kinetic segregation (KS), in which binding is not required, is also important. These models are mutually exclusive, and yet both appear to explain various aspects of T cell activation. Our work directly addresses this puzzle. We develop a computational modeling framework which can simulate TCR activation by both KP-based and KS-based models, making it possible to compare them in silico for the first time. Using this framework, we find conditions under which the two models provide different responses, and we show that the limited experimental evidence to date is consistent with KS, which should motivate further investigation.

immunology↗