Advanced searches left 3/3

Genome - BioRxiv

Summarized by Plex Scholar
Last Updated: 03 September 2022

* If you want to update the article please login/register

Reactivation of Epstein Barr Virus from Latency Involves Increased RNA Polymerase Activity at CTCF Binding Sites On The Viral Genome

The ability of Epstein-Barr Virus to switch between latent and lytic infection is crucial to its long-term survival, but the exact mechanisms underlying this conversion remain unclear. In latently infected Mutu-I cells at 1, 4 and 12 h post-reactivation, we used Precision nuclear Run On and Deep Sequencing to map cellular RNA polymerase activity during the latent to lytic switch. Unexpectedly at time-points post-reactivation, the EBV regions with the largest rise in Pol activity were LMP-2A, EBER-1, and RPMS1. CTCF bindment, transcription, and reactivation was demonstrated by an EBV mutant lacking the LMP-2A CTCF binding site. Multiple CTCF binding sites related to WT virus were unable to reactivate and had disrupted Pol activity at multiple CTCF binding sites relative to the WT virus.

Source link: https://doi.org/10.1101/2021.11.01.466781


The emergence of high-fitness variants accelerates the decay of genome heterogeneity in the coronavirus

The SARS-CoV-2 coronavirus accumulated a significant amount of genomic heterogeneity during the COVID-19 pandemic outbreak, which can be summarized by a measure of Sequence Composition Complexity. We compute SCC in high-quality coronavirus genomes from around the world, covering the entire pandemic period. We can determine evolutionary trends that could help us determine the virus evolution from its human host. Trends for SCC in the short time-span of SARS-CoV-2 pandemic expansion can be derived from phylogenetic ridge regression. We find no evidence for a trend in SCC values as predicted over time in early samples, though the virus genome seems to have progressed faster than Brownian Motions. Therefore, our findings show that phylogenetic timescales, which are typical of macroevolutionary timescales, can also be seen on shorter time spans typical of viral genomes.

Source link: https://doi.org/10.1101/2021.11.06.467547


The emergence of high-fitness variants accelerates the decay of genome heterogeneity in the coronavirus

The SARS-CoV-2 coronavirus carried a significant amount of genome heterogeneity during the COVID-19 pandemic outbreak, which can be summarized by a measure of Sequence Composition Complexity. We compute SCC in high-quality coronavirus genomes from around the world, covering the full range of the pandemic, in the hopes of identifying evolutionary trends that might guide us on the virus's evolution to its human host. Trends for SCC have emerged for the short time-span of SARS-CoV-2 pandemic expansion by using phylogenetic ridge regression. In early samples, there is no evidence for a trend in SCC values over time, and yet the virus genome appears to grow at a faster rate than Brownian Motion expectation. Hence, our findings show that phylogenetic trends, which are typical of macroevolutionary time scales, can also be revealed on shorter time spans typical of viral genomes.

Source link: https://doi.org/10.1101/2021.11.06.467547


Genome manipulation by guide-directed Argonaute cleavage

Many prokaryotic argonautes mediate DNA interference by using tiny DNA probes to cleave target DNA. The recombination rate correlates well with pAgo DNA cleavage activity, according to a mechanistic review, and it suggests that recombination involves both DSBs and RecBCD processing. According to these findings, the host genome's guide-directed cleavage pAgo on the host genome is mutagenic and can lead to a variety of outcomes, depending on the function of the host DNA repair machinery. Our research also finds an in vivo assay to assess or engineer pAgo DNA cleavage behaviour.

Source link: https://doi.org/10.1101/2021.11.17.469050

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions