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9 results for “APOBEC3”
otoole et al (2023) apobec3 published data
<p>Contents</p> <p>Data<br> - 3 XML files (epoch model, exponential model and skygrid model with 2 APOBEC3 partitions defined).<br> - 4 phylogenies (B.1 and Clade IIb, Clade I and Clade IIa, outgroup pruned)<br> - 4 state reconstruction files (B.1 and Clade IIb, Clade I and Clade IIa)<br> - 4 branch SNP reconstruction files (B.1 and Clade IIb, Clade I and Clade IIa)<br> - 4 amino acid reconstruction files (B.1 and Clade IIb, Clade I and Clade IIa)<br> - 4 snp count files (B.1 and Clade IIb, Clade I and Clade IIa) <br> - 2 heptamer count files for Clade IIb (internal and all branches)<br> - 4 root-to-tip data files (B.1 and Clade IIb, Clade I and Clade IIa)<br> - 1 mutation count file including data from Clade IIb and B.1<br> <br> Scripts<br> - all_in_one notebook (notebook of most work from the paper- reconstructs the branch snps from the state files, generates tree figures, calculates amino acid information, calculates root-to-tip data for regression, code for generating figures present in the manuscript, sliding window calculations)<br> - analysis_until_roottotip (stand alone notebook to get root-to-tip data)<br> - cleaner_apobec_work (earlier version of analysis, including sankey diagram code)<br> - get_ml_tree_with_reconstruction (shell commands for aligning, generating ml tree, reconstructing states and pruning off outgroup)<br> - make_partitions (extraction of code for generating the two partitions of the alignment, apobec3 and non-apobec3)<br> - roottotip.R (regression analysis using roottotip data)<br> - synonprob.R (probability of getting x synonymous mutations given the data)</p>
Footprint of the host restriction factors APOBEC3 on the genome of human viruses
<p><span><span>APOBEC3 enzymes are innate immune effectors that introduce mutations into viral genomes. These enzymes are cytidine deaminases which transform cytosine into uracil. They preferentially mutate cytidine preceded by thymidine making the 5'TC motif their favored target. Viruses have evolved different strategies to evade APOBEC3 restriction. Certain viruses actively encode viral proteins antagonizing the APOBEC3s, others passively face the APOBEC3 selection pressure thanks to a depleted genome for APOBEC3-targeted motifs. Hence, the APOBEC3s left on the genome of certain viruses an evolutionary footprint.</span></span></p> <p><span><span>The aim of our study is the identification of these viruses having a genome shaped by the APOBEC3s. We analyzed the genome of 33,400 human viruses for the depletion of APOBEC3-favored motifs. We demonstrate that the APOBEC3 selection pressure impacts at least 22% of all currently annotated human viral species. The <i>papillomaviridae</i> and <i>polyomaviridae</i> are the most intensively footprinted families; evidencing a selection pressure acting genome-wide and on both strands. Members of the <i>parvoviridae</i> family are differentially targeted in term of both magnitude and localization of the footprint. Interestingly, a massive APOBEC3 footprint is present on both strands of the B19 erythroparvovirus; making this viral genome one of the most cleaned sequences for APOBEC3-favored motifs. We also identified the endemic <i>coronaviridae</i> as significantly footprinted. Interestingly, no such footprint has been detected on the zoonotic MERS-CoV, SARS-CoV-1 and SARS-CoV-2 coronaviruses. In addition to viruses that are footprinted genome-wide, certain viruses are footprinted only on very short sections of their genome. That is the case for the <i>gamma-herpesviridae</i> and <i>adenoviridae</i> where the footprint is localized on the lytic origins of replication. A mild footprint can also be detected on the negative strand of the reverse transcribing HIV-1, HIV-2, HTLV-1 and HBV viruses.</span></span></p> <p><span><span>Together, our data illustrate the extent of the APOBEC3 selection pressure on the human viruses and identify new putatively APOBEC3-targeted viruses.</span></span></p>
Footprint of the host restriction factors APOBEC3 on the genome of human viruses
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APOBEC3 promotes squamous differentiation and metastases via IL1A/AP-1 signaling
GEO Series GSE237016. Homo sapiens; Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
APOBEC3-mediated mutagenic processes in DNA-repair-deficient HCT116 cells selectively induced by high-dose 5FdUR treatment.
GEO Series GSE285767. Homo sapiens. 5 samples. Type: Other.
CBFb Stabilizes HIV Vif to Counteract APOBEC3 at the Expense of RUNX1 Target Gene Expression
GEO Series GSE42576. Homo sapiens. 14 samples. Type: Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing.
CBFb Stabilizes HIV Vif to Counteract APOBEC3 at the Expense of RUNX1 Target Gene Expression [ChIP-seq]
GEO Series GSE42575. Homo sapiens. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Impact of proteasome inhibition on nascent transcription of APOBEC3 cytidine deaminases
GEO Series GSE248016. Homo sapiens. 10 samples. Type: Other.
CBFb Stabilizes HIV Vif to Counteract APOBEC3 at the Expense of RUNX1 Target Gene Expression [gene expression]
GEO Series GSE42574. Homo sapiens. 12 samples. Type: Expression profiling by array.
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