CAO indel evolution
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ABSTRACT:
PROVIDER: PRJEB36040 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Amino acid insertions and deletions (indels) are an abundant class of genetic variants. However, compared to substitutions, the effects of indels are not well understood and poorly predicted. Here we address this shortcoming by performing deep indel mutagenesis (DIM) of structurally diverse proteins. Indel tolerance is strikingly different to substitution tolerance and varies extensively both between different proteins and within different regions of the same protein. Although state of the art variant effect predictors perform poorly on indels, we show that both experimentally-measured and computationally-predicted substitution scores can be repurposed as good indel variant effect predictors by incorporating information on protein secondary structures. Quantifying the effects of indels on protein-protein interactions reveals that insertions can be an important class of gain-of-function variants. Our results provide an overview of the impact of indels on proteins and a method to predict their effects genome-wide.
2023-09-28 | GSE244096 | GEO
Project description:SpCas9 INDEL frequency was evaluated at both the on- and off-target sites of guideRNA targeting either the murine Rhodopsin or Albumin by Next Generation Sequencing. Minimal INDELs were found at the off target sites evaluted, while SpCas9 activity was predominantly on-target.
2021-11-11 | GSE180117 | GEO
Project description:We used microarrays to study the evolution of gene expression in two bacterial ecotypes that coexisted for more than 35000 generations of experimental evolution in an extremely simple environment We sampled four clones from each of two lineages at generations 6,500, 17,000 and 40,000 from the polymorphic Ara-2 population of the E. coli long-term evolution experiment. The four clones from each lineage and generation were mixed equally and used for global expression profiling, growth assays and competition experiments. Global expression profiles and growth assays were also performed on the ancestral strain. RNA extractions were done using cells in mid-exponential growth in the same glucose-limited minimal medium used in the evolution experiment. Global expression profiles were obtained by using Affymetrix arrays, with 5 or 6 biological replicates for each lineage-generation sample.
2012-01-01 | E-GEOD-30639 | biostudies-arrayexpress
Project description:Molecular phylogenomics investigates evolutionary relationships based on genomic data. However, despite genomic sequence conservation, changes in protein interactions can occur relatively rapidly and may cause strong functional diversification. To investigate such functional evolution, we here combine phylogenomics with interaction proteomics. We develop this concept by investigating the molecular evolution of the shelterin complex, which protects telomeres, across 16 vertebrate species from zebrafish to humans covering 450 million years of evolution. Our phylointeractomics screen discovers previously unknown telomere-associated proteins and reveals how homologous proteins undergo functional evolution. For instance, we show that TERF1 evolved as a telomere-binding protein in the common stem lineage of marsupial and placental mammals. Phylointeractomics is a versatile and scalable approach to investigate evolutionary changes in protein function and thus can provide experimental evidence for phylogenomic relationships.
2017-02-15 | PXD005517 | Pride
Project description:The transcription factor NRSF/REST represses many vertebrate neuronal genes in non-neuronal cells by binding to 3 distinct motif classes, which are the canonical 21bp NRSEs, longer non-canonical sites and solo half-sites. We used ChIP-seq in four mammalian species to determine the evolution of the NRSF binding repertoire. We show that while some NRSEs are deeply conserved, genes with several NRSEs show evidence of compensatory site turnover, suggesting that the association of the transcription factor to its target gene is more important than the specific binding site. We also found that many newborn sites in human are associated with primate specific indels and transposable elements. Our analysis of sites with conserved ChIP-binding in all 4 species demonstrates that both the non-canonical and solo half-sites convert preferentially to canonical motifs. These findings support a model of dynamic conversion between different motif types that account for the preferential accumulation of the canonical NRSE during evolution.
2024-01-01 | GSE77543 | GEO
Project description:Genome reorganization by large scale indels, gene displacements, and horizontal gene transfers allow an organism to re-organize genes into operons (“operonization”) and explore novel strategies for adapting to its changing environment. We have characterized the process of operonization by mapping and comparing transcriptome structures (TSs) of four phylogenetically diverse exptremophilic archaea: a hydrogenotrophic methanogen (Methanococcus maripaludis S2), an anaerobic thermophile (Pyrococcus furiosis DSM 3638), an acidophilic and aerobic thermophile (Sulfolobus solfataricus P2), and a photoheterotrophic halophile (Halobacterium salinarum NRC-1). We demonstrate how the evolution of new transcriptional elements (promoters and terminators) is utilized as a mechanism to incorporate translocated, inverted, and newly acquired genes into existing gene regulatory programs. This SuperSeries is composed of the following subset Series: GSE26777: Methanococcus maripaludis S2 growth curve, tiling arrays GSE26778: Pyrococcus furiosus DSM 3638 growth curve, tiling arrays GSE26779: Sulfolobus solfataricus P2 growth curve, tiling arrays Refer to individual Series
2011-06-27 | E-GEOD-26782 | biostudies-arrayexpress
Project description:Multidrug-resistant (MDR; resistance to >3 antimicrobial classes) Salmonella enterica serovar I 4,[5],12:i:- strains were linked to a 2015 foodborne outbreak from pork. Strain USDA15WA-1, associated with the outbreak, harbors an MDR module and the metal tolerance element Salmonella Genomic Island 4 (SGI-4). Characterization of SGI-4 revealed that conjugational transfer of SGI-4 resulted in the mobile genetic element (MGE) replicating as a plasmid or integrating into the chromosome. Tolerance to copper, arsenic, and antimony compounds was increased in Salmonella strains containing SGI-4 compared to strains lacking the MGE. Following Salmonella exposure to copper, RNA-seq transcriptional analysis demonstrated significant differential expression of diverse genes and pathways, including induction of numerous metal tolerance genes (copper, arsenic, silver, and mercury). Evaluation of swine administered elevated concentrations of zinc oxide (2,000 mg/kg) and copper sulfate (200 mg/kg) as an antimicrobial feed additive (Zn+Cu) in their diet for 4 weeks prior to and 3 weeks post-inoculation with serovar I 4,[5],12:i:- indicated that Salmonella shedding levels declined at a slower rate in pigs receiving in-feed Zn+Cu compared to control pigs (no Zn+Cu). The presence of metal tolerance genes in MDR Salmonella serovar I 4,[5],12:i:- may provide benefits for environmental survival or swine colonization in metal-containing settings.
2020-12-08 | GSE159054 | GEO
Project description:The evolution of human anatomical features likely involved changes in gene regulation during development. However, the nature and extent of human specific developmental regulatory functions remain unknown. We obtained a genome-wide view of cis regulatory evolution in human embryonic tissues by comparing the histone modification H3K27ac, which provides a quantitative readout of promoter and enhancer activity, during human, rhesus, and mouse limb development. Based on increased H3K27ac, we find that 13% of promoters and 11% of enhancers have gained activity on the human lineage since the human-rhesus divergence. These gains largely arose by modification of ancestral regulatory activities in the limb or potential co-option from other tissues and are likely to have heterogeneous genetic causes. Most enhancers that exhibit gain of activity in humans originated in mammals. Gains at promoters and enhancers in the human limb are associated with increased gene expression, suggesting they include molecular drivers of human morphological evolution. ChIP-Seq and RNA-Seq of autopod tissue of developing limb buds of Human (E33-E47), rhesus (E31-E36), and mouse (E10.5-E13.5). No raw data are provided for human samples. Human alignments were anonymized by removing sequence information and converting to bed format.
2013-07-02 | E-GEOD-42413 | biostudies-arrayexpress
Project description:Genome reorganization by large scale indels, gene displacements, and horizontal gene transfers allow an organism to re-organize genes into operons (“operonization”) and explore novel strategies for adapting to its changing environment. We have characterized the process of operonization by mapping and comparing transcriptome structures (TSs) of four phylogenetically diverse exptremophilic archaea: a hydrogenotrophic methanogen (Methanococcus maripaludis S2), an anaerobic thermophile (Pyrococcus furiosis DSM 3638), an acidophilic and aerobic thermophile (Sulfolobus solfataricus P2), and a photoheterotrophic halophile (Halobacterium salinarum NRC-1). We demonstrate how the evolution of new transcriptional elements (promoters and terminators) is utilized as a mechanism to incorporate translocated, inverted, and newly acquired genes into existing gene regulatory programs. This SuperSeries is composed of the SubSeries listed below.
2011-06-27 | GSE26782 | GEO