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Proceedings of the National Academy of... May 2022Collateral sensitivity (CS), which arises when resistance to one antibiotic increases sensitivity toward other antibiotics, offers treatment opportunities to constrain...
Collateral sensitivity (CS), which arises when resistance to one antibiotic increases sensitivity toward other antibiotics, offers treatment opportunities to constrain or reverse the evolution of antibiotic resistance. The applicability of CS-informed treatments remains uncertain, in part because we lack an understanding of the generality of CS effects for different resistance mutations, singly or in combination. Here, we address this issue in the gram-positive pathogen Streptococcus pneumoniae by measuring collateral and fitness effects of clinically relevant gyrA and parC alleles and their combinations that confer resistance to fluoroquinolones. We integrated these results in a mathematical model that allowed us to evaluate how different in silico combination treatments impact the dynamics of resistance evolution. We identified common and conserved CS effects of different gyrA and parC alleles; however, the spectrum of collateral effects was unique for each allele or allelic pair. This indicated that allelic identity can impact the evolutionary dynamics of resistance evolution during monotreatment and combination treatment. Our model simulations, which included the experimentally derived antibiotic susceptibilities and fitness effects, and antibiotic-specific pharmacodynamics revealed that both collateral and fitness effects impact the population dynamics of resistance evolution. Overall, we provide evidence that allelic identity and interactions can have a pronounced impact on collateral effects to different antibiotics and suggest that these need to be considered in models examining CS-based therapies.
Topics: Alleles; Anti-Bacterial Agents; Drug Resistance, Bacterial; Fluoroquinolones; Microbial Sensitivity Tests
PubMed: 35476512
DOI: 10.1073/pnas.2121768119 -
Epigenetics & Chromatin Oct 2023Epigenome editing refers to the targeted reprogramming of genomic loci using an EpiEditor which may consist of an sgRNA/dCas9 complex that recruits DNMT3A/3L to the...
BACKGROUND
Epigenome editing refers to the targeted reprogramming of genomic loci using an EpiEditor which may consist of an sgRNA/dCas9 complex that recruits DNMT3A/3L to the target locus. Methylation of the locus can lead to a modulation of gene expression. Allele-specific DNA methylation (ASM) refers to the targeted methylation delivery only to one allele of a locus. In the context of diseases caused by a dominant mutation, the selective DNA methylation of the mutant allele could be used to repress its expression but retain the functionality of the normal gene.
RESULTS
To set up allele-specific targeted DNA methylation, target regions were selected from hypomethylated CGIs bearing a heterozygous SNP in their promoters in the HEK293 cell line. We aimed at delivering maximum DNA methylation with highest allelic specificity in the targeted regions. Placing SNPs in the PAM or seed regions of the sgRNA, we designed 24 different sgRNAs targeting single alleles in 14 different gene loci. We achieved efficient ASM in multiple cases, such as ISG15, MSH6, GPD1L, MRPL52, PDE8A, NARF, DAP3, and GSPT1, which in best cases led to five to tenfold stronger average DNA methylation at the on-target allele and absolute differences in the DNA methylation gain at on- and off-target alleles of > 50%. In general, loci with the allele discriminatory SNP positioned in the PAM region showed higher success rate of ASM and better specificity. Highest DNA methylation was observed on day 3 after transfection followed by a gradual decline. In selected cases, ASM was stable up to 11 days in HEK293 cells and it led up to a 3.6-fold change in allelic expression ratios.
CONCLUSIONS
We successfully delivered ASM at multiple genomic loci with high specificity, efficiency and stability. This form of super-specific epigenome editing could find applications in the treatment of diseases caused by dominant mutations, because it allows silencing of the mutant allele without repression of the expression of the normal allele thereby minimizing potential side-effects of the treatment.
Topics: Humans; DNA Methylation; RNA, Guide, CRISPR-Cas Systems; Epigenesis, Genetic; Alleles; HEK293 Cells; Epigenome; CRISPR-Cas Systems; Gene Editing
PubMed: 37864244
DOI: 10.1186/s13072-023-00515-5 -
Proceedings of the National Academy of... Jul 2014Personal transcriptomes in which all of an individual's genetic variants (e.g., single nucleotide variants) and transcript isoforms (transcription start sites, splice...
Personal transcriptomes in which all of an individual's genetic variants (e.g., single nucleotide variants) and transcript isoforms (transcription start sites, splice sites, and polyA sites) are defined and quantified for full-length transcripts are expected to be important for understanding individual biology and disease, but have not been described previously. To obtain such transcriptomes, we sequenced the lymphoblastoid transcriptomes of three family members (GM12878 and the parents GM12891 and GM12892) by using a Pacific Biosciences long-read approach complemented with Illumina 101-bp sequencing and made the following observations. First, we found that reads representing all splice sites of a transcript are evident for most sufficiently expressed genes ≤3 kb and often for genes longer than that. Second, we added and quantified previously unidentified splicing isoforms to an existing annotation, thus creating the first personalized annotation to our knowledge. Third, we determined SNVs in a de novo manner and connected them to RNA haplotypes, including HLA haplotypes, thereby assigning single full-length RNA molecules to their transcribed allele, and demonstrated Mendelian inheritance of RNA molecules. Fourth, we show how RNA molecules can be linked to personal variants on a one-by-one basis, which allows us to assess differential allelic expression (DAE) and differential allelic isoforms (DAI) from the phased full-length isoform reads. The DAI method is largely independent of the distance between exon and SNV--in contrast to fragmentation-based methods. Overall, in addition to improving eukaryotic transcriptome annotation, these results describe, to our knowledge, the first large-scale and full-length personal transcriptome.
Topics: Alleles; Gene Expression; Haplotypes; Humans; Polymorphism, Single Nucleotide; RNA; Transcriptome
PubMed: 24961374
DOI: 10.1073/pnas.1400447111 -
Archives of Razi Institute Nov 2021Based on 16 STR-loci, the allele pool and interbreed differentiation of goat breeds of Russian and foreign breeding were investigated in this study. These breeds...
Based on 16 STR-loci, the allele pool and interbreed differentiation of goat breeds of Russian and foreign breeding were investigated in this study. These breeds included Karachai (KRCH-K, n=73, mountain zone; KRCH-Z, n=33, foothill zone), Dagestan Downy (DAGD, n=30), Dagestan Wool (DAGW, n=30), Soviet Wool (SOVW, n=30), Saanen (SAAN, n=34), Murciano-Granadina (MURS, n=37), as well as wild goats, represented by three species of mountain goats (n=52): Siberian Capricorn (Capra sibirica) of Altai (CSIB-S, n=6), Tajikistan (CSIB-T, n=4), Kyrgyzstan (CSIB-K, n=6), and the Himalayas (CSIB-H, n=4); Bezoar goat (Capa aegagrus) of Turkey (CAEG, n=3) and Pakistan (CAEG-S, n=3); West Caucasian tur (): western Caucasian (Kuban, CCAU-K, n=10), central Caucasian (CCAU-M, n=8), and eastern Caucasian (Dagestan, CCAU-D, n=8). The highest genetic diversity was observed in the North Caucasus breeds, such as Karachai, Dagestan Downy, and Dagestan Wool. The mean numbers of alleles per locus and allelic diversity were 7.385-9.154 and 7.353-7.713, respectively. The genetic proximity of Caucasian breeds was confirmed by cluster analysis, and they formed a common branch with the highest genetic affinity, while the Orenburg and Soviet Wool breeds formed another branch, and the third branch with the least affinity was the dairy breed of foreign selection.The analysis of the phylogenetic tree of domestic and wild species established the formation of three clusters formed by the subspecies of the West Caucasian tur, Siberian ibex, and breeds of domestic goats. At the same time, populations of the Bezoar goats were localized at the root of the last cluster, which confirmed their role as the ancestors of domestic goats.
Topics: Alleles; Animals; Genetic Variation; Goats; Phylogeny
PubMed: 35355766
DOI: 10.22092/ari.2021.355684.1709 -
Frontiers in Immunology 2023Patients in need of hematopoietic stem cell transplantation often rely on unrelated stem cell donors matched in certain human leukocyte antigen (HLA) genes. Donor search...
Patients in need of hematopoietic stem cell transplantation often rely on unrelated stem cell donors matched in certain human leukocyte antigen (HLA) genes. Donor search is complicated by the extensive allelic variability of the HLA system. Therefore, large registries of potential donors are maintained in many countries worldwide. Population-specific HLA characteristics determine the registry benefits for patients and also the need for further regional donor recruitment. In this work, we analyzed HLA allele and haplotype frequencies of donors of DKMS Chile, the first Chilean donor registry, with self-assessed "non-Indigenous" (=92,788) and "Mapuche" (=1,993) ancestry. We identified HLA alleles that were distinctly more abundant in the Chilean subpopulations than in worldwide reference populations, four of them particularly characteristic for the Mapuche subpopulation, namely B*39:09g, B*35:09, DRB1*04:07g, and DRB1*16:02g. Both population subsamples carried haplotypes of both Native American and European origin at high frequencies, reflecting Chile's complex history of admixture and immigration. Matching probability analysis revealed limited benefits for Chilean patients (both non-Indigenous and Mapuche) from donor registries of non-Chilean donors, thus indicating a need for ongoing significant donor recruitment efforts in Chile.
Topics: Humans; Chile; Alleles; Haplotypes; Hematopoietic Stem Cell Transplantation
PubMed: 37313414
DOI: 10.3389/fimmu.2023.1175135 -
Briefings in Functional Genomics Sep 2015Hundreds of copy number variants are complex and multi-allelic, in that they have many structural alleles and have rearranged multiple times in the ancestors who... (Review)
Review
Hundreds of copy number variants are complex and multi-allelic, in that they have many structural alleles and have rearranged multiple times in the ancestors who contributed chromosomes to current humans. Not only are the relationships of these multi-allelic CNVs (mCNVs) to phenotypes generally unknown, but many mCNVs have not yet been described at the basic levels-alleles, allele frequencies, structural features-that support genetic investigation. To date, most reported disease associations to these variants have been ascertained through candidate gene studies. However, only a few associations have reached the level of acceptance defined by durable replications in many cohorts. This likely stems from longstanding challenges in making precise molecular measurements of the alleles individuals have at these loci. However, approaches for mCNV analysis are improving quickly, and some of the unique characteristics of mCNVs may assist future association studies. Their various structural alleles are likely to have different magnitudes of effect, creating a natural allelic series of growing phenotypic impact and giving investigators a set of natural predictions and testable hypotheses about the extent to which each allele of an mCNV predisposes to a phenotype. Also, mCNVs' low-to-modest correlation to individual single-nucleotide polymorphisms (SNPs) may make it easier to distinguish between mCNVs and nearby SNPs as the drivers of an association signal, and perhaps, make it possible to preliminarily screen candidate loci, or the entire genome, for the many mCNV-disease relationships that remain to be discovered.
Topics: Alleles; DNA Copy Number Variations; Disease; Genes; Genetic Association Studies; Genome, Human; Humans; Phenotype
PubMed: 26163405
DOI: 10.1093/bfgp/elv028 -
American Journal of Human Genetics May 2017Recent successes in genome-wide association studies (GWASs) make it possible to address important questions about the genetic architecture of complex traits, such as...
Recent successes in genome-wide association studies (GWASs) make it possible to address important questions about the genetic architecture of complex traits, such as allele frequency and effect size. One lesser-known aspect of complex traits is the extent of allelic heterogeneity (AH) arising from multiple causal variants at a locus. We developed a computational method to infer the probability of AH and applied it to three GWASs and four expression quantitative trait loci (eQTL) datasets. We identified a total of 4,152 loci with strong evidence of AH. The proportion of all loci with identified AH is 4%-23% in eQTLs, 35% in GWASs of high-density lipoprotein (HDL), and 23% in GWASs of schizophrenia. For eQTLs, we observed a strong correlation between sample size and the proportion of loci with AH (R = 0.85, p = 2.2 × 10), indicating that statistical power prevents identification of AH in other loci. Understanding the extent of AH may guide the development of new methods for fine mapping and association mapping of complex traits.
Topics: Alleles; Databases, Genetic; Gene Frequency; Genetic Association Studies; Humans; Linkage Disequilibrium; Models, Molecular; Phenotype; Quantitative Trait Loci
PubMed: 28475861
DOI: 10.1016/j.ajhg.2017.04.005 -
Current Issues in Molecular Biology 2015Allele mining is a promising way to dissect naturally occurring allelic variants of candidate genes with essential agronomic qualities. With the identification,... (Review)
Review
Allele mining is a promising way to dissect naturally occurring allelic variants of candidate genes with essential agronomic qualities. With the identification, isolation and characterisation of blast resistance genes in rice, it is now possible to dissect the actual allelic variants of these genes within an array of rice cultivars via allele mining. Multiple alleles from the complex locus serve as a reservoir of variation to generate functional genes. The routine sequence exchange is one of the main mechanisms of R gene evolution and development. Allele mining for resistance genes can be an important method to identify additional resistance alleles and new haplotypes along with the development of allele-specific markers for use in marker-assisted selection. Allele mining can be visualised as a vital link between effective utilisation of genetic and genomic resources in genomics-driven modern plant breeding. This review studies the actual concepts and potential of mining approaches for the discovery of alleles and their utilisation for blast resistance genes in rice. The details provided here will be important to provide the rice breeder with a worthwhile introduction to allele mining and its methodology for breakthrough discovery of fresh alleles hidden in hereditary diversity, which is vital for crop improvement.
Topics: Alleles; Computational Biology; Data Mining; Disease Resistance; Genomics; Host-Pathogen Interactions; Oryza; Plant Diseases
PubMed: 25706446
DOI: No ID Found -
Plant Communications Jul 2021Hybrids are always a focus of botanical research and have a high practical value in agricultural production. To better understand allele regulation and differences in...
Hybrids are always a focus of botanical research and have a high practical value in agricultural production. To better understand allele regulation and differences in DNA methylation in hybrids, we developed a phasing pipeline for hybrid rice based on two parental genomes (PP2PG), which is applicable for Iso-Seq, RNA-Seq, and Bisulfite sequencing (BS-Seq). Using PP2PG, we analyzed differences in gene transcription, alternative splicing, and DNA methylation in an allele-specific manner between parents and progeny or different progeny alleles. The phasing of Iso-Seq data provided a great advantage in separating the whole gene structure and producing a significantly higher separation ratio than RNA-Seq. The interaction of hybrid alleles was studied by constructing an allele co-expression network that revealed the dominant allele effect in the network. The expression variation between parents and the parental alleles in progeny showed tissue- or environment-specific patterns, which implied a preference for -acting regulation under different conditions. In addition, by comparing allele-specific DNA methylation, we found that CG methylation was more likely to be inherited than CHG and CHH methylation, and its enrichment in genic regions was connected to gene structure. In addition to an effective phasing pipeline, we also identified differentiation in gene structure that may have led to the expansion of allele functions in hybrids. In summary, we developed a phasing pipeline and provided valuable insights into alternative splicing, interaction networks, acting regulation, and the inheritance of DNA methylation in hybrid rice.
Topics: Alleles; DNA Methylation; Epigenome; Gene Expression Regulation, Plant; Genome, Plant; Inheritance Patterns; Oryza; Transcriptome
PubMed: 34327321
DOI: 10.1016/j.xplc.2021.100185 -
Trends in Genetics : TIG Jun 2014Monoallelic gene expression is a remarkable process in which transcription occurs from only one of two homologous alleles in a diploid cell. Interestingly, between 0.5%... (Review)
Review
Monoallelic gene expression is a remarkable process in which transcription occurs from only one of two homologous alleles in a diploid cell. Interestingly, between 0.5% and 15% of autosomal genes exhibit random monoallelic gene expression, in which different cells express only one allele independently of the underlying genomic sequence, in a cell type-specific manner. Recently, genome-wide studies have increased our understanding of the cell type-specific incidence of random monoallelic gene expression, and how the imbalance in allelic expression is distinguished within the cell and potentially maintained across cell generations. Monoallelic gene expression is likely generated through stochastic independent regulation of the two alleles upon differentiation, and has varied implications for the cell and organism, in particular with respect to disease.
Topics: Alleles; Animals; Epigenesis, Genetic; Gene Expression; Gene Expression Regulation; Genome; Genome-Wide Association Study; Humans
PubMed: 24780084
DOI: 10.1016/j.tig.2014.03.003