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Cells Feb 2023PRUNE1 is a member of the aspartic acid-histidine-histidine (DHH) protein superfamily, which could display an exopolyphosphatase activity and interact with multiple...
PRUNE1 is a member of the aspartic acid-histidine-histidine (DHH) protein superfamily, which could display an exopolyphosphatase activity and interact with multiple cellular proteins involved in the cytoskeletal rearrangement. It is widely expressed during embryonic development and is essential for embryogenesis. PRUNE1 could also be critical for postnatal development of the nervous system as it was found to be mutated in patients with microcephaly, brain malformations, and neurodegeneration. To determine the cellular function of PRUNE1 during development and in disease, we have generated conditional mouse alleles of the in which P sites flank exon 6. Crossing these alleles with a ubiquitous Cre transgenic line resulted in a complete loss of PRUNE1 expression and embryonic defects identical to those previously described for null embryos. In addition, breeding these alleles with a Purkinje cell-specific Cre line () resulted in the loss of Purkinje cells similar to that observed in patients carrying a mutation with loss of PRUNE1 function. Therefore, the conditional mouse alleles generated in this study provide important genetic tools not only for dissecting the spatial and temporal roles of PRUNE1 during development but also for understanding the pathogenic role of PRUNE1 dysfunction in neurodegenerative or neurodevelopmental disease. In addition, from this work, we have described an approach that allows one to efficiently generate conditional mouse alleles based on mouse zygote electroporation.
Topics: Mice; Animals; Alleles; Mice, Knockout; Histidine; Plant Breeding; Mutation
PubMed: 36831191
DOI: 10.3390/cells12040524 -
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 -
Cell Reports Methods Sep 2023Reconstructing diploid sequences of human leukocyte antigen (HLA) genes, i.e., full-resolution HLA typing, from sequencing data is challenging. The high homogeneity...
Reconstructing diploid sequences of human leukocyte antigen (HLA) genes, i.e., full-resolution HLA typing, from sequencing data is challenging. The high homogeneity across HLA genes and the high heterogeneity within HLA alleles complicate the identification of genomic source loci for sequencing reads. Here, we present SpecHLA, which utilizes fine-tuned reads binning and local assembly to achieve accurate full-resolution HLA typing. SpecHLA accepts sequencing data from paired-end, 10×-linked-reads, high-throughput chromosome conformation capture (Hi-C), Pacific Biosciences (PacBio), and Oxford Nanopore Technology (ONT). It can also incorporate pedigree data and genotype frequency to refine typing. In 32 Human Genome Structural Variation Consortium, Phase 2 (HGSVC2) samples, SpecHLA achieved 98.6% accuracy for G-group-resolution HLA typing, inferring entire HLA alleles with an average of three mismatches fewer, ten gaps fewer, and 590 bp less edit distance than HISAT-genotype per allele. Additionally, SpecHLA exhibited a 2-field typing accuracy of 98.6% in 875 real samples. Finally, SpecHLA detected HLA loss of heterozygosity with 99.7% specificity and 96.8% sensitivity in simulated samples of cancer cell lines.
Topics: Humans; Alleles; Genotype; Cell Line; Diploidy; Histocompatibility Testing
PubMed: 37714157
DOI: 10.1016/j.crmeth.2023.100589 -
BMC Plant Biology Jan 2017The dwarfing gene sdw1 has been widely used throughout the world to develop commercial barley varieties. There are at least four different alleles at the sdw1 locus.
BACKGROUND
The dwarfing gene sdw1 has been widely used throughout the world to develop commercial barley varieties. There are at least four different alleles at the sdw1 locus.
RESULTS
Mutations in the gibberellin 20-oxidase gene (HvGA20ox2) resulted in multiple alleles at the sdw1 locus. The sdw1.d allele from Diamant is due to a 7-bp deletion in exon 1, while the sdw1.c allele from Abed Denso has 1-bp deletion and a 4-bp insertion in the 5' untranslated region. The sdw1.a allele from Jotun resulted from a total deletion of the HvGA20ox2 gene. The structural changes result in lower gene expression in sdw1.d and lack of expression in sdw1.a. There are three HvGA20ox genes in the barley genome. The partial or total loss of function of the HvGA20ox2 gene could be compensated by enhanced expression of its homolog HvGA20ox1and HvGA20ox3. A diagnostic molecular marker was developed to differentiate between the wild-type, sdw1.d and sdw1.a alleles and another molecular marker for differentiation of sdw1.c and sdw1.a. The markers were further tested in 197 barley varieties, out of which 28 had the sdw1.d allele and two varieties the sdw1.a allele. To date, the sdw1.d and sdw1.a alleles have only been detected in the modern barley varieties and lines.
CONCLUSIONS
The results provided further proof that the gibberellin 20-oxidase gene (HvGA20ox2) is the functional gene of the barley sdw1 mutants. Different deletions resulted in different functional alleles for different breeding purposes. Truncated protein could maintain partial function. Partial or total loss of function of the HvGA20ox2 gene could be compensated by enhanced expression of its homolog HvGA20ox1 and HvGA20ox3.
Topics: Alleles; Cloning, Molecular; Genes, Plant; Genetic Markers; Genetic Variation; Genome, Plant; Hordeum; Mixed Function Oxygenases; Transcription, Genetic
PubMed: 28086794
DOI: 10.1186/s12870-016-0964-4 -
Journal of Theoretical Biology May 2023Understanding the role of natural selection in driving evolutionary change requires accurate estimates of the strength of selection acting at the genetic level in the...
Understanding the role of natural selection in driving evolutionary change requires accurate estimates of the strength of selection acting at the genetic level in the wild. This is challenging to achieve but may be easier in the case of populations in migration-selection balance. When two populations are at equilibrium under migration-selection balance, there exist loci whose alleles are selected different ways in the two populations. Such loci can be identified from genome sequencing by their high values of F. This raises the question of what is the strength of selection on locally-adaptive alleles. To answer this question we analyse a 1-locus 2-allele model of a population distributed between two niches. We show by simulation of selected cases that the outputs from finite-population models are essentially the same as those from deterministic infinite-population models. We then derive theory for the infinite-population model showing the dependence of selection coefficients on equilibrium allele frequencies, migration rates, dominance and relative population sizes in the two niches. An Excel spreadsheet is provided for the calculation of selection coefficients and their approximate standard errors from observed values of population parameters. We illustrate our results with a worked example, with graphs showing the dependence of selection coefficients on equilibrium allele frequencies, and graphs showing how F depends on the selection coefficients acting on the alleles at a locus. Given the extent of recent progress in ecological genomics, we hope our methods may help those studying migration-selection balance to quantify the advantages conferred by adaptive genes.
Topics: Genetics, Population; Gene Frequency; Selection, Genetic; Chromosome Mapping; Biological Evolution; Alleles; Models, Genetic
PubMed: 36914112
DOI: 10.1016/j.jtbi.2023.111463 -
PloS One 2017Imputation of human leukocyte antigen (HLA) alleles from SNP-level data is attractive due to importance of HLA alleles in human disease, widespread availability of...
Imputation of human leukocyte antigen (HLA) alleles from SNP-level data is attractive due to importance of HLA alleles in human disease, widespread availability of genome-wide association study (GWAS) data, and expertise required for HLA sequencing. However, comprehensive evaluations of HLA imputations programs are limited. We compared HLA imputation results of HIBAG, SNP2HLA, and HLA*IMP:02 to sequenced HLA alleles in 3,265 samples from BioVU, a de-identified electronic health record database coupled to a DNA biorepository. We performed four-digit HLA sequencing for HLA-A, -B, -C, -DRB1, -DPB1, and -DQB1 using long-read 454 FLX sequencing. All samples were genotyped using both the Illumina HumanExome BeadChip platform and a GWAS platform. Call rates and concordance rates were compared by platform, frequency of allele, and race/ethnicity. Overall concordance rates were similar between programs in European Americans (EA) (0.975 [SNP2HLA]; 0.939 [HLA*IMP:02]; 0.976 [HIBAG]). SNP2HLA provided a significant advantage in terms of call rate and the number of alleles imputed. Concordance rates were lower overall for African Americans (AAs). These observations were consistent when accuracy was compared across HLA loci. All imputation programs performed similarly for low frequency HLA alleles. Higher concordance rates were observed when HLA alleles were imputed from GWAS platforms versus the HumanExome BeadChip, suggesting that high genomic coverage is preferred as input for HLA allelic imputation. These findings provide guidance on the best use of HLA imputation methods and elucidate their limitations.
Topics: Black or African American; Alleles; Female; Gene Frequency; Genome-Wide Association Study; Genotype; HLA Antigens; Haplotypes; Humans; Male; Middle Aged; Polymorphism, Single Nucleotide; White People
PubMed: 28207879
DOI: 10.1371/journal.pone.0172444 -
ELife Jul 2022Imprinting is a critical part of normal embryonic development in mammals, controlled by defined parent-of-origin (PofO) differentially methylated regions (DMRs) known as...
Imprinting is a critical part of normal embryonic development in mammals, controlled by defined parent-of-origin (PofO) differentially methylated regions (DMRs) known as imprinting control regions. Direct nanopore sequencing of DNA provides a means to detect allelic methylation and to overcome the drawbacks of methylation array and short-read technologies. Here, we used publicly available nanopore sequencing data for 12 standard B-lymphocyte cell lines to acquire the genome-wide mapping of imprinted intervals in humans. Using the sequencing data, we were able to phase 95% of the human methylome and detect 94% of the previously well-characterized, imprinted DMRs. In addition, we found 42 novel imprinted DMRs (16 germline and 26 somatic), which were confirmed using whole-genome bisulfite sequencing (WGBS) data. Analysis of WGBS data in mouse (), rhesus monkey (), and chimpanzee () suggested that 17 of these imprinted DMRs are conserved. Some of the novel imprinted intervals are within or close to imprinted genes without a known DMR. We also detected subtle parental methylation bias, spanning several kilobases at seven known imprinted clusters. At these blocks, hypermethylation occurs at the gene body of expressed allele(s) with mutually exclusive H3K36me3 and H3K27me3 allelic histone marks. These results expand upon our current knowledge of imprinting and the potential of nanopore sequencing to identify imprinting regions using only parent-offspring trios, as opposed to the large multi-generational pedigrees that have previously been required.
Topics: Alleles; Animals; DNA Methylation; Female; Genomic Imprinting; Germ Cells; Mammals; Mice; Nanopore Sequencing; Pregnancy
PubMed: 35787786
DOI: 10.7554/eLife.77898 -
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 -
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