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Nucleic Acids Research Jul 2022We present ANANASTRA, https://ananastra.autosome.org, a web server for the identification and annotation of regulatory single-nucleotide polymorphisms (SNPs) with...
We present ANANASTRA, https://ananastra.autosome.org, a web server for the identification and annotation of regulatory single-nucleotide polymorphisms (SNPs) with allele-specific binding events. ANANASTRA accepts a list of dbSNP IDs or a VCF file and reports allele-specific binding (ASB) sites of particular transcription factors or in specific cell types, highlighting those with ASBs significantly enriched at SNPs in the query list. ANANASTRA is built on top of a systematic analysis of allelic imbalance in ChIP-Seq experiments and performs the ASB enrichment test against background sets of SNPs found in the same source experiments as ASB sites but not displaying significant allelic imbalance. We illustrate ANANASTRA usage with selected case studies and expect that ANANASTRA will help to conduct the follow-up of GWAS in terms of establishing functional hypotheses and designing experimental verification.
Topics: Alleles; Binding Sites; Genome-Wide Association Study; Polymorphism, Single Nucleotide; Protein Binding; Transcription Factors; DNA-Binding Proteins
PubMed: 35446421
DOI: 10.1093/nar/gkac262 -
HLA May 2020The identification of null or questionably expressed HLA allelic variants is a major issue in HLA diagnostics, because the mistyping of the aberrant expression of such...
The identification of null or questionably expressed HLA allelic variants is a major issue in HLA diagnostics, because the mistyping of the aberrant expression of such alleles can have a major impact on the outcome of both hematopoietic stem cell transplantation (HSCT) and solid organ transplants. It is debated how questionable (Q) alleles, because of their unknown expression profile, should be considered in an allogenic HSCT setting. The HLA-B*38:55Q allele was detected as an HLA-B blank specificity; DNA sequencing identified a single polymorphism at position 373 in exon 3 (TGC > CGC), which results in the replacement of cysteine 101 with an arginine in the HLA-B heavy chain, thus, impairing disulfide bridge formation in the alpha-2 domain, essential for the normal expression of the HLA molecules. In order to determine the RNA and protein expression profile of this allelic variant, we analyzed antigenic expression at different levels, transcriptional and transductional, using a combination of cellular methods, such as serological testing and flow cytometric analysis, polymerase chain reaction (PCR) sequence-specific primer (SSP) cDNA group-specific amplification and immunocytochemical assay, demonstrating the prevalent cytoplasmatic distribution of the HLA-B*38:55Q protein. Our findings suggest that in matching process the HLA-B*38:55Q allele needs to be considered as a low expressed allele, able to elicit an allogenic T-cell response in vivo and impair the transplant outcome.
Topics: Alleles; Exons; Genes, MHC Class I; HLA-B Antigens; Hematopoietic Stem Cell Transplantation
PubMed: 31891446
DOI: 10.1111/tan.13790 -
Frontiers in Endocrinology 2023Interspecies hybridization is an important breeding method to generate fishes with heterosis in aquaculture. Using this method, hybrid Nile tilapia (, ♀) × blue...
BACKGROUND
Interspecies hybridization is an important breeding method to generate fishes with heterosis in aquaculture. Using this method, hybrid Nile tilapia (, ♀) × blue tilapia (, ♂) has been produced and widely farmed due to its growth and appetite superiorities. However, the genetic mechanism of these advanced traits is still not well understood. is a crucial gene that regulates growth and appetite in fishes. In the present study, we focused on the expression characteristics and its regulation of in the hybrid.
RESULTS
The tissue distribution analysis showed that was predominantly expressed in the stomach in the hybrid. was more highly expressed in the stomach in the hybrid and Nile tilapia, compared to blue tilapia, showing a nonadditive pattern. Two single-nucleotide polymorphism (SNP) sites were identified including T/C and C/G from the second exon in the gene from Nile tilapia and blue tilapia. By pyrosequencing based on the SNP sites, the allele-specific expression (ASE) of in the hybrid was assayed. The result indicated that in the hybrid showed higher maternal allelic transcript ratios. Fasting significantly increased overall expression at 4, 8, 12, 24, and 48 h. In addition, higher maternal allelic transcript ratios were not changed in the fasting hybrids at 48 h. The and effects were determined by evaluating the overall expression and ASE values in the hybrid. The expression of was mediated by compensating and effects in hybrid.
CONCLUSION
In summary, the present lines of evidence showed the nonadditive expression of in the hybrid tilapia and its regulation by subgenomes, offering new insight into gene expression characteristics in hybrids.
Topics: Animals; Tilapia; Alleles; Ghrelin; Cichlids
PubMed: 38152137
DOI: 10.3389/fendo.2023.1292730 -
Journal of Integrative Plant Biology May 2021In rice (Oryza sativa), amylose content (AC) is the major factor that determines eating and cooking quality (ECQ). The diversity in AC is largely attributed to natural...
In rice (Oryza sativa), amylose content (AC) is the major factor that determines eating and cooking quality (ECQ). The diversity in AC is largely attributed to natural allelic variation at the Waxy (Wx) locus. Here we identified a rare Wx allele, Wx , which combines a favorable AC, improved ECQ and grain transparency. Based on a phylogenetic analysis of Wx genomic sequences from 370 rice accessions, we speculated that Wx may have derived from recombination between two important natural Wx alleles, Wx and Wx . We validated the effects of Wx on rice grain quality using both transgenic lines and near-isogenic lines (NILs). When introgressed into the japonica Nipponbare (NIP) background, Wx resulted in a moderate AC that was intermediate between that of NILs carrying the Wx allele and NILs with the Wx allele. Notably, mature grains of NILs fixed for Wx had an improved transparent endosperm relative to soft rice. Further, we introduced Wx into a high-yielding japonica cultivar via molecular marker-assisted selection: the introgressed lines exhibited clear improvements in ECQ and endosperm transparency. Our results suggest that Wx is a promising allele to improve grain quality, especially ECQ and grain transparency of high-yielding japonica cultivars, in rice breeding programs.
Topics: Alleles; Gene Expression Regulation, Plant; Oryza; Plant Proteins
PubMed: 32886440
DOI: 10.1111/jipb.13010 -
Bioinformatics (Oxford, England) Nov 2021The sparse allele vectors file format is an efficient storage format for large-scale DNA variation data and is designed for high throughput association analysis by...
SUMMARY
The sparse allele vectors file format is an efficient storage format for large-scale DNA variation data and is designed for high throughput association analysis by leveraging techniques for fast deserialization of data into computer memory. A command line interface has been developed to complement the storage format and supports basic features like importing, exporting and subsetting. Additionally, a C++ programming API is available allowing for easy integration into analysis software.
AVAILABILITY AND IMPLEMENTATION
https://github.com/statgen/savvy.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Alleles; Software
PubMed: 33989384
DOI: 10.1093/bioinformatics/btab378 -
Molecular Ecology Feb 2022The sequencing depth required to genotype autopolyploid populations is a very controversial topic. Different studies have adopted variable depth values without a clear...
The sequencing depth required to genotype autopolyploid populations is a very controversial topic. Different studies have adopted variable depth values without a clear guide on the optimal sequencing depth value. Many studies suggest high depth thresholds for different ploidies that may not be practical and substantially increase the overall genotyping cost for different projects. However, such conservative thresholds may not be required to achieve the most common research goals. In fact, some recent reports in the field of quantitative genetics found that much lower sequencing depth thresholds could achieve the same accuracy as high depth thresholds. In this manuscript, I discuss when researchers need to use stringent sequencing depth thresholds and when they can use more relaxed ones. I support my argument by calculating the probabilities of sampling different homologues at a given sequencing depth. I also discuss the uses and the uncertainty in calculating a continuous allelic dosage as the proportion of sequencing reads that hold the alternative allele, which is becoming a common method now in quantitative genetics to replace discrete dosage estimation.
Topics: Alleles; Genotype; High-Throughput Nucleotide Sequencing; Polymorphism, Single Nucleotide
PubMed: 34875138
DOI: 10.1111/mec.16313 -
Physical Chemistry Chemical Physics :... Jan 2023Recent advances in direct inhibition of Ras benefit from the protein's intrinsic dynamic nature that derives therapeutically vulnerable conformers bearing transiently...
Recent advances in direct inhibition of Ras benefit from the protein's intrinsic dynamic nature that derives therapeutically vulnerable conformers bearing transiently formed cryptic pockets. Hotspot mutants of Ras are major tumor drivers and are hyperactivated in cells at variable levels, which may require allele-specific strategies for effective targeting. However, it remains unclear how the prevalent oncogenic mutations and activation states perturb the free energy landscape governing the protein dynamics and druggability. Here we characterized the nucleotide state- and allele-dependent alterations of Ras conformational dynamics using a combined NMR experimental and computational approach and constructed quantitative ensembles revealing the conservation of the cryptic SI/II-P and SII-P pockets in different states and alleles. Highly local but critical conformational reorganizations that undermine the SII-P accessibility to residue 12 have been identified as a common mechanism resulting in the low reactivities of Ras·GTP as well as Ras(G12D)·GDP with covalent SII-P inhibitors. Our results strongly support the conformational selection scenario for interactions between Ras and the previously reported binders and offer insights for the future development of state- and allele-specific, as well as pan-Ras, inhibitors.
Topics: Alleles; Protein Conformation; Nucleotides; Magnetic Resonance Spectroscopy; Mutation
PubMed: 36537570
DOI: 10.1039/d2cp04964c -
Cell Systems Feb 2022Pan-cancer studies sketched the genomic landscape of the tumor types spectrum. We delineated the purity- and ploidy-adjusted allele-specific profiles of 4,950 patients...
Pan-cancer studies sketched the genomic landscape of the tumor types spectrum. We delineated the purity- and ploidy-adjusted allele-specific profiles of 4,950 patients across 27 tumor types from the Cancer Genome Atlas (TCGA). Leveraging allele-specific data, we reclassified as loss of heterozygosity (LOH) 9% and 7% of apparent copy-number wild-type and gain calls, respectively, and overall observed more than 18 million allelic imbalance somatic events at the gene level. Reclassification of copy-number events revealed associations between driver mutations and LOH, pointing out the timings between the occurrence of point mutations and copy-number events. Integrating allele-specific genomics and matched transcriptomics, we observed that allele-specific gene status is relevant in the regulation of TP53 and its targets. Further, we disclosed the role of copy-neutral LOH in the impairment of tumor suppressor genes and in disease progression. Our results highlight the role of LOH in cancer and contribute to the understanding of tumor progression.
Topics: Alleles; Genomics; Humans; Loss of Heterozygosity; Neoplasms
PubMed: 34731645
DOI: 10.1016/j.cels.2021.10.001 -
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 -
DNA Research : An International Journal... Feb 2019The current RNA-Seq method analyses fragments of mRNAs, from which it is occasionally difficult to reconstruct the entire transcript structure. Here, we performed and...
The current RNA-Seq method analyses fragments of mRNAs, from which it is occasionally difficult to reconstruct the entire transcript structure. Here, we performed and evaluated the recent procedure for full-length cDNA sequencing using the Nanopore sequencer MinION. We applied MinION RNA-Seq for various applications, which would not always be easy using the usual RNA-Seq by Illumina. First, we examined and found that even though the sequencing accuracy was still limited to 92.3%, practically useful RNA-Seq analysis is possible. Particularly, taking advantage of the long-read nature of MinION, we demonstrate the identification of splicing patterns and their combinations as a form of full-length cDNAs without losing precise information concerning their expression levels. Transcripts of fusion genes in cancer cells can also be identified and characterized. Furthermore, the full-length cDNA information can be used for phasing of the SNPs detected by WES on the transcripts, providing essential information to identify allele-specific transcriptional events. We constructed a catalogue of full-length cDNAs in seven major organs for two particular individuals and identified allele-specific transcription and splicing. Finally, we demonstrate that single-cell sequencing is also possible. RNA-Seq on the MinION platform should provide a novel approach that is complementary to the current RNA-Seq.
Topics: Alleles; DNA, Complementary; Gene Expression Profiling; High-Throughput Nucleotide Sequencing; Humans; Polymorphism, Single Nucleotide; RNA Splicing; Sequence Analysis, RNA
PubMed: 30462165
DOI: 10.1093/dnares/dsy038