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At least 721 records · Page 40Linked to original sources
PubMed2026

ALPINE: a scalable pipeline for comprehensive classification of gene-editing outcomes from long-read amplicon sequencing.

SUMMARY: CRISPR genome editing has enabled precise genetic modification for gene and cell therapies, but edits often produce heterogeneous on-target outcomes, including homology-directed repair (HDR) knock-ins, DNA repair template integrations, and structural variants. Existing tools are frequently limited to short reads or lack viral vector-specific integration categories needed for therapeutic development. Here, we present ALPINE (Amplicon Long-read Pipeline for INtegration Evaluation), a scalable and reproducible pipeline for classifying and quantifying gene-editing outcomes from long-read amplicon sequencing supporting both PacBio HiFi and Oxford Nanopore platforms. ALPINE classifies reads into 10+ categories, including DNA repair vector integration subtypes, and performs variant calling near the gene-edited site with batch, multi-sample reporting. Uniquely, ALPINE can distinguish between cells treated with multiple DNA repair vectors and identify distinct molecular features, such as inverted terminal repeats (ITRs), enabling comprehensive characterization of complex gene editing outcomes. Dual-target benchmarking on simulated datasets demonstrated high accuracy for transgene integration events. Independent validation on public crosslinked-HDR dataset confirmed ALPINE's integration detection capabilities, and application to edited T cell samples demonstrated comprehensive gene-editing outcome profiling. AVAILABILITY: ALPINE is available under MIT license at https://github.com/Maggi-Chen/ALPINE and https://doi.org/10.5281/zenodo.20272510. All analysis scripts and visualization code used in this manuscript are available at https://github.com/Maggi-Chen/ALPINE-manuscript-analysis. Simulated datasets are deposited at Zenodo (https://doi.org/10.5281/zenodo.20260865). Public dataset PRJNA913199 is available through NCBI SRA.

Gene Editing↗
PubMed2026

map3C: a computational tool for processing multiomic single-cell Hi-C data.

SUMMARY: The emergence of multiomic single-cell Hi-C (scHi-C) methods, which simultaneously profile chromatin conformation and other modalities such as gene expression or DNA methylation, creates tremendous opportunities for studying the genome's structure-function relationships. Existing tools for processing multiomic scHi-C datasets lack certain key functions for downstream bioinformatics analysis. We present map3C, a software tool that incorporates additional key functions. Specifically, we demonstrate that map3C facilitates multiomic scHi-C processing, quality control, and identification of structural variant locations in the genome. AVAILABILITY AND IMPLEMENTATION: map3C is available at https://github.com/luogenomics/map3C and is archived at https://doi.org/10.5281/zenodo.20724719.

Software↗
PubMed2026

nf-core/pacsomatic: a scalable somatic analytic pipeline using PacBio HiFi data.

MOTIVATION: Pacific Biosciences (PacBio) HiFi long-read sequencing enables robust characterization of complex genomic regions, repetitive elements, and structural variants (SVs) that are often inaccessible to short-read technologies. To fully leverage HiFi reads to advance cancer genomics and epigenetics, researchers require an end-to-end, scalable and optimized bioinformatics workflow. The nf-core framework meets this need by providing rigorously tested, community-curated pipelines that ensure reproducibility, transparency, and broad compatibility across computational environments. RESULTS: We present nf-core/pacsomatic, an automated Nextflow DSL2 pipeline designed for comprehensive paired tumor-normal somatic analysis using PacBio HiFi data. The workflow includes steps for read alignments against reference genome, somatic SNV/indel, SV, and CNV calling, CpG methylation profiling and differential methylation region (DMR) detection. Additional downstream modules support functional annotation, mutational signature analysis, tumor purity and ploidy estimation, and homologous recombination deficiency (HRD) assessment. Utilizing nf-core's modular design and containerized execution, nf-core/pacsomatic provides a stable framework for the reproducible discovery of biological insights. AVAILABILITY: nf-core/pacsomatic is available under the MIT License at nf-core (https://nf-co.re/pacsomatic) and github (https://github.com/nf-core/pacsomatic).

Software↗
PubMed2006

Genome comparison in silico in Neisseria suggests integration of filamentous bacteriophages by their own transposase.

We have identified filamentous prophages, Nf (Neisserial filamentous phages), during an in silico genome comparison in Neisseria. Comparison of three genomes of Neisseria meningitidis and one of Neisseria gonorrhoeae revealed four subtypes of Nf. Eleven intact copies are located at different loci in the four genomes. Each intact copy of Nf is flanked by duplication of 5'-CT and, at its right end, carries a transposase homologue (pivNM/irg) of RNaseH/Retroviral integrase superfamily. The phylogeny of these putative transposases and that of phage-related proteins on Nfs are congruent. Following circularization of Nfs, a promoter-like sequence forms. The sequence at the junction of these predicted circular forms (5'-atCTtatat) was found in a related plasmid (pMU1) at a corresponding locus. Several structural variants of Nfs--partially inverted, internally deleted and truncated--were also identified. The partial inversion seems to be a product of site-specific recombination between two 5'-CTtat sequences that are in inverse orientation, one at its end and the other upstream of pivNM/irg. Formation of internally deleted variants probably proceeded through replicative transposition that also involved two 5'-CTtat sequences. We concluded that the PivNM/Irg transposase on Nfs integrated their circular forms into the chromosomal 5'-CT-containing sequences and probably mediated the above rearrangements.

Base Sequence↗
PubMed2025

The genetic basis of chloride exclusion in grapevines.

Mediterranean regions are among the most important areas for global grape production, characterized by dry climates and frequent challenges associated with soil salinity. In these environments, chloride toxicity is a major factor limiting vine growth and fruit quality. Despite the critical role of chloride exclusion in salinity tolerance, the genetic mechanisms underlying this trait remain poorly understood. In this study, we analyzed natural variation in chloride exclusion using a diverse panel of 335 accessions representing 18 wild and cultivated Vitis species. This panel, comprising accessions from the southwestern United States and Mexico, captures a broad range of evolutionary adaptations to abiotic stress and provides a valuable genetic resource for breeding efforts aimed at introducing novel traits. Using genome-wide association and quantitative trait loci (QTL) mapping, we identified a major QTL on chromosome 8, now designated qClEx8.1, containing candidate genes encoding cation/H⁺ exchangers (CHXs), which are involved in ion transport and homeostasis. To validate these findings, we analyzed a mapping population derived from Vitis acerifolia longii 9018 and the commercial rootstock GRN3, confirming the chromosome 8 locus as a major determinant of chloride exclusion. Structural variant analysis revealed nonsynonymous substitutions within CHX genes that may influence protein function and salinity tolerance. Additionally, we discovered a novel QTL on chromosome 19 enriched with G-type lectin S-receptor-like serine/threonine-protein kinases, known regulators of stress signaling. By integrating phenotypic and genomic data across a diverse Vitis collection, this study advances our understanding of the genetic architecture underlying chloride exclusion and highlights candidate genes for breeding salt-tolerant rootstocks.

Vitis↗
PubMed2026

Screening for dual sgRNAs with comparable indel efficiencies enhances CRISPR-mediated large-fragment deletion.

CRISPR-mediated large-fragment deletion provides a powerful approach for gene clusters, noncoding regions and structural variants, but its broader application is limited by low and variable deletion efficiency. Here, we systematically designed and evaluated 78 sgRNAs targeting nine representative gene clusters (ttn.1-ttn.2 cluster, 7 hox clusters and nppb-nppa cluster), containing 31 large fragments (5 kb-340 kb) to investigate the determinants of deletion efficiency. We found two key rules for achieving high deletion efficiency: (i) using dual sgRNAs with similar indel efficiencies, and (ii) applying a single sgRNA pair rather than multiple sgRNAs. Based on those rules, a 340 kb deletion is detected in the progenies of 95% of founders. Whereas the deletion size showed no significant linear correlation with deletion efficiency within the tested range. Implementing these rules resulted in an average of 70% of founders transmitting deletions across all tested sgRNA pairs. Therefore, screening sgRNAs can effectively enhance CRISPR utility in deletions, thereby facilitating the application of genomic manipulation in vertebrates and other species.

CRISPR↗
PubMed2003

Structural investigation of chondroitin/dermatan sulfate oligosaccharides from human skin fibroblast decorin.

Hybrid chondroitin/dermatan sulfate (CS/DS) glycosaminoglycan chains, derived from decorin secreted by human skin fibroblasts, were shown to interact with FGF-2, as did oligosaccharides derived therefrom by chondroitin B lyase digestion. In a first attempt to identify the biologically active sequence, a novel protocol for structural analysis of enzyme-resistant oligosaccharides larger than standard trisulfated hexasaccharides was developed. The method bases on capillary electrophoresis (CE) for separating oversulfated species in offline combination with nanoelectrospray ionization quadrupole time-of-flight tandem mass spectrometry (nanoESI-QTOF-MS/MS) in the negative ion mode. Under optimized CE and ESI-MS conditions, up to 12-mer oligosaccharides with different degrees of sulfation were identified. A novel tandem MS protocol (CID-VE) was applied to elucidate the structure of a previously undescribed pentasulfated CS/DS hexasaccharide, Delta-4,5-IdoAGalNAc[GlcAGalNAc]2(5S). In this molecular species, detected as a triply charged ion at m/z 511.38, three sulfates are found in the IdoAGalNAcGlcA moiety offering two structural variants: one containing sulfated IdoA together with a disulfated GalNAc moiety and in the other one both uronic acids, that is, GlcA and IdoA and the amino sugar each carry a sulfate ester group.

Chondroitin Sulfates↗
PubMed2026

Genetic architecture of endometriosis: risk factors, comorbidities and clinical implications.

BACKGROUND: In 1999, Dr Susan Treloar and colleagues conducted a landmark twin study in Australia and reported their estimate of 51% for the heritability of endometriosis. This important result led several groups to begin mapping genetic factors contributing to increased endometriosis risk. Despite early challenges, advances in genome-wide association studies (GWAS) have identified multiple genetic risk factors and some target genes implicated in follow-up studies on genetic regulation of transcription. Access to large publicly available genetic datasets and analysis with endometriosis GWAS results is also providing new opportunities to answer important questions about comorbid conditions associated with endometriosis and their implications for clinical practice. OBJECTIVE AND RATIONALE: The objective of the review is to summarize the last 25 years of genetic studies in endometriosis, outline contributions to our understanding of the disease, and suggest future directions to accelerate biological insights from genetic studies to improve clinical outcomes. SEARCH METHODS: A comprehensive review of scientific literature on the genetics of endometriosis was conducted through searches in PubMed and Google Scholar up to June 2026. Search terms included "endometriosis AND (genetics OR GWAS OR genetic risk factors)", For studies addressing the functional characterization of genetic risk loci, additional searches employed the terms "endometriosis AND (genotype-phenotype associations OR colocalization OR eQTL OR mQTL OR multi omics methods)". To identify studies examining shared genetic risk between endometriosis and comorbid conditions, the search strategy included "endometriosis AND (genetic correlation OR colocalization OR Mendelian randomisation)". Publications reporting discoveries related to genetic risk factors for endometriosis and studies interpreting their biological and clinical significance were critically evaluated, and 144 publications were discussed in the review. OUTCOMES: Discovery of genetic risk factors started slowly and has accelerated in recent years with developments in technology and international collaborations to combine data and increase statistical power. GWAS have mapped 80 genetic risk factors that implicate gene regulation of hormonal targets, development of the reproductive tract, regulation of cell proliferation, and regulation of epithelial cell differentiation. In common with most other complex diseases, effects of individual common genetic risk factors are small. However, several examples demonstrate that small effect sizes are not a good predictor for the impact of drugs developed against genetically validated targets. Genetic risk factors implicate five genes regulating gonadotrophin release and oestrogen action, the major target pathway of current drugs for treatment of endometriosis demonstrating proof-of-principal for biologically meaningful results. Genetic correlation and Mendelian Randomization studies highlight important causal relationships between endometriosis and comorbid conditions including a possible role for testosterone during development and shared genetic risk factors for gynaecological, gastrointestinal, pain, psychiatric, and inflammatory conditions. Understanding causal relationships between endometriosis and related conditions will aid clinical management and more personalized treatments. WIDER IMPLICATIONS: Genetic studies provide novel insights into endometriosis pathogenesis and associations with related comorbid conditions. Genetic factors modifying gene regulation and disease risk likely act in specific cell types, and access to datasets from genetically informed cell-based models, single-cell and spatial omics data are needed to accelerate progress. Future studies should address critical questions of heterogeneity and disease subtypes, expand the search for genetic risk factors to non-European populations, evaluate the role of rare and structural variants, and better integrate data from functional, genomics, genetics, and clinical studies to reduce diagnostic delay, develop novel treatment strategies, and translate discoveries into personalized management strategies for affected individuals. REGISTRATION NUMBER: N/A.

comorbid conditions↗
PubMed1991

Identification and characterization of a prolactin-like polypeptide synthesized by mitogen-stimulated murine lymphocytes.

Previously, we have reported that concanavalin A (Con A)-stimulated murine splenocytes synthesize and secrete into the medium a substance with prolactin (PRL)-like properties. Western blot analysis of the culture medium of Con A-stimulated murine splenocytes identified a PRL-like polypeptide (Ly-PLP) with an apparent molecular weight (Mr) of 46 kd. Rabbit anti-rat PRL antibody (S-9, NIDDK) was used for immunostaining. Specificity was proved by the absence of a band in properly preabsorbed primary and secondary antibodies. Electroeluted Ly-PLP enhanced the mitogenic response of lymphocytes to Con A. In situ hybridization analysis of dispersed lymphocyte smears demonstrated the presence of an mRNA that hybridized with a rat PRL cDNA probe. The size of the mRNA species was 1.4 kb on Northern blot analysis. Two-dimensional peptide map analysis of pituitary PRL and Ly-PLP showed three peptides with identical migration characteristics. Western blot analysis of lymphocyte culture medium following Con-A-affinity column treatment provided evidence that the Ly-PLP was a non-glycoprotein. Therefore, we conclude that Ly-PLP represents a structural variant of pituitary-PRL (Pit-PRL), and provide evidence to strongly suggest that it is a novel lymphokine.

Animals↗
PubMed2026

Rapid derivation of cloning-competent cells from peripheral blood advances conservation biobanking.

Establishing viable cell lines from endangered species is essential for conservation, yet traditional fibroblast derivation from skin biopsies faces challenges including contamination risk and extended culture timelines. Here, we demonstrate that endothelial progenitor cells (EPCs) and pericytes isolated from peripheral blood represent robust alternatives to fibroblasts for biobanking. Compared to canid fibroblasts, canid blood-derived cells exhibit 2- to 3-fold faster doubling rates (15 to 20 h vs. ~35 h for fibroblasts) and reduced time to banked cell lines (1.5 to 2 wks vs. 3 to 4 wks for fibroblasts). Proteomic profiling of 32 canonical markers confirmed EPCs and pericytes represent distinct populations with lineage-specific molecular signatures. Optical genome mapping demonstrated equivalent genomic stability across cell types with no detectable structural variants or aneuploidies. Finally, interspecific somatic cell nuclear transfer (iSCNT) experiments confirmed both EPCs and pericytes generate viable canid embryos with efficiency meeting or exceeding fibroblasts. As a proof of concept for conservation cloning, iSCNT embryos made with gray wolf blood-derived cells had a 15% implantation rate following embryo transfer and resulted in six viable fetuses. These findings support integrating blood-derived cell banking into conservation programs, which enables opportunistic genetic preservation during standard management activities and expands options for genetic rescue through assisted reproductive technologies.

Animals↗
PubMed2004

Selection footprint in the FimH adhesin shows pathoadaptive niche differentiation in Escherichia coli.

Spread of biological species from primary into novel habitats leads to within-species adaptive niche differentiation and is commonly driven by acquisition of point mutations in individual genes that increase fitness in the alternative environment. However, finding footprints of adaptive niche differentiation in specific genes remains a challenge. Here we describe a novel method to analyze the footprint of pathogenicity-adaptive, or pathoadaptive, mutations in the Escherichia coli gene encoding FimH-the major, mannose-sensitive adhesin. Analysis of distribution of mutations across the nodes and branches of the FimH phylogenetic network shows (1) zonal separation of evolutionary primary structural variants of FimH and recently derived ones, (2) dramatic differences in the ratio of synonymous and nonsynonymous changes between nodes from different zones, (3) evidence for replacement hot-spots in the FimH protein, (4) differential zonal distribution of FimH variants from commensal and uropathogenic E. coli, and (5) pathoadaptive functional changes in FimH brought by the mutations. The selective footprint in fimH indicates that the pathoadaptive niche differentiation of E. coli is either in its initial stages or undergoing an evolutionary "source/sink" dynamic.

Adaptation, Biological↗
PubMed1991

Detection of an unusual distortion in A-tract DNA using KMnO4: effect of temperature and distamycin on the altered conformation.

The chemical probes potassium permanganate (KMnO4) and diethylpyrocarbonate (DEPC) can be used to study the conformational flexibility of short tracts of adenine (A-tracts) present in DNA. With these probes, we demonstrate that a novel distortion is induced in a 5 base pair A-tract at low temperature. Formation of this distorted A-tract structure, which occurs in a DNA fragment from the promoter region of the plasmid pBR322, is distinguished by a dramatic increase in the KMnO4 reactivity of the central thymines in this tract at 12 degrees C. This alteration occurs in the absence of any detectable rearrangement in the conformation of the adenines in the complementary strand. Induction of this low temperature A-tract structure is blocked by the minor groove binding drug distamycin. Hydroxyl radical footprinting of distamycin binding to the fragment containing the d(A)5 tract at 12 degrees C suggests that this drug has two different modes of binding to DNA in agreement with recent NMR data. These experiments show that short A-tracts are capable of forming more than one structural variant of B DNA in solution. The possible relationship between the intrinsic bending of DNA containing short phased A-tracts and the low temperature A-tract conformation is discussed.

Adenine↗
PubMed1991

Manipulation of the 'zinc cluster' region of transcriptional activator LEU3 by site-directed mutagenesis.

The transcriptional activator LEU3 of Saccharomyces cerevisiae belongs to a family of lower eukaryotic DNA binding proteins with a well-conserved DNA binding motif known as the Zn(II)2Cys6 binuclear cluster. We have constructed mutations in LEU3 that affect either one of the conserved cysteines (Cys47) or one of several amino acids located within a variable subregion of the DNA binding motif. LEU3 proteins with a mutation at Cys47 were very poor activators which could not be rescued by supplying Zn(II) to the growth medium. Mutations within the variable subregion were generally well-tolerated. Only two of seven mutations in this region generated poor activators, and both could be reactivated by Zn(II) supplements. Three of the other five mutations gave rise to activators that were better than wild type. One of these, His50Cys, exhibited a 1.5 fold increase in in vivo target gene activation and a notable increase in the affinity for target DNA. The properties of the His50Cys mutant are discussed in terms of a variant structure of the DNA binding motif. During the course of this work, evidence was obtained suggesting that only one of the two LEU3 protein-DNA complexes routinely seen actually activates transcription. The other (which may contain an additional protein factor) does not.

Amino Acid Sequence↗
PubMed2005

Facile FMR1 mRNA structure regulation by interruptions in CGG repeats.

RNA metabolism is a major contributor to the pathogenesis of clinical disorders associated with premutation size alleles of the fragile X mental retardation (FMR1) gene. Herein, we determined the structural properties of numerous FMR1 transcripts harboring different numbers of both CGG repeats and AGG interruptions. The stability of hairpins formed by uninterrupted repeat-containing transcripts increased with the lengthening of the repeat tract. Even a single AGG interruption in the repeated sequence dramatically changed the folding of the 5'UTR fragments, typically resulting in branched hairpin structures. Transcripts containing different lengths of CGG repeats, but sharing a common AGG pattern, adopted similar types of secondary structures. We postulate that interruption-dependent structure variants of the FMR1 mRNA contribute to the phenotype diversity, observed in premutation carriers.

5' Untranslated Regions↗
PubMed1990

DNA based diagnostic tests: recombinant DNA and cardiovascular disease risk factors.

Advances in molecular biology and medical biotechnology are continuously creating exciting possibilities for DNA based diagnostics. It is now possible by simple procedures to detect polymorphic DNA markers, structural variants and regulatory mutants of human genes, allowing detailed genotyping of patients. The innovative combination of immunoenzymatic techniques, monoclonal antibodies and recombinant tracer proteins, results in new DNA based tests for the determination of important biochemical parameters, in order to define more precisely the phenotype and hence assess the individual risk. The application of these technologies to the analysis of dyslipidemias, atherosclerosis and cardiovascular diseases may not only lead to a better understanding of the molecular and genetic basis of these pathologies, but also to their early recognition and better management.

Base Sequence↗
PubMed2000

Gestational changes in uterine L-type calcium channel function and expression in guinea pig.

Pregnancy can influence both the resting membrane potential and the ion channel composition of the uterine myometrium. Calcium flux is essential for excitation-contraction coupling in pregnant uterus. The uterine L-type calcium channel is an important component in mediating calcium flux and is purported to play a role in parturition. This study was undertaken to characterize gestational changes in 1) the uterine contractile response to the L-type calcium channel agonist, Bay K 8644; 2) the mRNA expression of channel subunits by semiquantitative reverse transcriptase-polymerase chain reaction; and 3) estimate channel protein levels by measuring (3)H-isradipine binding at the dihydropyridine binding site of the alpha(1c) subunit utilizing saturation binding methods. Sensitivity to Bay K 8644 increases beginning at 0.8 of gestation and persists through term. The change in sensitivity is coincident with an increased mRNA expression of the alpha(1c) and beta(2) subunits but with the least detectable amounts of isradipine binding. The expressed alpha(1c) transcript represents a novel structural variant with a 118-amino acid deletion in the III-IV linker and repeats IVS1-S3 of the protein sequence. The guinea pig uterine L-type calcium channel activity is highly regulated through gestation, but the regulation of mRNA expression may be different from regulation of protein levels, estimated by isradipine binding. The up-regulation of function, alpha(1c) subunit mRNA expression, and isradipine binding at term gestation are consistent with a role for this ion channel in parturition.

3-Pyridinecarboxylic acid, 1,4-dihydro-2,6-dimethy↗
PubMed1990

Complex and diversified regulatory programs control the expression of vertebrate collagen genes.

The collagens represent a family of structurally related but genetically distinct proteins whose function is essential to maintaining the integrity of vertebrate organs. In addition to their supportive roles, collagens influence a variety of developmental programs and physiological processes. Transcription of collagen genes is controlled by a series of complex interactions between cis-acting regulatory elements and trans-acting nuclear factors that have positive or negative effects on gene expression. Collagen synthesis relies on the timely utilization of diversified regulatory programs that employ tissue and cell-type specific promoters and enhancers. Some of these programs lead to the production of structurally variant chains in different tissues, while others shut down synthesis of a specific collagen type during cell differentiation. Still others control collagen expression in distinct cell lineages. The number, complexity, and variety of the mechanisms leading to the diversified expression of the collagen genes illustrate the unique contribution of this family of proteins to multicellular organogenesis.

Animals↗
PubMed1985

Lowered prealbumin levels in patients with familial amyloid polyneuropathy (FAP) and their non-affected but at risk relatives.

Amyloid fibrils in familial amyloid polyneuropathy, the familial (AF) form of systemic amyloidosis, are composed of the monomeric unit (14,000 MW) of prealbumin molecules. By radioimmunoassay, the serum level of prealbumin was measured in 25 patients from 12 different kinships with this dominantly inherited form of amyloidosis and 56 unaffected, but at risk, relatives from two of the kinships. Results were compared to prealbumin levels in normal individuals and patients with primary (AL) and secondary (AA) forms of systemic amyloidosis. Significantly lowered prealbumin levels were found in the AF patients (149.2 micrograms/ml) and their at risk relatives (169.0 micrograms/ml) when compared to normal individuals (232.9 micrograms/ml), AL patients (221.9 micrograms/ml) and AA patients (211.7 micrograms/ml). No abnormality was found in levels of retinol binding protein (RBP), which is carried by prealbumin, in the serum of either the AF patients or their relatives. The depressed prealbumin levels may indicate a structural variant molecular form, an extra hepatic synthesis or an abnormality in catabolism of this protein that is present prior to the clinical or histopathologic onset of the AF disease.

Amyloidosis↗