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At least 19 recordsLinked to original sources
PubMed1989

A general system of resistance to malaria infection in Anopheles gambiae controlled by two main genetic loci.

Genetic analysis of a system of Plasmodium refractoriness in Anopheles gambia suggests that the joint action of 2 unlinked genetic loci substantially controls expression of the susceptible and refractory phenotypes. One genetic component, here named Pif-B (for Plasmodium infectivity factor), is closely linked or identical to a polymorphic autosomal esterase locus which can be visualized by gel electrophoresis. This locus exerts the major controlling effect on susceptibility to Plasmodium cynomolgi B. The other genetic component is independent of esterase and exerts major control over refractoriness to the P. cynomolgi Ceylon strain parasite. Genetic assortment of the esterase-independent component suggests that it is controlled by 1 principal locus, here named Pif-C. The 2 genetic components of Plasmodium refractoriness appear to contribute to the same phenotype through physiologically independent means.

Animals↗
PubMed2025

Endogenous fine-mapping and prioritization of functional regulatory elements in complex genetic loci.

Most genetic loci linked to polygenic traits are in non-coding regions, with complex regulation and linkage disequilibrium (LD), complicating causal variant and gene prioritization. We used multiplexed single-cell CRISPR interference and activation perturbations to investigate cis-regulatory element (CRE) and gene expression relationships within tight LD in the endogenous chromatin context. We demonstrated the prevalence of multiple causality in perfect LD (pLD) for independent expression quantitative trait loci (eQTLs) and uncovered fine-grained genetic effects on gene expression within pLD, which are difficult to decipher using traditional eQTL fine-mapping or existing computational methods. We found that over one-third of the causal CREs lack classical epigenetic markers prior to perturbation, and we functionally validated one of these hidden regulatory mechanisms. Leveraging Multiome single-cell epigenetic and sequence perturbations, we highlighted the regulatory plasticity of the human genome. Our study will guide the exploration of missing causal mechanisms underlying molecular trait regulation and disease development.

Humans↗
PubMed2005

Integrative genetic analysis of transcription modules: towards filling the gap between genetic loci and inherited traits.

Genetic loci that regulate inherited traits are routinely identified using quantitative trait locus (QTL) mapping methods. However, the genotype-phenotype associations do not provide information on the gene expression program through which the genetic loci regulate the traits. Transcription modules are 'self-consistent regulatory units' and are closely related to the modular components of gene regulatory network [Ihmels, J., Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y. and Barkai, N. (2002) Revealing modular organization in the yeast transcriptional network. Nat. Genet., 31, 370-377; Segal, E., Shapira, M., Regev, A., Pe'er, D., Botstein, D., Koller, D. and Friedman, N. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet., 34, 166-176]. We used genome-wide genotype and gene expression data of a genetic reference population that consists of mice of 32 recombinant inbred strains to identify the transcription modules and the genetic loci regulating them. Twenty-nine transcription modules defined by genetic variations were identified. Statistically significant associations between the transcription modules and 18 classical physiological and behavioral traits were found. Genome-wide interval mapping showed that major QTLs regulating the transcription modules are often co-localized with the QTLs regulating the associated classical traits. The association and the possible co-regulation of the classical trait and transcription module indicate that the transcription module may be involved in the gene pathways connecting the QTL and the classical trait. Our results show that a transcription module may associate with multiple seemingly unrelated classical traits and a classical trait may associate with different modules. Literature mining results provided strong independent evidences for the relations among genes of the transcription modules, genes in the regions of the QTLs regulating the transcription modules and the keywords representing the classical traits.

Animals↗
PubMed1993

The transcriptional organization of the Bacillus subtilis 168 chromosome region between the spoVAF and serA genetic loci.

The genetic organization of the spoVAF-serA area of the Bacillus subtilis chromosome and its putative transcription map have been derived from analysis of the nucleotide sequence. In order to confirm this transcription map as regards size of transcripts and to determine growth conditions for their appearance, we undertook Northern hybridization analysis of total RNA from vegetatively growing and sporulating cells. Twenty-three distinct transcripts were thus identified, 14 of which were predicted from sequence analysis and nine of which were not predicted. Eight of the latter are homologous to open reading frames identified by sequence analysis but were not expected, since no obvious promoter or terminator was found in the sequence. The last unexpected transcript does not correspond to an ORF and might identify a novel gene. Three predicted transcripts were not detected. The transcripts were classified in four groups as (i) constitutive, (ii) regulated by nutritional depletion, (iii) specific for sporulation, and (iv) possibly regulated temporally. These studies demonstrate that systematic Northern analysis of a bacterial chromosome region is a useful complement to sequence analysis.

Bacillus subtilis↗
PubMed2026

Mining of important genetic loci and evaluation of genetic effects for growth traits in Baicheng You Chicken.

The Baicheng You Chicken is a precious indigenous breed in Xinjiang, China, prized for its strong disease and stress resistance and superior meat quality. However, the lack of scientific breeding and conservation has led to poor production performance, particularly in growth traits. In this study, we collected phenotypic and whole-genome resequencing data from 1,535 18-week-old Baicheng You Chickens (180 males and 1,355 females). After stringent quality control (SNP call rate > 95%, minor allele frequency > 1%), we constructed the breed's first comprehensive SNP-based genome-wide variation map, which comprised 2,020,743 high-quality SNPs across the genome. The filtered SNPs had high mapping quality (99.73% mapped to the bGalGal1.mat.broiler.GRCg7b reference genome, Q30 = 93.26%) and a reasonable Ti/Tv ratio (2.596), guaranteeing the reliability of subsequent analyses. We estimated genetic effects (SNP-based heritability and phenotypic variance explained (PVE) by individual loci) via the restricted maximum likelihood (REML) method, and performed a genome-wide association study (GWAS) using a mixed linear model (MLM) - with sex as a fixed effect and principal components to correct for population stratification - to identify significant loci and their effect sizes (Beta). All eight growth traits showed moderate to high heritability: body weight (BW) had the highest heritability (0.86±0.11), while chest width (CW, 0.41±0.08) and body slanting length (BSL, 0.43±0.09) were the lowest; keel length (KL), chest girth (CG), pelvic width (PW), chest depth (CD) and shank length (SL) had heritabilities of 0.50±0.09, 0.46±0.09, 0.54±0.09, 0.67±0.10 and 0.74±0.10, respectively. GWAS identified 145 significant SNPs, with a maximum Beta value of 0.39 and PVE ranging from 1.25% to 6.25%. We annotated 22 candidate genes, with TAPT1, IGF2BP1, ADGRB3, LDB2, NCAPG and LCORL as key candidates. These quantifiable genetic markers and effect estimates provide direct targets for marker-assisted selection (MAS) and valuable resources for future genomic selection (GS) programs, offering a practical approach to improve the breed's slow growth while preserving its unique meat quality.

Baicheng You Chicken↗
PubMed2001

Use of radiation hybrid panels to map genetic loci.

The mapping of genetic loci within organisms has been accelerated by the advent of Radiation Hybrid (RH) panels. These panels are available for humans and non-humans including mice, baboon, rat, and canine. This article contains a general protocol for the use of the Genebridge 4 whole genome RH panel to map a human locus. This protocol may also be adjusted to suit the other RH panels currently available.

Chromosome Mapping↗
PubMed2024

Polycystic Ovary Syndrome Physiologic Pathways Implicated Through Clustering of Genetic Loci.

CONTEXT: Polycystic ovary syndrome (PCOS) is a heterogeneous disorder, with disease loci identified from genome-wide association studies (GWAS) having largely unknown relationships to disease pathogenesis. OBJECTIVE: This work aimed to group PCOS GWAS loci into genetic clusters associated with disease pathophysiology. METHODS: Cluster analysis was performed for 60 PCOS-associated genetic variants and 49 traits using GWAS summary statistics. Cluster-specific PCOS partitioned polygenic scores (pPS) were generated and tested for association with clinical phenotypes in the Mass General Brigham Biobank (MGBB, N = 62 252). Associations with clinical outcomes (type 2 diabetes [T2D], coronary artery disease [CAD], and female reproductive traits) were assessed using both GWAS-based pPS (DIAMANTE, N = 898,130, CARDIOGRAM/UKBB, N = 547 261) and individual-level pPS in MGBB. RESULTS: Four PCOS genetic clusters were identified with top loci indicated as following: (i) cluster 1/obesity/insulin resistance (FTO); (ii) cluster 2/hormonal/menstrual cycle changes (FSHB); (iii) cluster 3/blood markers/inflammation (ATXN2/SH2B3); (iv) cluster 4/metabolic changes (MAF, SLC38A11). Cluster pPS were associated with distinct clinical traits: Cluster 1 with increased body mass index (P = 6.6 × 10-29); cluster 2 with increased age of menarche (P = 1.5 × 10-4); cluster 3 with multiple decreased blood markers, including mean platelet volume (P = 3.1 ×10-5); and cluster 4 with increased alkaline phosphatase (P = .007). PCOS genetic clusters GWAS-pPSs were also associated with disease outcomes: cluster 1 pPS with increased T2D (odds ratio [OR] 1.07; P = 7.3 × 10-50), with replication in MGBB all participants (OR 1.09, P = 2.7 × 10-7) and females only (OR 1.11, 4.8 × 10-5). CONCLUSION: Distinct genetic backgrounds in individuals with PCOS may underlie clinical heterogeneity and disease outcomes.

Humans↗
PubMed1982

Mutagenic responses of five independent genetic loci in CHO cells to a variety of mutagens. Development and characteristics of a mutagen screening system based on selection for multiple drug-resistant markers.

With the aim of developing a sensitive mutagen screening system, the responses of 15 different chemical mutagens at 5 independent genetic loci in Chinese hamster ovary (CHO) cells have been determined. The genetic markers which have been employed include resistance to thioguanine (Thgr), ouabain (OuaR), the protein synthesis inhibitor emetine (Emtr), the polyamine synthesis inhibitor methylglyoxal bisguanylhydrazone (Mbgr) and the nucleoside analog 5,6-dichlororibofuranosyl benzimidazole (DrbR). The optimal selection conditions for all of these genetic markers in CHO cells have been described. The chemicals whose response was investigated in these studies include direct-acting alkylating agents (ethyl methane-sulfonate, methyl methanesulfonate, beta-propiolactone, ethyleneimine, N-nitrosomethylurea and 4-nitroquinoline-N-oxide), DNA intercalating and cross-linking agents (ICR-170, acridine orange, ethidium bromide, mitomycin C and actinomycin D), polycyclic hydrocarbons (benzo[a]pyrene (B(a)P) and 7,12-dimethylbenz[a]anthracene (DMBA)) and aromatic amines (benzidine and beta-naphthylamine). Simultaneous examination of the response of the set of genetic markers to these chemicals revealed that although all of these chemicals caused a dose-dependent increase in the frequency of mutations at many of the above genetic loci, the magnitude of the mutagenic response at different genetic loci varied greatly depending upon the chemical. Of the genetic loci examined, no one single locus showed higher response to all of the above chemicals, instead, depending upon the chemical, specific loci were found to be more responsive than others. The polycyclic hydrocarbons and aromatic amines were weakly mutagenic in this system at several genetic loci even without any exogenous microsomal activation, although in the presence of a rat liver S9 fraction similar toxic and mutagenic effects of B(a)P and DMBA were observed at 5-20-fold lower concentrations. These results indicate that CHO cells may possess significant capacity for the metabolic activation of many procarcinogens, and also underscore the merits of measuring the mutagenic response at multiple genetic loci in mutagen screening studies.

Animals↗
PubMed2006

Mouse bone marrow and peripheral blood erythroid cell counts are regulated by different autosomal genetic loci.

Erythropoiesis is under fine control and genetic loci that affect it are likely to be important in a range of conditions. To assess the relative contributions of different genetic loci to parameters of erythropoiesis, we have measured RBC counts in the peripheral circulation and committed erythroid cells (RBC and small normoblasts) in the bone marrow in a cohort of (CBA/H x C57BL/6) F2 mice to map quantitative trait loci (QTL). Candidate genes were assessed using bioinformatics and DNA sequencing. Different autosomal loci affect bone marrow (chromosomes 5, 11 and 19) and peripheral blood (chromosome 4) erythroid cell counts but there may be a common chromosome X locus. Spleen weight QTL were found on chromosomes 3, 15 and 17. Surprisingly, erythropoietin (Epo) is the best candidate quantitative trait gene (QTG) in the chromosome 5 locus that affects bone marrow but not peripheral blood erythroid cell counts. Epo gene expression is known to be genetically regulated in mice, but our data suggest a tissue-specific role for epo in mouse erythropoiesis that is also genetically determined. The identity of the other QTG will be important both to further knowledge of the control of erythropoiesis and as potential modifier genes for haematological disorders.

Animals↗
PubMed1982

Mutagenic response to ultraviolet light and X-rays at five independent genetic loci in Chinese hamster ovary cells.

The mutagenic response to ultraviolet light and X-irradiation at a number of well characterized independent genetic loci, viz those conferring resistance to 6-thioguanine, ouabain, emetine, methylglyoxal (bis) guanylhydrazone (MGBG), and 5, 6-dichlororibofuranosyl benzimidazole (DRB), has been determined. Upon exposure of cells to UV light in the range of 70 to 180 ergs/mm2, the frequency of mutants at all of the above genetic loci increased in a linear dose-dependent manner. However, some genetic-locus-specific differences in response to UV light were observed in these studies. In contrast to UV light, exposure of cells to X-rays caused a linear dose-dependent increase in the frequency of mutants at only the thioguanine-resistant (Thgr) locus, which affects the purine salvage pathway enzyme hypoxanthine-guanine phosphoribosyltransferase, that is not essential for growth under these conditions. The other genetic loci that affect essential cellular functions (and hence should detect only specific base substitution types of mutations), however, showed no increase in the frequencies of mutants upon X-irradiation of cells. These results are in accordance with the nature of the genetic lesions which are caused by these agents and the properties of these genetic markers.

Animals↗
PubMed1993

A 1.5-megabase yeast artificial chromosome contig from human chromosome 10q11.2 connecting three genetic loci (RET, D10S94, and D10S102) closely linked to the MEN2A locus.

The genetic loci RET, D10S94, and D10S102 from human chromosome 10q11.2 are very closely linked to a locus responsible for the multiple endocrine neoplasia type 2 (MEN2A and MEN2B) and medullary thyroid carcinoma (MTC1) familial cancer syndromes. We have constructed a 1.5-megabase contig consisting of six genomic yeast artificial chromosome clones which include these loci and define their physical order. A critical crossover event has been identified within the map interval; this event places the MEN2A locus centromeric to D10S102 and defines the orientation of the physical map on the chromosome. The orientation of the contig and order of the markers are centromere-RET-D10S94-D10S102-telomere. In addition, a microsatellite repeat polymorphism with a heterozygosity of 71% at the RET locus and a restriction fragment length polymorphism with a heterozygosity of 42% detected by a lambda clone from the D10S94 locus have been developed for high-resolution genetic linkage mapping and predictive diagnostic testing. These data place three important markers on a contiguous physical map, narrow the MEN2 disease locus interval, and provide a framework for further candidate gene identification efforts. Placement of these genetic loci along a clone-based map and continued expansion of the contig will also facilitate efforts to determine the relationship of physical to genetic distance near the centromeres of human chromosomes.

Base Sequence↗
PubMed1983

Mutagenic responses of thirteen anticancer drugs on mutation induction at multiple genetic loci and on sister chromatid exchanges in Chinese hamster ovary cells.

The mutagenic responses of 13 antineoplastic drugs, namely, chlorambucil, busulfan, lomustine, dacarbazine, Adriamycin, daunomycin, bleomycin, VM-26, VP16-213, ellipticine, actinomycin D, mitomycin C, and cis-diamminedichloroplatinum(II) have been determined in two different assay systems in Chinese hamster ovary cells which measure mutation induction at multiple genetic loci and the frequencies of sister chromatid exchanges. The five genetic loci whose responses have been measured include those conferring resistance to 6-thioguanine (Thgr or TGr), ouabain, emetine, methylglyoxal bis(guanylhydrazone), and 5,6-dichlororibofuranosylbenzimidazole; of these, only the Thgr marker affects a function (hypoxanthine-guanine phosphoribosyltransferase, hgprt locus) which is not essential for cellular growth. All of these drugs showed a dose-dependent increase in mutation frequency at the hgprt locus, but their responses at other genetic loci differed greatly and showed marked specificity for different chemical classes of the drugs. The observed locus-specific differences in response to these drugs suggest that they may differ in terms of their accessibility or affinity to different chromosomal regions. All of these drugs also led to a significant increase in the frequency of sister chromatid exchanges, and a very good correlation was observed between the activity of these drugs in the sister chromatid exchange assay and the mutagenic response of the hgprt locus. Of the drugs which were examined, VM-26, VP16-213, chlorambucil, mitomycin C, and cis-diamminedichloroplatinum(II) showed a particularly strong response in both of these assay systems. In terms of the minimum concentration which gave a mutagenic response, the drugs differed from each other by a factor of about 100,000, with actinomycin D, VM-26, and daunomycin being mutagenic in the range of 3 x 10(-8) to 1 x 10(-7) M, whereas dacarbazine produced a weak mutagenic response only at about 2 x 10(-3) M.

Animals↗
PubMedDate not supplied

New genetic loci in neuroblastoma.

Neuroblastoma has been associated genetically with amplification of the MYCN gene and with alteration of the short arm of chromosome 1 (1p). In pursuit of determining the spectrum of genetic loci damaged recurrently in neuroblastoma cells we have recently encountered two additional types of genomic abnormalities: i.) duplication of the MYCN gene on chromosome 2p24; and ii.) amplification of the gene MDM2. These alterations extend the spectrum of genetic lesions in neuroblastoma cells, although their incidence in primary tumor tissues has not been determined as yet.

Child↗
PubMed2000

Topography of genetic loci in tissue samples: towards new diagnostic tool using interphase FISH and high-resolution image analysis techniques.

Using single and dual colour fluorescence in situ hybridisation (FISH) combined with image analysis techniques the topographic characteristics of genes and centromeres in nuclei of human colon tissue cells were investigated. The distributions of distances from the centre-of-nucleus to genes (centromeres) and from genes to genes (centromeres to centromeres) were studied in normal colon tissue cells found in the neighbourhood of tumour samples, in tumour cell line HT-29 and in promyelocytic HL-60 cell line for comparison. Our results show that the topography of genetic loci determined in 3D-fixed cell tissue corresponds to that obtained for 2D-fixed cells separated from the tissue. The distributions of the centre-of-nucleus to gene (centromere) distances and gene to gene (centromere to centromere) distances and their average values are different for various genetic loci but similar for normal colon tissue cells, HT-29 colon tumour cell line and HL-60 promyelocytic cell line. It suggests that the arrangement of genetic loci in cell nucleus is conserved in different types of human cells. The investigations of trisomic loci in HT-29 cells revealed that the location of the third genetic element is not different from the location of two homologues in diploid cells. We have shown that the topographic parameters used in our experiments for different genetic elements are not tissue or tumour specific. In order to validate high-resolution cytometry for oncology, further investigations should include more precise parameters reflecting the state of chromatin in the neighbourhood of critical oncogenes or tumour suppresser genes.

Cell Nucleus↗
PubMed1986

X-rays mutate human lymphoblast cells at genetic loci that should respond only to point mutagens.

We have demonstrated that X-rays induce mutations at 4 of 5 genetic loci. 2 of these loci, which code for a mRNA synthesis factor (resistance to 5,6-dichlororibofuranosylbenzimidazole) and tubulin (resistance to podophyllotoxin), are "small-marker" loci, in that they theoretically respond only to mutations which eliminate a toxin-binding site while leaving the major function of the protein intact. Thus mutations induced by X-rays in these two loci are most likely due to base-pair substitution-type alterations. X-Rays did not induce mutations in the Na+/K+ ATPase (resistance to ouabain), another small-marker locus. Two other loci, hypoxanthine guanine phosphoribosyl transferase (resistance to 6-thioguanine) and thymidine kinase (resistance to trifluorothymidine), are "whole-gene" targets in that they theoretically respond to a wide variety of mutagenic changes. X-Rays induced dose-dependent increases in mutant fraction at both of these loci. Ethyl methanesulfonate (EMS), an agent thought to produce mutations primarily through a base-pair substitution mechanism, induced mutations at all genetic loci tested. The pattern of mutations at the small-marker loci induced by EMS was different than that induced by X-rays, suggesting that the specificities of the mutagens and/or of the loci are different.

Dichlororibofuranosylbenzimidazole↗
PubMed2003

[A search for genetic loci responsible for emotional stress-induced arterial hypertension in the ISIAH rats].

Hypertension is a widespread human disease caused by a complex interaction of a series of the genetic factors with both each other and the environmental conditions. In this study we aimed at determining the candidate genetic loci responsible for hypertension in the ISIAH rats and studying the dynamics of the relevant genetic and physiological mechanisms in rat ontogeny. The candidate genetic loci were identified from association of the microsatellite markers linked to these loci with arterial hypertension in rat F2 hybrids exposed to stress. Two populations of F2 hybrids of different age (3-4 and 6 months) were obtained by crossing hypertensive ISIAH and normotensive WAG rats. We present the results of cosegregation analysis for the following loci: the gene for the Na+, K(+)-ATPase alpha 1 subunit isoform (Atp1a1), the endothelin-2 gene (Edn2), the low affinity nerve growth factor receptor gene (Lngfr), and a region of chromosome 10 marked with the D10Rat58 microsatellile located 3 cM away of the aldolase C gene (AldC). The results obtained allowed us to localize the genes responsible for the stress-induced arterial hypertension in the ISIAH rats to the Atp1a1 locus (P < 0.05), chromosome 2 and to the Lngfr gene locus (P < 0.05), chromosome 10. The association of hypertensive status with the Lngfr gene was found only in young ISIAH rats whereas in adult rats of this line, hypertension was associated with the Atp1a1 locus.

Age Factors↗
PubMed2005

Possible genomic imprinting of three human obesity-related genetic loci.

To detect potentially imprinted, obesity-related genetic loci, we performed genomewide parent-of-origin linkage analyses under an allele-sharing model for discrete traits and under a family regression model for obesity-related quantitative traits, using a European American sample of 1,297 individuals from 260 families, with 391 microsatellite markers. We also used two smaller, independent samples for replication (a sample of 370 German individuals from 89 families and a sample of 277 African American individuals from 52 families). For discrete-trait analysis, we found evidence for a maternal effect in chromosome region 10p12 across the three samples, with LOD scores of 5.69 (single-point) and 4.52 (multipoint) for the pooled sample. For quantitative-trait analysis, we found the strongest evidence for a maternal effect (single-point LOD of 2.85; multipoint LOD of 4.01 for body mass index [BMI] and 3.69 for waist circumference) in region 12q24 and for a paternal effect (single-point LOD of 4.79; multipoint LOD of 3.72 for BMI) in region 13q32, in the European American sample. The results suggest that parent-of-origin effects, perhaps including genomic imprinting, may play a role in human obesity.

Adipose Tissue↗
PubMed1980

Control of natural resistance to Salmonella typhimurium and Leishmania donovani in mice by closely linked but distinct genetic loci.

Inbred strains of mice vary in their sensitivity to infection with both Salmonella typhimurium and Leishmania donovani. In both cases, this differential susceptibility is genetically controlled. Resistance to the intracellular parasite L. donovani is determined by a single locus on chromosome 1, designated Lsh (ref. 4). The primary regulator of resistance to S. typhimurium is a single, dominant autosomal gene, named Ity (for immunity to typhimurium), and it has also been recently mapped to chromosome 1 (ref. 6). In addition, two other genetic loci regulate resistance to S. typhimurium in mice. These genes, Lpsd and xid, are mutant alleles that render C3H/HeJ and CBA/N mice, respectively, salmonella susceptible. Both Bradley and his colleagues, and Plant and Glynn, noted similar patterns of resistance or susceptibility of inbred strains of mice to L. donovani and S. typhimurium, and therefore suggested that Lsh and Ity might be the same gene. Mapping of both genes to the same region of chromosome 1 supported this hypothesis but no linkage studies have been used to test it. Since recombinant inbred (RI) mouse strains are, in effect, permanent segregant populations, they are ideal for determing linkage between resistance genes to two different pathogens. Therefore, we determined the S. typhimurium susceptibility of five sets of RI mouse strains that had been previously typed for Lsh and conclude that Lsh and Ity are closely linked but distinct genetic loci.

Animals↗