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Fa Yi Xue Za Zhi Jun 2023To study the detection efficiency of trio full sibling with another known full sibling reference added under different number of autosomal STR typing systems.
OBJECTIVES
To study the detection efficiency of trio full sibling with another known full sibling reference added under different number of autosomal STR typing systems.
METHODS
Based on 43 detection systems consisting of 13 to 55 representative autosomal STR loci, 10 000 true families (full sibling group) and 10 000 false families (unrelated individual group) were randomly simulated. The full sibling index (FSI) was calculated based on the method of family reconstruction. The cumulative sibling relationship index (CFSI) of 0.000 1 and 10 000 were used as the evaluation thresholds, and the detection efficiency parameters were calculated and compared with the identification of the duo full sibling testing.
RESULTS
With the increasing number of STR loci, the error rate and inability of judgement rate gradually decreased; the sensitivity, specificity, correct rate of judgment and other parameters gradually increased, and the system efficiency gradually improved. Under the same detection system, trio full sibling testing showed higher sensitivity, specificity, system efficiency and lower inability of judgement rate compared with duo full sibling testing. When the system efficiency was higher than 0.85 and inability of judgement rate was less than 0.01%, at least 20 STRs should be detected for trio full sibling testing, which was less than 29 STRs required by duo full sibling testing.
CONCLUSIONS
The detection efficiency of trio full sibling testing is superior to that of duo full sibling testing with the same detection system, which is an effective identification scheme for laboratories with inadequate detection systems or for materials with limited conditions.
Topics: Humans; Siblings; Microsatellite Repeats; DNA Fingerprinting; Gene Frequency
PubMed: 37517012
DOI: 10.12116/j.issn.1004-5619.2023.530203 -
Proceedings of the National Academy of... Apr 2022Admixture appears increasingly ubiquitous in the evolutionary history of various taxa, including humans. Such gene flow likely also occurred among our closest living...
Admixture appears increasingly ubiquitous in the evolutionary history of various taxa, including humans. Such gene flow likely also occurred among our closest living relatives: bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). However, our understanding of their evolutionary history has been limited by studies that do not consider all Pan lineages or do not analyze all lineages simultaneously, resulting in conflicting demographic models. Here, we investigate this gap in knowledge using nucleotide site patterns calculated from whole-genome sequences from the autosomes of 71 bonobos and chimpanzees, representing all five extant Pan lineages. We estimated demographic parameters and compared all previously proposed demographic models for this clade. We further considered sex bias in Pan evolutionary history by analyzing the site patterns from the X chromosome. We show that 1) 21% of autosomal DNA in eastern chimpanzees derives from western chimpanzee introgression and that 2) all four chimpanzee lineages share a common ancestor about 987,000 y ago, much earlier than previous estimates. In addition, we suggest that 3) there was male reproductive skew throughout Pan evolutionary history and find evidence of 4) male-biased dispersal from western to eastern chimpanzees. Collectively, these results offer insight into bonobo and chimpanzee evolutionary history and suggest considerable differences between current and historic chimpanzee biogeography.
Topics: Animals; Biological Evolution; Female; Genome; Male; Nucleotides; Pan paniscus; Pan troglodytes
PubMed: 35452306
DOI: 10.1073/pnas.2200858119 -
Zhongguo Xue Xi Chong Bing Fang Zhi Za... May 2021To investigate the karyotypes and C bands of in China, so as to understand its chromosome number, morphology and C-band staining of .
OBJECTIVE
To investigate the karyotypes and C bands of in China, so as to understand its chromosome number, morphology and C-band staining of .
METHODS
The testis specimens were sampled from male collected from Shunde City, Guangdong Province, prepared into slides of metaphase chromosomes and subjected to Giemsa staining and C-band staining. The morphology of metaphase chromosomes and the location of heterochromatin were observed using microscopy, and the long arm and short arm of each chromosome and total chromosome length were recorded to analyze the karyotypes and C bands of .
RESULTS
The male presented a chromosome number of 2 = 25, including 22 autosomes and 3 sex chromosomes. The relative length of chromosomes ranged from 3.59% to 12.76%, the arm ratio was 1.06 to 1.24, and the centromere index was 44.76% to 48.47%. All chromosomes were metacentric chromosomes and the karyotype formula was 2 = 22 metacentric + XXY, and the C bands varied on different chromosomes. No heterochromatin was found in the X chromosome, and the overall staining appeared pale, while heterochromatin was detected in all regions of the Y chromosome, and the overall staining appeared dark. In addition, heterochromatin was present in both ends of the autosome.
CONCLUSIONS
The male presents a chromosome number of 2 = 25 in China, and the karyotype formula is 2 = 22 metacentric + XXY. C-banding shows dark staining of the Y chromosome, pale staining of the X chromosome, and dark staining of both ends of the autosome. Our data may provide insights into the investigation on the origin, evolution and gene mapping of in China.
Topics: Animals; China; Heterochromatin; Karyotype; Karyotyping; Male; Triatoma
PubMed: 34286533
DOI: 10.16250/j.32.1374.2021036 -
Journal of Translational Medicine Nov 2022Previous studies on European (EUR) samples have obtained inconsistent results regarding the genetic correlation between type 2 diabetes mellitus (T2DM) and Schizophrenia...
BACKGROUND
Previous studies on European (EUR) samples have obtained inconsistent results regarding the genetic correlation between type 2 diabetes mellitus (T2DM) and Schizophrenia (SCZ). A large-scale trans-ethnic genetic analysis may provide additional evidence with enhanced power.
OBJECTIVE
We aimed to explore the genetic basis for both T2DM and SCZ based on large-scale genetic analyses of genome-wide association study (GWAS) data from both East Asian (EAS) and EUR subjects.
METHODS
A range of complementary approaches were employed to cross-validate the genetic correlation between T2DM and SCZ at the whole genome, autosomes (linkage disequilibrium score regression, LDSC), loci (Heritability Estimation from Summary Statistics, HESS), and causal variants (MiXeR and Mendelian randomization, MR) levels. Then, genome-wide and transcriptome-wide cross-trait/ethnic meta-analyses were performed separately to explore the effective shared organs, cells and molecular pathways.
RESULTS
A weak genome-wide negative genetic correlation between SCZ and T2DM was found for the EUR (r = - 0.098, P = 0.009) and EAS (r =- 0.053 and P = 0.032) populations, which showed no significant difference between the EUR and EAS populations (P = 0.22). After Bonferroni correction, the r remained significant only in the EUR population. Similar results were obtained from analyses at the levels of autosomes, loci and causal variants. 25 independent variants were firstly identified as being responsible for both SCZ and T2DM. The variants associated with the two disorders were significantly correlated to the gene expression profiles in the brain (P = 1.1E-9) and pituitary gland (P = 1.9E-6). Then, 61 protein-coding and non-coding genes were identified as effective genes in the pituitary gland (P < 9.23E-6) and were enriched in metabolic pathways related to glutathione mediated arsenate detoxification and to D-myo-inositol-trisphosphate.
CONCLUSION
Here, we show that a negative genetic correlation exists between SCZ and T2DM at the whole genome, autosome, locus and causal variant levels. We identify pituitary gland as a common effective organ for both diseases, in which non-protein-coding effective genes, such as lncRNAs, may be responsible for the negative genetic correlation. This highlights the importance of molecular metabolism and neuroendocrine modulation in the pituitary gland, which may be responsible for the initiation of T2DM in SCZ patients.
Topics: Humans; Schizophrenia; Genome-Wide Association Study; Diabetes Mellitus, Type 2; Ethnicity; Pituitary Gland; Polymorphism, Single Nucleotide; Genetic Predisposition to Disease
PubMed: 36329495
DOI: 10.1186/s12967-022-03704-0 -
Seminars in Cell & Developmental Biology Aug 2016Genes are generally expressed from their two alleles, except in some particular cases such as random inactivation of one of the two X chromosomes in female mammals or... (Review)
Review
Genes are generally expressed from their two alleles, except in some particular cases such as random inactivation of one of the two X chromosomes in female mammals or imprinted genes which are expressed only from the maternal or the paternal allele. A lesser-known phenomenon is random monoallelic expression (RME) of autosomal genes, where genes can be stably expressed in a monoallelic manner, from either one of the parental alleles. Studies on autosomal RME face several challenges. First, RME that is based on epigenetic mechanisms has to be distinguished from biased expression of one allele caused by a DNA sequence polymorphism in a regulatory element. Second, RME should not be confused with transient monoallelic expression often observed in single cell analyses, and that often corresponds to dynamic bursting of expression. Thanks to analyses on clonal cell populations, the existence of RME in cultured cells is now well established. Future studies of RME in vivo will have to overcome tissue heterogeneity and certain technical limitations. Here, we discuss current knowledge on autosomal RME, as well as possible mechanisms controlling these expression patterns and potential implications for development and disease, drawing parallels with what is known for X-chromosome inactivation, a paradigm of random monoallelic expression.
Topics: Alleles; Animals; Chromosomes; Disease; Humans; Single-Cell Analysis; X Chromosome Inactivation
PubMed: 27101886
DOI: 10.1016/j.semcdb.2016.04.007 -
Clinical Epigenetics May 2022Sex differences are known to play a role in disease aetiology, progression and outcome. Previous studies have revealed autosomal epigenetic differences between males and...
BACKGROUND
Sex differences are known to play a role in disease aetiology, progression and outcome. Previous studies have revealed autosomal epigenetic differences between males and females in some tissues, including differences in DNA methylation patterns. Here, we report for the first time an analysis of autosomal sex differences in DNAme using the Illumina EPIC array in human whole blood by performing a discovery (n = 1171) and validation (n = 2471) analysis.
RESULTS
We identified and validated 396 sex-associated differentially methylated CpG sites (saDMPs) with the majority found to be female-biased CpGs (74%). These saDMP's are enriched in CpG islands and CpG shores and located preferentially at 5'UTRs, 3'UTRs and enhancers. Additionally, we identified 266 significant sex-associated differentially methylated regions overlapping genes, which have previously been shown to exhibit epigenetic sex differences, and novel genes. Transcription factor binding site enrichment revealed enrichment of transcription factors related to critical developmental processes and sex determination such as SRY and ESR1.
CONCLUSION
Our study reports a reliable catalogue of sex-associated CpG sites and elucidates several characteristics of these sites using large-scale discovery and validation data sets. This resource will benefit future studies aiming to investigate sex specific epigenetic signatures and further our understanding of the role of DNA methylation in sex differences in human whole blood.
Topics: CpG Islands; DNA Methylation; Epigenesis, Genetic; Epigenomics; Female; Humans; Male; Sex Characteristics
PubMed: 35568878
DOI: 10.1186/s13148-022-01279-7 -
Cells Dec 2021Although the pericentromeric regions of chromosomes that are enriched in tandemly repeated satellite DNA represent a significant part of eukaryotic genomes, they remain...
Although the pericentromeric regions of chromosomes that are enriched in tandemly repeated satellite DNA represent a significant part of eukaryotic genomes, they remain understudied, which is mainly due to interdisciplinary knowledge gaps. Recent studies suggest their important role in genome regulation, karyotype stability, and evolution. Thus, the idea of satellite DNA as a junk part of the genome has been refuted. The integration of data regarding molecular composition, chromosome behaviour, and the details of the in situ organization of pericentromeric regions is of great interest. The objective of this work was a cytogenetic analysis of the interactions between pericentromeric regions from non-homologous chromosomes in mouse spermatocytes using immuno-FISH. We analysed two events: the associations between centromeric regions of the X chromosome and autosomes and the associations between the centromeric regions of the autosomal bivalents that form chromocenters. We concluded that the X chromosome forms temporary synaptic associations with different autosomes in early meiotic prophase I, which can normally be found until the pachytene-diplotene, without signs of pachytene arrest. These associations are formed between the satellite-DNA-rich centromeric regions of the X chromosome and different autosomes but do not involve the satellite-DNA-poor centromeric region of the Y chromosome. We suggest the hypothetical model of X chromosome competitive replacement from such associations during synaptic correction. We showed that the centromeric region of the X chromosome in association remains free of γH2Ax-dependent chromatin inactivation, while the Y chromosome is completely inactivated. This finding highlights the predominant role of associations between satellite DNA-rich regions of different chromosomes, including the X chromosome. We suppose that X-autosomal transient associations are a manifestation of an additional synaptic disorder checkpoint. These associations are normally corrected before the late diplotene stage. We revealed that the intense spreading conditions that were applied to the spermatocyte I nuclei did not lead to the destruction of stretched chromatin fibers of elongated chromocenters enriched in satellite DNA. The tight associations that we revealed between the pericentromeric regions of different autosomal bivalents and the X chromosome may represent the basis for a mechanism for maintaining the repeats stability in the autosomes and in the X chromosome. The consequences of our findings are discussed.
Topics: Animals; Centromere; Chromosomes, Mammalian; DNA; DNA, Satellite; Histones; Meiosis; Mice, Inbred BALB C; Mice, Inbred CBA; X Chromosome; Mice
PubMed: 34943883
DOI: 10.3390/cells10123375 -
Molecular Cytogenetics 2017Reciprocal Y autosome translocations are rare but frequently associated with male infertility. We report on the meiotic outcome in embryos fathered by two males with the...
BACKGROUND
Reciprocal Y autosome translocations are rare but frequently associated with male infertility. We report on the meiotic outcome in embryos fathered by two males with the karyotypes 46,X,t(Y;4)(q12;p15.32) and 46,X,t(Y;16)(q12;q13). The two couples underwent preimplantation genetic diagnosis (PGD) enabling determination of the segregation types that were compatible with fertilization and preimplantation embryo development. Both PGD and follow up analysis were carried out via fluorescence in situ hybridization (FISH) or array comparative genomic hybridization (aCGH) allowing the meiotic segregation types to be determined in a total of 27 embryos.
RESULTS
Interestingly, it was seen that the number of female embryos resulting from alternate segregation with the chromosome combination of X and the autosome from the carrier gamete differed from the corresponding balanced males with derivative Y and the derivative autosome by a ratio of 7:1 in each case ( = 0.003) while from the adjacent-1 mode of segregation, the unbalanced male embryos with the combination of der Y and the autosome were seen in all embryos from couple A and in couple B with the exception of one embryo only that had the other chromosome combination of X and derivative autosome ( = 0.011). In both cases the deficit groups have in common the der autosome chromosome that includes the segment Yq12 to qter.
CONCLUSION
The most likely explanation may be that this chromosome is associated with the X chromosome at PAR2 (pseudoautosomal region 2) in the sex-body leading to inactivation of genes on the autosomal segment that are required for the meiotic process and that this has led to degeneration of this class of spermatocytes during meiosis.
PubMed: 28184250
DOI: 10.1186/s13039-017-0303-y -
Animals : An Open Access Journal From... May 2022The regulation of gene expression is a complex process involving organism function and phenotypic diversity, and is caused by cis- and trans- regulation. While prior...
The regulation of gene expression is a complex process involving organism function and phenotypic diversity, and is caused by cis- and trans- regulation. While prior studies identified the regulatory pattern of the autosome rewiring in hybrids, the role of gene regulation in W sex chromosomes is not clear due to their degradation and sex-limit expression. Here, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, which exhibited broad differences in gender-related traits, and assessed the expression of the genes on the W chromosome to disentangle the contribution of cis- and trans-factors to expression divergence. We found that female-specific selection does not have a significant effect on W chromosome gene-expression patterns. For different tissues, there were most parental divergence expression genes in muscle, and also more heterosis compared with two other tissues. Notably, a broader pattern of trans regulation in the W chromosome was observed, which is consistent with autosomes. Taken together, this work describes the regulatory divergence of W-linked genes between two contrasting breeds and indicates sex chromosomes have a unique regulation and expression mechanism.
PubMed: 35565645
DOI: 10.3390/ani12091218 -
Nature Ecology & Evolution Dec 2021Sex chromosomes are susceptible to the evolution of selfish meiotic drive elements that bias transmission and distort progeny sex ratios. Conflict between such sex-ratio...
Sex chromosomes are susceptible to the evolution of selfish meiotic drive elements that bias transmission and distort progeny sex ratios. Conflict between such sex-ratio drivers and the rest of the genome can trigger evolutionary arms races resulting in genetically suppressed 'cryptic' drive systems. The Winters cryptic sex-ratio drive system of Drosophila simulans comprises a driver, Distorter on the X (Dox) and an autosomal suppressor, Not much yang, a retroduplicate of Dox that suppresses via production of endogenous small interfering RNAs (esiRNAs). Here we report that over 22 Dox-like (Dxl) sequences originated, amplified and diversified over the ~250,000-year history of the three closely related species, D. simulans, D. mauritiana and D. sechellia. The Dxl sequences encode a rapidly evolving family of protamines. Dxl copy numbers amplified by ectopic exchange among euchromatic islands of satellite DNAs on the X chromosome and separately spawned four esiRNA-producing suppressors on the autosomes. Our results reveal the genomic consequences of evolutionary arms races and highlight complex interactions among different classes of selfish DNAs.
Topics: Animals; DNA, Satellite; Drosophila; Evolution, Molecular; Sex Ratio; X Chromosome
PubMed: 34489561
DOI: 10.1038/s41559-021-01543-8