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This review investigates the role of aneuploidy and chromosome instability (CIN) in the aging brain. Aneuploidy refers to an abnormal chromosomal count, deviating from the normal diploid set. It can manifest as either a deficiency or excess of chromosomes. CIN encompasses a broader range of chromosomal alterations, including aneuploidy as well as structural modifications in DNA. We provide an overview of the state-of-the-art methodologies utilized for studying aneuploidy and CIN in non-tumor somatic tissues devoid of clonally expanded populations of aneuploid cells.CIN and aneuploidy, well-established hallmarks of cancer cells, are also associated with the aging process. In non-transformed cells, aneuploidy can contribute to functional impairment and developmental disorders. Despite the importance of understanding the prevalence and specific consequences of aneuploidy and CIN in the aging brain, these aspects remain incompletely understood, emphasizing the need for further scientific investigations.This comprehensive review consolidates the present understanding, addresses discrepancies in the literature, and provides valuable insights for future research efforts.
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Aneuploidia , Neoplasias , Animais , Humanos , Instabilidade Cromossômica , Aberrações Cromossômicas , Encéfalo , Cromossomos , Neoplasias/genética , Mamíferos/genéticaRESUMO
De novo mutations, a consequence of errors in DNA repair or replication, have been reported to accumulate with age in normal tissues of humans and model organisms. This accumulation during development and aging has been implicated as a causal factor in aging and age-related pathology, including but not limited to cancer. Due to their generally very low abundance mutations have been difficult to detect in normal tissues. Only with recent advances in DNA sequencing of single-cells, clonal lineages or ultra-high-depth sequencing of small tissue biopsies, somatic mutation frequencies and spectra have been unveiled in several tissue types. The rapid accumulation of such data prompted us to develop a platform called SomaMutDB (https://vijglab.einsteinmed.org/SomaMutDB) to catalog the 2.42 million single nucleotide variations (SNVs) and 0.12 million small insertions and deletions (INDELs) thus far identified using these advanced methods in nineteen human tissues or cell types as a function of age or environmental stress conditions. SomaMutDB employs a user-friendly interface to display and query somatic mutations with their functional annotations. Moreover, the database provides six powerful tools for analyzing mutational signatures associated with the data. We believe such an integrated resource will prove valuable for understanding somatic mutations and their possible role in human aging and age-related diseases.
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Bases de Dados Genéticas , Genoma Humano/genética , Mutação/genética , Distribuição Tecidual/genética , Envelhecimento/genética , Reparo do DNA/genética , Humanos , Taxa de Mutação , Neoplasias/classificação , Neoplasias/genéticaRESUMO
MethBank (http://bigd.big.ac.cn/methbank) is a database that integrates high-quality DNA methylomes across a variety of species and provides an interactive browser for visualization of methylation data. Here, we present an updated implementation of MethBank (version 3.0) by incorporating more DNA methylomes from multiple species and equipping with more enhanced functionalities for data annotation and more friendly web interfaces for data presentation, search and visualization. MethBank 3.0 features large-scale integration of high-quality methylomes, involving 34 consensus reference methylomes derived from a large number of human samples, 336 single-base resolution methylomes from different developmental stages and/or tissues of five plants, and 18 single-base resolution methylomes from gametes and early embryos at multiple stages of two animals. Additionally, it is enhanced by improving the functionalities for data annotation, which accordingly enables systematic identification of methylation sites closely associated with age, sites with constant methylation levels across different ages, differentially methylated promoters, age-specific differentially methylated cytosines/regions, and methylated CpG islands. Moreover, MethBank provides tools to estimate human methylation age online and to identify differentially methylated promoters, respectively. Taken together, MethBank is upgraded with significant improvements and advances over the previous version, which is of great help for deciphering DNA methylation regulatory mechanisms for epigenetic studies.
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Metilação de DNA , Bases de Dados Genéticas , Animais , Ilhas de CpG , Citosina/metabolismo , Humanos , Camundongos , Regiões Promotoras Genéticas , Sequenciamento Completo do GenomaRESUMO
DNA methylation plays crucial roles during embryonic development. Here we present MethBank (http://dnamethylome.org), a DNA methylome programming database that integrates the genome-wide single-base nucleotide methylomes of gametes and early embryos in different model organisms. Unlike extant relevant databases, MethBank incorporates the whole-genome single-base-resolution methylomes of gametes and early embryos at multiple different developmental stages in zebrafish and mouse. MethBank allows users to retrieve methylation levels, differentially methylated regions, CpG islands, gene expression profiles and genetic polymorphisms for a specific gene or genomic region. Moreover, it offers a methylome browser that is capable of visualizing high-resolution DNA methylation profiles as well as other related data in an interactive manner and thus is of great helpfulness for users to investigate methylation patterns and changes of gametes and early embryos at different developmental stages. Ongoing efforts are focused on incorporation of methylomes and related data from other organisms. Together, MethBank features integration and visualization of high-resolution DNA methylation data as well as other related data, enabling identification of potential DNA methylation signatures in different developmental stages and accordingly providing an important resource for the epigenetic and developmental studies.
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Metilação de DNA , Bases de Dados de Ácidos Nucleicos , Desenvolvimento Embrionário/genética , Animais , Ilhas de CpG , Células Germinativas/metabolismo , Sequenciamento de Nucleotídeos em Larga Escala , Internet , Camundongos , Polimorfismo Genético , Análise de Sequência de DNA , Transcriptoma , Peixe-Zebra/genéticaRESUMO
High-throughput sequencing at the single-cell and single-molecule level has shown that mutation rate is much higher in somatic cells than in the germline, with thousands of mutations accumulating with age in most human tissues. While there is now ample evidence that some of these mutations can clonally amplify and lead to disease, most notably cancer, the total burden of mutations a cell can tolerate without functional decline remains unknown. Here we addressed this question by exposing human primary fibroblasts multiple times to low doses of N-ethyl-N-nitrosourea (ENU) and quantitatively analyzing somatic mutation burden using single-cell whole genome sequencing. The results indicate that individual cells can sustain â¼60,000 single-nucleotide variants (SNVs) with only a slight adverse effect on growth rate. We found evidence for selection against potentially deleterious variants in gene coding regions as well as depletion of mutations in sequences associated with genetic pathways expressed in these human fibroblasts, most notably those relevant for maintaining basic cellular function and growth. However, no evidence of negative selection was found for variants in non-coding regions. We conclude that actively proliferating fibroblasts can tolerate very high levels of somatic mutations without major adverse effects on growth rate via negative selection against damaging coding mutations. Since most tissues in adult organisms have very limited capacity to select against mutations based on a growth disadvantage, these results suggest that a causal effect of somatic mutations in aging and disease cannot be ruled out.
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SUMMARY: With the rapid development of DNA sequencing technology, increasing bacteria genome data enable the biologists to dig the evolutionary and genetic information of prokaryotic species from pan-genome sight. Therefore, the high-efficiency pipelines for pan-genome analysis are mostly needed. We have developed a new pan-genome analysis pipeline (PGAP), which can perform five analytic functions with only one command, including cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis of functional genes, species evolution analysis and function enrichment analysis of gene clusters. PGAP's performance has been evaluated on 11 Streptococcus pyogenes strains. AVAILABILITY: PGAP is developed with Perl script on the Linux Platform and the package is freely available from http://pgap.sf.net. CONTACT: junyu@big.ac.cn; xiaojingfa@big.ac.cn SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Genoma Bacteriano , Software , Streptococcus pyogenes/genética , Algoritmos , Streptococcus pyogenes/classificaçãoRESUMO
Retrotransposons are a class of transposable elements capable of self-replication and insertion into new genomic locations. Across species, the mobilization of retrotransposons in somatic cells has been suggested to contribute to the cell and tissue functional decline that occurs during aging. Retrotransposons are broadly expressed across cell types, and de novo insertions have been observed to correlate with tumorigenesis. However, the extent to which new retrotransposon insertions occur during normal aging and their effect on cellular and animal function remains understudied. Here, we use a single nucleus whole genome sequencing approach in Drosophila to directly test whether transposon insertions increase with age in somatic cells. Analyses of nuclei from thoraces and indirect flight muscles using a newly developed pipeline, Retrofind, revealed no significant increase in the number of transposon insertions with age. Despite this, reducing the expression of two different retrotransposons, 412 and Roo, extended lifespan, but did not alter indicators of health such as stress resistance. This suggests a key role for transposon expression and not insertion in regulating longevity. Transcriptomic analyses revealed similar changes to gene expression in 412 and Roo knockdown flies and highlighted changes to genes involved in proteolysis and immune function as potential contributors to the observed changes in longevity. Combined, our data show a clear link between retrotransposon expression and aging.
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Drosophila , Retroelementos , Animais , Retroelementos/genética , Drosophila/genética , Drosophila melanogaster/genética , Envelhecimento/genética , GenômicaRESUMO
The pinning synchronization scheme is investigated for stochastic multi-layer networks under the intra-layer coupling disturbance and stochastic noise. To save the control cost, a pinning control scheme is proposed. And some sufficient conditions in the form of the LMI are given, based on Lyapunov theory and stochastic analysis, to make sure that the multi-layer networks synchronize to a desired trajectory. Next, the selection scheme of pinned nodes is designed according to the structure of considered multi-layer networks. Finally, simulation examples are shown to illustrate the feasibility and availability of the designed pinning scheme.
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Conductive carbon black (CCB) is an important filler in stretchable conductive silicone rubber (CSR) composites. However, due to the active oxygen-containing groups on CCB, introducing it into silicone rubber (SR) may cause SR to not completely cure. Surface modification of CCB may ease the problem but at the cost of reducing the electrical conductivity of pristine CCB. In this work, the curing and crosslinking performance of CCB/SR is detected in detail, the hydroxyl groups (-OH) carried by CCB can react with the silicon-hydrogen group (Si-H) with the existence of Pt catalyst, causing insufficiency of the hydrosilylation reaction thus hindering the solidifying process of silicon rubber. To take advantage of this reaction, more hydrogen silicone oil (PHMS) possessing silicon-hydrogen bonds is introduced into the system to improve the curing degree as well as fix the CCB in the crosslinked network. Due to the lock-in effect of CCB, the resistance of CSR samples is stable after several hundred bending cycles, and the composite's tensile strength is three times that of the pure SR samples. Besides, the size of the composites can expand to dozens of centimeters or even a few meters with uniform electric conductivity. This composite has resistance as low as 10.20 Ω and is suitable to make electroplating mold, and a rapid plating rate of 2.4 mm/24 h can be achieved. Meanwhile, the overall properties make this CSR composite have potential applications in mold manufacture, flexible electronics, and other related fields.
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Postzygotic somatic mutations have been found associated with human disease, including diseases other than cancer. Most information on somatic mutations has come from studying clonally amplified mutant cells, based on a growth advantage or genetic drift. However, almost all somatic mutations are unique for each cell, and the quantitative analysis of these low-abundance mutations in normal tissues remains a major challenge in biology. Here, we introduce single-molecule mutation sequencing (SMM-seq), a novel approach for quantitative identification of point mutations in normal cells and tissues.
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Sequenciamento de Nucleotídeos em Larga Escala , Neoplasias , Humanos , Mutação , Neoplasias/genéticaRESUMO
Inherited germline mutations in the breast cancer gene 1 (BRCA1) or BRCA2 genes (herein BRCA1/2) greatly increase the risk of breast and ovarian cancer, presumably by elevating somatic mutational errors as a consequence of deficient DNA repair. However, this has never been directly demonstrated by a comprehensive analysis of the somatic mutational landscape of primary, noncancer, mammary epithelial cells of women diagnosed with pathogenic BRCA1/2 germline mutations. Here, we used an accurate, single-cell whole-genome sequencing approach to first show that telomerized primary mammary epithelial cells heterozygous for a highly penetrant BRCA1 variant displayed a robustly elevated mutation frequency as compared with their isogenic control cells. We then demonstrated a small but statistically significant increase in mutation frequency in mammary epithelial cells isolated from the breast of BRCA1/2 mutation carriers as compared with those obtained from age-matched controls with no genetically increased risk for breast cancer.
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Neoplasias da Mama , Neoplasias Ovarianas , Proteína BRCA1/genética , Proteína BRCA2/genética , Neoplasias da Mama/genética , Neoplasias da Mama/patologia , Células Epiteliais/patologia , Feminino , Predisposição Genética para Doença , Mutação em Linhagem Germinativa , Humanos , Mutação , Neoplasias Ovarianas/patologia , Análise de Célula ÚnicaRESUMO
Although lung cancer risk among smokers is dependent on smoking dose, it remains unknown if this increased risk reflects an increased rate of somatic mutation accumulation in normal lung cells. Here, we applied single-cell whole-genome sequencing of proximal bronchial basal cells from 33 participants aged between 11 and 86 years with smoking histories varying from never-smoking to 116 pack-years. We found an increase in the frequency of single-nucleotide variants and small insertions and deletions with chronological age in never-smokers, with mutation frequencies significantly elevated among smokers. When plotted against smoking pack-years, mutations followed the linear increase in cancer risk until about 23 pack-years, after which no further increase in mutation frequency was observed, pointing toward individual selection for mutation avoidance. Known lung cancer-defined mutation signatures tracked with both age and smoking. No significant enrichment for somatic mutations in lung cancer driver genes was observed.
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Neoplasias Pulmonares , Análise de Célula Única , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Envelhecimento/genética , Criança , Células Epiteliais , Receptores ErbB/genética , Humanos , Neoplasias Pulmonares/genética , Pessoa de Meia-Idade , Mutação , Fumar/efeitos adversos , Fumar/genética , Adulto JovemRESUMO
Conductive silicone rubber (CSR) is an outstanding stretchable conductive composite due to its excellent mechanical properties and stable conductivity. In this paper, silver nanoparticles were deposited on carbon black (CB) through a reduction reaction. The uniform dispersion of silver particles on the surface of CB as well as the grape-like branch structure of hybrid particles was formed by the condensation reaction of the hydroxyl groups of CB with (3-mercaptopropyl) trimethoxysilane (KH-590), along with the interattraction between sulfhydryl groups of KH-590 and silver ions. This sulfhydryl modified conductive carbon black/Ag hybrid filler (SMCB@Ag) avoided the high processing viscosity of CSR caused by the hydroxyl groups of CB. The percolation threshold of CSR made from SMCB@Ag was 5.5 wt% according to the percolation equation. With the addition amount of SMCB@Ag increasing to 10 wt%, the conductivity of CSR increased from 10-5 to about 101. Moreover, the conductivity of this CSR showed excellent stability with extension of storage time and increase of stretching-recovery cycles.
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Telomere attrition has been proposed as a biomarker and causal factor in aging. In addition to causing cellular senescence and apoptosis, telomere shortening has been found to affect gene expression in subtelomeric regions. Here, we analyzed the distribution of age-related differentially expressed genes from the GTEx RNA sequencing database of 54 tissue types from 979 human subjects and found significantly more upregulated than downregulated genes in subtelomeric regions as compared to the genome-wide average. Our data demonstrate spatial relationships between telomeres and gene expression in aging.
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Senescência Celular/genética , Expressão Gênica/genética , Telômero/genética , Adulto , Idoso , Envelhecimento , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Adulto JovemRESUMO
Freshwater polyps of the genus Hydra do not age. However, temperature stress induces aging and a shift from reproduction by asexual budding to sexual gamete production in a cold-sensitive (CS) strain of H. oligactis. We sequenced the transcriptome of a male CS strain before and after this life history shift and compared changes in gene expression relative to those seen in a cold-resistant (CR) strain that does not undergo a life history shift in response to altered temperature. We found that the switch from non-aging asexual reproduction to aging and sexual reproduction involves upregulation of genes not only involved in gametogenesis but also genes involved in cellular senescence, apoptosis, and DNA repair accompanied by a downregulation of genes involved in stem cell maintenance. These results suggest that aging is a byproduct of sexual reproduction-associated cellular reprogramming and underscore the power of these H. oligactis strains to identify intrinsic mechanisms of aging.
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Hydra , Envelhecimento/genética , Animais , Masculino , Reprodução/genética , Reprodução Assexuada , Células-TroncoRESUMO
Enterovirus 71 (EV71) and coxsackievirus A16 (CVA16) have been considered major pathogens of hand, foot and mouth disease (HFMD) throughout the world for decades. In recent years, coxsackievirus A6 (CVA6) and coxsackievirus A10 (CVA10) have raised attention as two other serious pathogens of HFMD. The present study focused on the synonymous codon usage of four viruses isolated from 2008 to 2015, with particular attention on P1 (encoding capsid proteins) and P2-P3 regions (both encoding non-structural proteins) in the genomic RNA. Relative synonymous codon usage, effective number of codons, neutrality and correspondence were analyzed. The results indicated that these viruses prefer A/T at the third position in codons rather than G/C. The most frequent codons of 4 essential and 2 semi-essential amino acids, as well as a key amino acid of metabolic junctions (Glu) used in the four viruses are also the most frequently used in humans. Effective number of codons (ENC) values indicated weak codon usage bias in all the viruses. Relatively, the force of mutation pressure in the P1 region was found to be stronger than that in the P2-P3 region, and this force in the P1 region of CVA6 and EV71 was stronger than that of CVA10 and A16. The neutrality analysis results implied that mutation pressure plays a minor role in shaping codon bias of these viruses. Correspondence analysis indicated that the codon usage of EV71 strains varied much more than that of other viruses. In conclusion, the present study provides novel and comparative insight into the evolution of HFMD pathogens at the codon level.
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Proteínas do Capsídeo/genética , Códon/metabolismo , Enterovirus Humano A/genética , Genoma Viral , Proteínas não Estruturais Virais/genética , Aminoácidos/genética , Aminoácidos/metabolismo , Proteínas do Capsídeo/metabolismo , Códon/química , Enterovirus Humano A/isolamento & purificação , Expressão Gênica , Código Genético , Doença de Mão, Pé e Boca/virologia , Humanos , Análise de Sequência de DNA , Proteínas não Estruturais Virais/metabolismoRESUMO
The second law of thermodynamics states that entropy, as a measure of randomness in a system, increases over time. Although studies have investigated biological sequence randomness from different aspects, it remains unknown whether sequence randomness changes over time and whether this change consists with the second law of thermodynamics. To capture the dynamics of randomness in molecular sequence evolution, here we detect sequence randomness based on a collection of eight statistical random tests and investigate the randomness variation of coding sequences with an application to Escherichia coli. Given that core/essential genes are more ancient than specific/non-essential genes, our results clearly show that core/essential genes are more random than specific/non-essential genes and accordingly indicate that sequence randomness indeed increases over time, consistent well with the second law of thermodynamics. We further find that an increase in sequence randomness leads to increasing randomness of GC content and longer sequence length. Taken together, our study presents an important finding, for the first time, that sequence randomness increases over time, which may provide profound insights for unveiling the underlying mechanisms of molecular sequence evolution.
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Composição de Bases , Escherichia coli/genética , Evolução Molecular , Modelos GenéticosRESUMO
[This corrects the article DOI: 10.1371/journal.pone.0155935.].
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Codon usage bias, as a combined interplay from mutation and selection, has been intensively studied in Escherichia coli. However, codon usage analysis in an E. coli pangenome remains unexplored and the relative importance of mutation and selection acting on core genes and strain-specific genes is unknown. Here we perform comprehensive codon usage analyses based on a collection of multiple complete genome sequences of E. coli. Our results show that core genes that are present in all strains have higher codon usage bias than strain-specific genes that are unique to single strains. We further explore the forces in influencing codon usage and investigate the difference of the major force between core and strain-specific genes. Our results demonstrate that although mutation may exert genome-wide influences on codon usage acting similarly in different gene sets, selection dominates as an important force to shape biased codon usage as genes are present in an increased number of strains. Together, our results provide important insights for better understanding genome plasticity and complexity as well as evolutionary mechanisms behind codon usage bias.
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Cassava is a major tropical food crop in the Euphorbiaceae family that has high carbohydrate production potential and adaptability to diverse environments. Here we present the draft genome sequences of a wild ancestor and a domesticated variety of cassava and comparative analyses with a partial inbred line. We identify 1,584 and 1,678 gene models specific to the wild and domesticated varieties, respectively, and discover high heterozygosity and millions of single-nucleotide variations. Our analyses reveal that genes involved in photosynthesis, starch accumulation and abiotic stresses have been positively selected, whereas those involved in cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been negatively selected in the cultivated varieties, reflecting the result of natural selection and domestication. Differences in microRNA genes and retrotransposon regulation could partly explain an increased carbon flux towards starch accumulation and reduced cyanogenic glucoside accumulation in domesticated cassava. These results may contribute to genetic improvement of cassava through better understanding of its biology.