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1.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 38(11): 1045-1050, 2021 Nov 10.
Artigo em Chinês | MEDLINE | ID: mdl-34729740

RESUMO

OBJECTIVE: To assess the clinical value of non-invasive prenatal testing (NIPT) for the screening of trisomy and copy number variations (CNVs) of chromosomes 21, 18 and 13. METHODS: From January 2015 to December 2019, 40 628 pregnant women underwent NIPT testing using high-throughput sequencing and bioinformatics analysis to test the cell-free fetal DNA in maternal plasma. High-risk pregnant women underwent invasive prenatal diagnosis, while low-risk ones were followed up by telephone. RESULTS: The three most common indications included intermediate risk of serological screening, high risk of serological screening and advanced maternal age. Among all pregnant women, 257 cases were detected as trisomy 21, 18 and 13 (170, 49 and 38 cases, respectively). 227 cases chose invasive prenatal diagnosis, with respectively 122, 28 and 10 cases confirmed. The positive predictive value (PPV) was 81.33% (122/150), 65.12% (28/43), 29.41% (10/34), respectively. Two false negative cases of trisomy 18 were found during follow-up. Meanwhile, NIPT has detected 46 cases (15, 16 and 15 cases, respectively) CNVs on chromosomes 21, 18 and 13, among which 37 cases underwent invasive prenatal diagnosis. There were 5, 3 and 5 positive cases, which yielded a PPV of 41.67% (5/12), 25%(3/12) and 33.33%(5/15), respectively. Two other chromosome CNVs were accidentally discovered among the false positive samples. CONCLUSION: The incidence of chromosomal abnormalities in the serological screening high-risk group was 52.02%, which was significantly higher than other groups. NIPT has a high sensitivity and specificity for the screening of trisomies 21, 18 and 13, while its accuracy for detecting CNVs of chromosomes 21, 18 and 13 needs to be improved. As a screening method, NIPT has a great clinical value, though there are still limitations of false positive and false negative results.Comprehensive pre- and post-test genetic counseling should be provided to the patients.


Assuntos
Transtornos Cromossômicos , Síndrome de Down , Aneuploidia , Transtornos Cromossômicos/diagnóstico , Transtornos Cromossômicos/genética , Cromossomos , Variações do Número de Cópias de DNA , Síndrome de Down/diagnóstico , Síndrome de Down/genética , Feminino , Humanos , Gravidez , Diagnóstico Pré-Natal , Trissomia/diagnóstico , Trissomia/genética , Síndrome da Trissomía do Cromossomo 18/genética
2.
BMC Genomics ; 22(1): 794, 2021 Nov 04.
Artigo em Inglês | MEDLINE | ID: mdl-34736418

RESUMO

BACKGROUND: The present availability of full genome sequences of a broad range of animal species across the whole range of evolutionary history enables one to ask questions as to the distribution of genes across the chromosomes. Do newly recruited genes, as new clades emerge, distribute at random or at non-random locations? RESULTS: We extracted values for the ages of the human genes and for their current chromosome locations, from published sources. A quantitative analysis showed that the distribution of newly-added genes among and within the chromosomes appears to be increasingly non-random if one observes animals along the evolutionary series from the precursors of the tetrapoda through to the great apes, whereas the oldest genes are randomly distributed. CONCLUSIONS: Randomization will result from chromosome evolution, but less and less time is available for this process as evolution proceeds. Much of the bunching of recently-added genes arises from new gene formation as paralogues in gene families, near the location of genes that were recruited in the preceding phylostratum. As examples we cite the KRTAP, ZNF, OR and some minor gene families. We show that bunching can also result from the evolution of the chromosomes themselves when, as for the KRTAP genes, blocks of genes that had previously been on disparate chromosomes become linked together.


Assuntos
Evolução Molecular , Genoma , Animais , Cromossomos/genética , Humanos
3.
Mol Biol (Mosk) ; 55(6): 999-1010, 2021.
Artigo em Russo | MEDLINE | ID: mdl-34837704

RESUMO

A fundamental difference between somatic nuclei (macronuclei) of ciliates and cell nuclei of higher eukaryotes is that the macronuclear genome is a huge number (up to tens or hundreds of thousands) of gene-sized (0.5-25 kb) or subchromosomal (up to 2000 kb) minichromosomes. Electron microscopy shows that macronuclear chromatin usually looks like chromatin bodies or fibrils 200-300 nm thick in the interphase. However, the question of how many DNA molecules are contained in an individual chromatin body remains open. The organization of chromatin in macronuclei was studied in the ciliates Didinium nasutum and three Paramecium sp, which differ in pulsed-field gel electrophoresis (PFGE) karyotype, and compared with the model of topologically associated domains (TADs) of higher eukaryotic nuclei. PFGE showed that the sizes of macronuclear DNAs ranged from 50 to 1700 kb, while the majority of the molecules were less than 500 kb in length. A comparative quantitative analysis of the PFGE and electron microscopic data showed that each chromatin body contained one minichromosome in P. multimicronucleatum in the logarithmic growth phase, while bodies in the D. nasutum macronucleus contained two or more DNA molecules each. Chromatin bodies aggregated during starvation, when activity of the macronuclei decreased, leading to an increase of chromatin body size or the formation of 200- to 300-nm fibrils of several chromatin bodies. A model was proposed to explain the formation of such structures. In terms of topological characteristics, macronuclear chromatin bodies with subchromosomal DNA molecules were found to correspond to higher eukaryotic TADs.


Assuntos
Cilióforos , Macronúcleo , Núcleo Celular/genética , Cromatina/genética , Cromossomos/genética , Cilióforos/genética , DNA , Macronúcleo/genética
4.
BMC Bioinformatics ; 22(1): 569, 2021 Nov 27.
Artigo em Inglês | MEDLINE | ID: mdl-34837944

RESUMO

BACKGROUND: Efficient and effective genome scaffolding tools are still in high demand for generating reference-quality assemblies. While long read data itself is unlikely to create a chromosome-scale assembly for most eukaryotic species, the inexpensive Hi-C sequencing technology, capable of capturing the chromosomal profile of a genome, is now widely used to complete the task. However, the existing Hi-C based scaffolding tools either require a priori chromosome number as input, or lack the ability to build highly continuous scaffolds. RESULTS: We design and develop a novel Hi-C based scaffolding tool, pin_hic, which takes advantage of contact information from Hi-C reads to construct a scaffolding graph iteratively based on N-best neighbors of contigs. Subsequent to scaffolding, it identifies potential misjoins and breaks them to keep the scaffolding accuracy. Through our tests on three long read based de novo assemblies from three different species, we demonstrate that pin_hic is more efficient than current standard state-of-art tools, and it can generate much more continuous scaffolds, while achieving a higher or comparable accuracy. CONCLUSIONS: Pin_hic is an efficient Hi-C based scaffolding tool, which can be useful for building chromosome-scale assemblies. As many sequencing projects have been launched in the recent years, we believe pin_hic has potential to be applied in these projects and makes a meaningful contribution.


Assuntos
Genoma , Genômica , Cromossomos/genética , Sequenciamento de Nucleotídeos em Larga Escala , Análise de Sequência de DNA
5.
Zootaxa ; 5005(2): 101-144, 2021 Jul 26.
Artigo em Inglês | MEDLINE | ID: mdl-34811274

RESUMO

Bush-crickets (or katydids) of the genus Mecopoda are relatively large insects well-known for their sounds for centuries. Bioacoustic studies in India and China revealed a surprisingly large diversity of sound patterns. We extend these studies into the tropics of South East Asia using integrative taxonomy, combining song analysis, morphology of sound producing organs and male genitalia as well as chromosomes, to get a better understanding of the phylogeny and evolution of this widespread group. Besides the closely related genus Eumecopoda, the genus Mecopoda contains some isolated species and a large group of species which we assign to the Mecopoda elongata group. Some species of this group have broad tegmina and stridulatory files with different tooth spacing patterns and produce continuous, often relatively complicated, trill-like songs. The species of another subgroup with narrower wings have all similar files. Their songs consist of echemes (groups of syllables) which differ in syllable number and syllable repetition rate and also in echeme repetition rate. Our results show that South East Asia harbours a large and certainly not yet fully explored number of Mecopoda species which are most easily and clearly identified by song. Based on the data, five new forms are described: Mecopoda mahindai Heller sp. nov., Mecopoda paucidens Ingrisch, Su Heller sp. nov., Mecopoda sismondoi Heller sp. nov., Mecopoda niponensis vietnamica Heller Korsunovskaya subsp. nov., Eumecopoda cyrtoscelis zhantievi Heller subsp. nov. In addition, some taxonomic changes are proposed: Eumecopoda Hebard, 1922 stat. rev., Paramecopoda Gorochov, 2020, syn. nov. of Eumecopoda Hebard, 1922, Mecopoda javana (Johansson, 1763) stat. nov. (neotype selected) with M. javana minahasa Gorochov, 2020 stat. nov., M. javana darevskyi Gorochov, 2020 stat. nov., M. javana buru Gorochov, 2020 stat. nov., Mecopoda macassariensis (Haan, 1843) stat. rev., Mecopoda ampla malayensis Gorochov, 2020 syn. nov., Mecopada ampla javaensis Gorochov, 2020 syn. nov., Mecopoda fallax aequatorialis Gorochov, 2020 syn. nov., the last three are all synonyms of Mecopoda himalaya Liu, 2020, Mecopoda yunnana Liu 2020, stat. nov.


Assuntos
Ortópteros , Distribuição Animal , Estruturas Animais , Animais , Cromossomos , Insetos , Masculino , Tamanho do Órgão , Ortópteros/genética
6.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 38(12): 1165-1170, 2021 Dec 10.
Artigo em Chinês | MEDLINE | ID: mdl-34839499

RESUMO

The International System for Human Cytogenomic Nomenclature (ISCN) is an international standard used for describing genome rearrangement detected by chromosomal karyotyping, fluorescence in situ hybridization, microarray, a variety of specific region detection technologies and high-throughput sequencing. In 2019, the ISCN standing committee has revised the ISCN and officially published it in October 2020. This article has summarized the updated content of ISCN 2020.


Assuntos
Cromossomos , Sequenciamento de Nucleotídeos em Larga Escala , Aberrações Cromossômicas , Humanos , Hibridização in Situ Fluorescente , Cariotipagem
7.
F1000Res ; 10: 289, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34621505

RESUMO

Background: Seagrasses (Alismatales) are the only fully marine angiosperms.  Zostera marina (eelgrass) plays a crucial role in the functioning of coastal marine ecosystems and global carbon sequestration. It is the most widely studied seagrass and has become a marine model system for exploring adaptation under rapid climate change. The original draft genome (v.1.0) of the seagrass  Z. marina (L.) was based on a combination of Illumina mate-pair libraries and fosmid-ends. A total of 25.55 Gb of Illumina and 0.14 Gb of Sanger sequence was obtained representing 47.7× genomic coverage. The assembly resulted in ~2000 unordered scaffolds (L50 of 486 Kb), a final genome assembly size of 203MB, 20,450 protein coding genes and 63% TE content. Here, we present an upgraded chromosome-scale genome assembly and compare v.1.0 and the new v.3.1, reconfirming previous results from Olsen et al. (2016), as well as pointing out new findings.   Methods: The same high molecular weight DNA used in the original sequencing of the Finnish clone was used. A high-quality reference genome was assembled with the MECAT assembly pipeline combining PacBio long-read sequencing and Hi-C scaffolding.  Results: In total, 75.97 Gb PacBio data was produced. The final assembly comprises six pseudo-chromosomes and 304 unanchored scaffolds with a total length of 260.5Mb and an N50 of 34.6 MB, showing high contiguity and few gaps (~0.5%). 21,483 protein-encoding genes are annotated in this assembly, of which 20,665 (96.2%) obtained at least one functional assignment based on similarity to known proteins.  Conclusions: As an important marine angiosperm, the improved  Z. marina genome assembly will further assist evolutionary, ecological, and comparative genomics at the chromosome level. The new genome assembly will further our understanding into the structural and physiological adaptations from land to marine life.


Assuntos
Zosteraceae , Cromossomos , Ecossistema , Genoma , Anotação de Sequência Molecular , Zosteraceae/genética
8.
Nat Commun ; 12(1): 6030, 2021 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-34654815

RESUMO

For millions of years, plants evolve plenty of structurally diverse secondary metabolites (SM) to support their sessile lifestyles through continuous biochemical pathway innovation. While new genes commonly drive the evolution of plant SM pathway, how a full biosynthetic pathway evolves remains poorly understood. The evolution of pathway involves recruiting new genes along the reaction cascade forwardly, backwardly, or in a patchwork manner. With three chromosome-scale Papaver genome assemblies, we here reveal whole-genome duplications (WGDs) apparently accelerate chromosomal rearrangements with a nonrandom distribution towards SM optimization. A burst of structural variants involving fusions, translocations and duplications within 7.7 million years have assembled nine genes into the benzylisoquinoline alkaloids gene cluster, following a punctuated patchwork model. Biosynthetic gene copies and their total expression matter to morphinan production. Our results demonstrate how new genes have been recruited from a WGD-induced repertoire of unregulated enzymes with promiscuous reactivities to innovate efficient metabolic pathways with spatiotemporal constraint.


Assuntos
Vias Biossintéticas , Cromossomos/metabolismo , Morfinanos/metabolismo , Noscapina/metabolismo , Papaver/genética , Papaver/metabolismo , Alcaloides/química , Alcaloides/metabolismo , Benzilisoquinolinas/metabolismo , Vias Biossintéticas/genética , Evolução Molecular , Genoma , Genômica , Família Multigênica , Proteínas de Plantas/genética
9.
Int J Mol Sci ; 22(19)2021 Sep 30.
Artigo em Inglês | MEDLINE | ID: mdl-34638945

RESUMO

The quest for the discovery and validation of radiosensitivity biomarkers is ongoing and while conventional bioassays are well established as biomarkers, molecular advances have unveiled new emerging biomarkers. Herein, we present the validation of a new 4-gene signature panel of CDKN1, FDXR, SESN1 and PCNA previously reported to be radiation-responsive genes, using the conventional G2 chromosomal radiosensitivity assay. Radiation-induced G2 chromosomal radiosensitivity at 0.05 Gy and 0.5 Gy IR is presented for a healthy control (n = 45) and a prostate cancer (n = 14) donor cohort. For the prostate cancer cohort, data from two sampling time points (baseline and Androgen Deprivation Therapy (ADT)) is provided, and a significant difference (p > 0.001) between 0.05 Gy and 0.5 Gy was evident for all donor cohorts. Selected donor samples from each cohort also exposed to 0.05 Gy and 0.5 Gy IR were analysed for relative gene expression of the 4-gene signature. In the healthy donor cohort, there was a significant difference in gene expression between IR dose for CDKN1, FXDR and SESN1 but not PCNA and no significant difference found between all prostate cancer donors, unless they were classified as radiation-induced G2 chromosomal radiosensitive. Interestingly, ADT had an effect on radiation response for some donors highlighting intra-individual heterogeneity of prostate cancer donors.


Assuntos
Inibidor de Quinase Dependente de Ciclina p21/genética , Proteínas de Choque Térmico/genética , Proteínas Mitocondriais/genética , Oxirredutases atuantes sobre Doadores de Grupo Enxofre/genética , Antígeno Nuclear de Célula em Proliferação/genética , Neoplasias da Próstata/genética , Tolerância a Radiação/genética , Transcriptoma , Adulto , Idoso , Idoso de 80 Anos ou mais , Antagonistas de Androgênios/farmacologia , Antagonistas de Androgênios/uso terapêutico , Estudos de Casos e Controles , Cromossomos/efeitos da radiação , Estudos de Coortes , Humanos , Masculino , Pessoa de Meia-Idade , Reação em Cadeia da Polimerase Multiplex/métodos , Prognóstico , Neoplasias da Próstata/sangue , Neoplasias da Próstata/tratamento farmacológico , Doses de Radiação , Tolerância a Radiação/efeitos dos fármacos , Reação em Cadeia da Polimerase em Tempo Real/métodos , Adulto Jovem
10.
PLoS Genet ; 17(10): e1009870, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34669718

RESUMO

Reduction of genome ploidy from diploid to haploid necessitates stable pairing of homologous chromosomes into bivalents before the start of the first meiotic division. Importantly, this chromosome pairing must avoid interlocking of non-homologous chromosomes. In spermatocytes of Drosophila melanogaster, where homolog pairing does not involve synaptonemal complex formation and crossovers, associations between non-homologous chromosomes are broken up by chromosome territory formation in early spermatocytes. Extensive non-homologous associations arise from the coalescence of the large blocks of pericentromeric heterochromatin into a chromocenter and from centromere clustering. Nevertheless, during territory formation, bivalents are moved apart into spatially separate subnuclear regions. The condensin II subunits, Cap-D3 and Cap-H2, have been implicated, but the remarkable separation of bivalents during interphase might require more than just condensin II. For further characterization of this process, we have applied time-lapse imaging using fluorescent markers of centromeres, telomeres and DNA satellites in pericentromeric heterochromatin. We describe the dynamics of the disruption of centromere clusters and the chromocenter in normal spermatocytes. Mutations in Cap-D3 and Cap-H2 abolish chromocenter disruption, resulting in excessive chromosome missegregation during M I. Chromocenter persistence in the mutants is not mediated by the special system, which conjoins homologs in compensation for the absence of crossovers in Drosophila spermatocytes. However, overexpression of Cap-H2 precluded conjunction between autosomal homologs, resulting in random segregation of univalents. Interestingly, Cap-D3 and Cap-H2 mutant spermatocytes displayed conspicuous stretching of the chromocenter, as well as occasional chromocenter disruption, suggesting that territory formation might involve forces unrelated to condensin II. While the molecular basis of these forces remains to be clarified, they are not destroyed by inhibitors of F actin and microtubules. Our results indicate that condensin II activity promotes chromosome territory formation in co-operation with additional force generators and that careful co-ordination with alternative homolog conjunction is crucial.


Assuntos
Adenosina Trifosfatases/genética , Cromossomos/genética , Proteínas de Ligação a DNA/genética , Proteínas de Drosophila/genética , Drosophila melanogaster/genética , Complexos Multiproteicos/genética , Espermatócitos/fisiologia , Animais , Centrômero/genética , Cromatina/genética , Pareamento Cromossômico/genética , Segregação de Cromossomos/genética , Drosophila melanogaster/metabolismo , Feminino , Heterocromatina/genética , Interfase/genética , Masculino
11.
Genet Sel Evol ; 53(1): 78, 2021 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-34620094

RESUMO

BACKGROUND: Genomic selection using single nucleotide polymorphism (SNP) markers has been widely used for genetic improvement of livestock, but most current methods of genomic selection are based on SNP models. In this study, we investigated the prediction accuracies of haplotype models based on fixed chromosome distances and gene boundaries compared to those of SNP models for genomic prediction of phenotypic values. We also examined the reasons for the successes and failures of haplotype genomic prediction. METHODS: We analyzed a swine population of 3195 Duroc boars with records on eight traits: body judging score (BJS), teat number (TN), age (AGW), loin muscle area (LMA), loin muscle depth (LMD) and back fat thickness (BF) at 100 kg live weight, and average daily gain (ADG) and feed conversion rate (FCR) from 30 to100 kg live weight. Ten-fold validation was used to evaluate the prediction accuracy of each SNP model and each multi-allelic haplotype model based on 488,124 autosomal SNPs from low-coverage sequencing. Haplotype blocks were defined using fixed chromosome distances or gene boundaries. RESULTS: Compared to the best SNP model, the accuracy of predicting phenotypic values using a haplotype model was greater by 7.4% for BJS, 7.1% for AGW, 6.6% for ADG, 4.9% for FCR, 2.7% for LMA, 1.9% for LMD, 1.4% for BF, and 0.3% for TN. The use of gene-based haplotype blocks resulted in the best prediction accuracy for LMA, LMD, and TN. Compared to estimates of SNP additive heritability, estimates of haplotype epistasis heritability were strongly correlated with the increase in prediction accuracy by haplotype models. The increase in prediction accuracy was largest for BJS, AGW, ADG, and FCR, which also had the largest estimates of haplotype epistasis heritability, 24.4% for BJS, 14.3% for AGW, 14.5% for ADG, and 17.7% for FCR. SNP and haplotype heritability profiles across the genome identified several genes with large genetic contributions to phenotypes: NUDT3 for LMA, LMD and BF, VRTN for TN, COL5A2 for BJS, BSND for ADG, and CARTPT for FCR. CONCLUSIONS: Haplotype prediction models improved the accuracy for genomic prediction of phenotypes in Duroc pigs. For some traits, the best prediction accuracy was obtained with haplotypes defined using gene regions, which provides evidence that functional genomic information can improve the accuracy of haplotype genomic prediction for certain traits.


Assuntos
Genoma , Genômica , Animais , Cromossomos/genética , Haplótipos , Masculino , Fenótipo , Polimorfismo de Nucleotídeo Único , Suínos/genética
12.
Am J Intellect Dev Disabil ; 126(6): 505-510, 2021 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-34700346

RESUMO

Duplication of chromosome 15q11.2-q13.1 (dup15q syndrome) results in hypotonia, intellectual disability (ID), and autism symptomatology. Clinical electroencephalography has shown abnormal sleep physiology, but no studies have characterized sleep behaviors. The present study used the Children's Sleep Habits Questionnaire (CSHQ) in 42 people with dup15q syndrome to examine the clinical utility of this questionnaire and quantify behavioral sleep patterns in dup15q syndrome. Individuals with fully completed forms (56%) had higher cognitive abilities than those with partially completed forms. Overall, caregivers indicated a high rate of sleep disturbance, though ratings differed by epilepsy status. Results suggest that clinicians should use caution when using standardized questionnaires and consider epilepsy status when screening for sleep problems in dup15q syndrome.


Assuntos
Epilepsia , Deficiência Intelectual , Criança , Cromossomos , Eletroencefalografia , Epilepsia/genética , Humanos , Deficiência Intelectual/genética , Sono
13.
Zhonghua Yu Fang Yi Xue Za Zhi ; 55(10): 1220-1227, 2021 Oct 06.
Artigo em Chinês | MEDLINE | ID: mdl-34706508

RESUMO

Objective: The purpose of this study is to use the next-generation sequencing (NGS) technology platform to detect the methylation rate of phosphatase and tensin homolog deleted on chromosome ten (PTEN) promoter region in hepatocellular carcinoma (HCC) tissue samples, and to analyze the clinical significance of its correlation with the prognosis of patients receiving sorafenib treatment. Methods: The 52 pairs of tumor tissue and para-cancerous tissue samples from HCC patients treated with sorafenib alone, which were collected and preserved in the Liver Tumor Diagnosis and Research Center of the former 302 Hospital of the People's Liberation Army by the National Natural Science Foundation of China Youth Project with the project batch number 81702986 in 2018, were extracted total DNA from the samples. Then the DNA samples were treated with bisulfite and specific primers were designed to amplify the PTEN promoter region. Finally, the amplified products were analyzed by second-generation sequencing. In the analysis of clinical significance of PTEN methylation, log-rank statistical analysis was used to calculate whether there was a statistical difference in survival between the patient groups. Results: The methylation rate of PTEN promoter region in tumor tissues (29.17%±9.58%) was significantly higher than that in paracancer tissues (4.17%±2.86%)(t=19.970,P<0.05). At the same time, in HCC tissues, the methylation rate of the PTEN promoter region is negatively correlated with its expression (F=47.270,P<0.000 1;Y=-1 800×X+38.03), and the PTEN methylation rate is negatively correlated with the prognosis of patients receiving the molecularly targeted drug Sorafenib (χ²=4.313,P<0.05). Conclusion: This study successfully established a new method for detecting methylation in the promoter region of PTEN, and the methylation rate of PTEN can be used as one of the targets of HCC diagnosis and targeted therapy.


Assuntos
Carcinoma Hepatocelular , Metilação de DNA , Neoplasias Hepáticas , PTEN Fosfo-Hidrolase/genética , Carcinoma Hepatocelular/genética , Cromossomos , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Neoplasias Hepáticas/genética , Regiões Promotoras Genéticas
14.
Nat Commun ; 12(1): 5876, 2021 10 07.
Artigo em Inglês | MEDLINE | ID: mdl-34620865

RESUMO

Chromosomal recombinant gene expression offers a number of advantages over plasmid-based synthetic biology. However, the methods applied for bacterial genome engineering are still challenging and far from being standardized. Here, in an attempt to realize the simplest recombinant genome technology imaginable and facilitate the transition from recombinant plasmids to genomes, we create a simplistic methodology and a comprehensive strain collection called the Standardized Genome Architecture (SEGA). In its simplest form, SEGA enables genome engineering by combining only two reagents: a DNA fragment that can be ordered from a commercial vendor and a stock solution of bacterial cells followed by incubation on agar plates. Recombinant genomes are identified by visual inspection using green-white colony screening akin to classical blue-white screening for recombinant plasmids. The modular nature of SEGA allows precise multi-level control of transcriptional, translational, and post-translational regulation. The SEGA architecture simultaneously supports increased standardization of genetic designs and a broad application range by utilizing well-characterized parts optimized for robust performance in the context of the bacterial genome. Ultimately, its adaption and expansion by the scientific community should improve predictability and comparability of experimental outcomes across different laboratories.


Assuntos
Bactérias/genética , Engenharia Genética/métodos , Genoma Bacteriano , Biologia Sintética/métodos , Cromossomos , Escherichia coli/genética , Citometria de Fluxo/métodos , Regulação Bacteriana da Expressão Gênica , Vetores Genéticos , Plasmídeos , Regiões Promotoras Genéticas , Recombinação Genética , Padrões de Referência
15.
Nat Commun ; 12(1): 5865, 2021 10 07.
Artigo em Inglês | MEDLINE | ID: mdl-34620869

RESUMO

Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular biological phenomenon. This process is driven by the formation of chromosome loops. The ATP consuming motor, condensin, interacts with chromatin segments to actively extrude loops. Motivated by real-time imaging of loop extrusion (LE), we created an analytically solvable model, predicting the LE velocity and step size distribution as a function of external load. The theory fits the available experimental data quantitatively, and suggests that condensin must undergo a large conformational change, induced by ATP binding, bringing distant parts of the motor to proximity. Simulations using a simple model confirm that the motor transitions between an open and a closed state in order to extrude loops by a scrunching mechanism, similar to that proposed in DNA bubble formation during bacterial transcription. Changes in the orientation of the motor domains are transmitted over ~50 nm, connecting the motor head and the hinge, thus providing an allosteric basis for LE.


Assuntos
Adenosina Trifosfatases/metabolismo , Proteínas de Ligação a DNA/metabolismo , DNA/metabolismo , Complexos Multiproteicos/metabolismo , Bactérias/genética , Cromatina , Cromossomos/metabolismo , DNA/química , Técnicas Genéticas , Humanos , Cinética , Modelos Genéticos , Transcrição Genética
16.
J Transl Med ; 19(1): 416, 2021 10 09.
Artigo em Inglês | MEDLINE | ID: mdl-34625066

RESUMO

BACKGROUND: In vitro oocyte maturation (IVM) is being increasingly approached in assisted reproductive technology (ART). This study aimed to evaluate the quality of embryos generated by in-vitro matured immature follicles, as a guideline for further clinical decision-making. METHODS: A total of 52 couples with normal karyotypes underwent in vitro fertilization, and 162 embryos were donated for genetic screening. Embryos in IVF group were generated by mature follicles retrieved during gonadotrophin-stimulated in vitro fertilization (IVF) cycles. And embryos in IVM group were fertilized from IVM immature oocytes. RESULTS: The average age of the women was 30.50 ± 4.55 years (range 21-42 years) with 87 embryos from IVF group and 75 embryos from IVM group. The rate of aneuploid with 28 of the 87 (32.2%) embryos from IVF group and 21 of the 75 (28%) embryos from IVM group, with no significant difference. The frequency of aneuploid embryos was lowest in the youngest age and increased gradually with women's age, whether in IVF group or IVM group and risen significantly over 35 years old. The embryos with morphological grade 1 have the lowest aneuploidy frequency (16.6%), and increase by the grade, especially in IVF group. In grade 3, embryos in IVM group were more likely to be euploid than IVF group (60% vs 40%, respectively). CONCLUSIONS: IVM does not affect the quality of embryos and does not increase the aneuploidy rate of embryos. It is clinically recommended that women more than 35 years have a high aneuploidy rate and recommended to test by PGS (strongly recommended to screened by PGS for women more than 40 years). Women aged less than 35 years old for PGS according to their physical and economic conditions. Embryo with poor quality is also recommended to test by PGS, especially for grade III embryos.


Assuntos
Aneuploidia , Técnicas de Maturação in Vitro de Oócitos , Adulto , Cromossomos , Feminino , Fertilização In Vitro , Humanos , Oócitos , Adulto Jovem
17.
BMC Genomics ; 22(1): 644, 2021 Sep 06.
Artigo em Inglês | MEDLINE | ID: mdl-34488632

RESUMO

BACKGROUND: Inversion Symmetry is a generalization of the second Chargaff rule, stating that the count of a string of k nucleotides on a single chromosomal strand equals the count of its inverse (reverse-complement) k-mer. It holds for many species, both eukaryotes and prokaryotes, for ranges of k which may vary from 7 to 10 as chromosomal lengths vary from 2Mbp to 200 Mbp. Building on this formalism we introduce the concept of k-mer distances between chromosomes. We formulate two k-mer distance measures, D1 and D2, which depend on k. D1 takes into account all k-mers (for a single k) appearing on single strands of the two compared chromosomes, whereas D2 takes into account both strands of each chromosome. Both measures reflect dissimilarities in global chromosomal structures. RESULTS: After defining the various distance measures and summarizing their properties, we also define proximities that rely on the existence of synteny blocks between chromosomes of different bacterial strains. Comparing pairs of strains of bacteria, we find negative correlations between synteny proximities and k-mer distances, thus establishing the meaning of the latter as measures of evolutionary distances among bacterial strains. The synteny measures we use are appropriate for closely related bacterial strains, where considerable sections of chromosomes demonstrate high direct or reversed equality. These measures are not appropriate for comparing different bacteria or eukaryotes. K-mer structural distances can be defined for all species. Because of the arbitrariness of strand choices, we employ only the D2 measure when comparing chromosomes of different species. The results for comparisons of various eukaryotes display interesting behavior which is partially consistent with conventional understanding of evolutionary genomics. In particular, we define ratios of minimal k-mer distances (KDR) between unmasked and masked chromosomes of two species, which correlate with both short and long evolutionary scales. CONCLUSIONS: k-mer distances reflect dissimilarities among global chromosomal structures. They carry information which aggregates all mutations. As such they can complement traditional evolution studies , which mainly concentrate on coding regions.


Assuntos
Cromossomos , Genômica , Inversão Cromossômica , Cromossomos/genética , Eucariotos , Evolução Molecular , Humanos , Sintenia
18.
BMC Genomics ; 22(1): 665, 2021 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-34521340

RESUMO

BACKGROUND: It is important to resolve the evolutionary history of species genomes as it has affected both genome organization and chromosomal architecture. The rapid innovation in sequencing technologies and the improvement in assembly algorithms have enabled the creation of highly contiguous genomes. DNA Zoo, a global organization dedicated to animal conservation, offers more than 150 chromosome-length genome assemblies. This database has great potential in the comparative genomics field. RESULTS: Using the donkey (Equus asinus asinus, EAS) genome provided by DNA Zoo as an example, the scaffold N50 length and Benchmarking Universal Single-Copy Ortholog score reached 95.5 Mb and 91.6%, respectively. We identified the cytogenetic nomenclature, corrected the direction of the chromosome-length sequence of the donkey genome, analyzed the genome-wide chromosomal rearrangements between the donkey and horse, and illustrated the evolution of the donkey chromosome 1 and horse chromosome 5 in perissodactyls. CONCLUSIONS: The donkey genome provided by DNA Zoo has relatively good continuity and integrity. Sequence-based comparative genomic analyses are useful for chromosome evolution research. Several previously published chromosome painting results can be used to identify the cytogenetic nomenclature and correct the direction of the chromosome-length sequence of new assemblies. Compared with the horse genome, the donkey chromosomes 1, 4, 20, and X have several obvious inversions, consistent with the results of previous studies. A 4.8 Mb inverted structure was first discovered in the donkey chromosome 25 and plains zebra chromosome 11. We speculate that the inverted structure and the tandem fusion of horse chromosome 31 and 4 are common features of non-caballine equids, which supports the correctness of the existing Equus phylogeny to an extent.


Assuntos
Cromossomos Humanos Par 1 , Equidae , Animais , Cromossomos/genética , Cromossomos Humanos Par 5 , Equidae/genética , Genoma , Cavalos/genética , Humanos
19.
Medicina (Kaunas) ; 57(9)2021 Aug 24.
Artigo em Inglês | MEDLINE | ID: mdl-34577783

RESUMO

Background and objectives: The chromosome locus 20q11.21 is a commonly amplified locus in colorectal cancer, with a prevalence of 8% to 9%. Several candidate cancer-associated genes are transcribed from the locus. The therapeutic implications of the amplification in colorectal cancer remain unclear. Materials and Methods: Preclinical cell line models of colorectal cancer included in the Cancer Cell Line Encyclopedia (CCLE) collection were examined for the presence of amplifications in 20q11.21 genes. Correlations of the presence of 20q11.21 amplifications with gene essentialities and drug sensitivities were surveyed on salient databases for determination of therapeutic leads. Results: A significant subset of colorectal cancer cell lines in the CCLE (12 of 63 cell lines, 19%) bear amplifications of genes located at 20q11.21. Cancer-associated genes of the locus include ASXL1, DNMT3B, BCL2L1, TPX2, KIF3B and POFUT1. These genes are all amplified in the 12 cell lines, but they are variably over-expressed at the mRNA level, compared to non-amplified lines. 20q11.21 amplified cell lines are sensitive to various tyrosine kinase inhibitors and are resistant to chemotherapy drugs targeting the mitotic apparatus and microtubules. CRISPR and RNAi dependencies screening revealed, besides the ß-catenin and KRAS genes, a few recurrent gene dependencies in more than one cell line, including YAP1 and JUP. Conclusions: Cell line models of colorectal cancer with 20q11.21 gene amplifications display dependencies on the presence of specific genes and resistance or sensitivity to specific drugs and drug categories. Observations from in vitro models may form the basis for clinical drug development in this subtype of colorectal cancer. Genetic lesions conferring synthetic lethality to certain drugs or categories of drugs could be discovered with this approach.


Assuntos
Neoplasias Colorretais , Preparações Farmacêuticas , Linhagem Celular Tumoral , Cromossomos , Neoplasias Colorretais/tratamento farmacológico , Neoplasias Colorretais/genética , Amplificação de Genes , Humanos , Cinesina , Fatores de Transcrição
20.
Zool Res ; 42(5): 660-665, 2021 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-34472227

RESUMO

Flatheads are valuable commercial fish species endemic to the Indo-West Pacific. Due to their economic value and unique biological traits, such as metamorphosis and camouflage, they serve as ideal marine organisms for studies on demersal adaptation and evolution. The brown-spotted flathead (Platycephalus sp.1) is the most widely distributed in the northwestern Pacific. Despite the lack of a valid scientific name, it has been long recognized and exploited in the marine fisheries of China, Japan, and Korea. In the current study, we applied Illumina, PacBio, and Hi-C sequencing to assemble a chromosome-scale genome for this species. The assembled genome was 660.63 Mb long with a scaffold N50 of 28.65 Mb and 100% of the contigs were anchored onto 24 chromosomes. We predicted 22 743 protein-coding genes, 94.8% of which were functionally annotated. Comparative genomic analyses suggested that Platycephalus sp.1 diverged from its common ancestor with Gasterosteus aculeatus ~88.4 million years ago. The expanded gene families were significantly enriched in immune, biosynthetic, and metabolic pathways. Furthermore, three shared Gene Ontology terms and 377 common positively selected genes were identified between flathead and flatfish species, suggesting that these genes may contribute to demersal adaptation in flatheads. The assembled genomic data provide a valuable molecular resource for further research on the biological and adaptive evolution of flathead species.


Assuntos
Adaptação Fisiológica/genética , Cromossomos/genética , Peixes/genética , Genoma , Genômica/métodos , Animais , Oceano Pacífico , Filogenia
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