Unstable Allotetraploid Tobacco Genome due to Frequent Homeologous Recombination, -. Segmental Deletion, and Chromosome Loss

The types of mutations and their corresponding frequencies are difficult to measure in complex genomes. In this study, a high-throughput method was developed to identify spontaneous loss-of-function alleles for the resistance gene N and the transgenic avirulence gene P50 in allotetraploid tobacco. A total of 2134 loss- of-function alleles of the N gene were identified after screening 14 million F1 hybrids. Analysis of these mutants revealed striking evolutionary patterns for genes in polyploids. Only 14 of the loss-of-function mutations were caused by spontaneous point mutations or indels, while the others were caused by home- ologous recombination （with a frequency of 1/12 000） or chromosome loss （1/15 000）. Loss of the chromosome with the PS0 insertion occurred at a similar frequency （1/13 000）, and the frequency of spon- taneous segmental deletion in this chromosome was 1/16 000. Both homeologous recombination and chromosome loss considerably decreased the viability of the mutants. Our data suggest that the high mutation rate in polyploids is probably due to the occurrence of homeologous recombination and the toler- ance of large mutations such as chromosome loss in polyploid genomes. Frequent mutations tend to drive polyploids to extinction unless a novel mutation helps the polyploid to effectively compete with diploids or find a new ecological niche.

Loss of heterozygosity for loci on chromosome arms 1p and 10q in oligoden-droglial tumors: relationship to outcome and chemosensitivity

Oligodendroglial tumors frequently have deletions ofchromosomal loci on lp and l9q.Loas of heterozygosity(LOH)of chromosome 10 may be a negative prognostic factor.We reviewed 23 patients with oligodendroglial tumors,toevaluate the frequency of lp and 10q LOH and correlate with clinical outcome.Three loci(DlS402,DlSl 172,MCT118)on lp and 2 loci(Dl0S520 and D10S521)on 10q were analyzed for LOH using PCR techniques.

Roles of Loss of Chromosome 14q Allele in the Prognosis of Renal Cell Carcinoma with C-reactive Protein Abnormity

Background：Renal cell carcinoma （RCC） is frequently associated with paraneoplastic inflammatory syndrome （PIS）.This study aimed at exploring the connections between the survival rate and specific gene alterations and the potential mechanism.Methods：We retrospectively studied 69 surgical RCC cases from August 2014 to February 2016,including 18 cases of clear cell RCC （ccRCC） demonstrating elevated pretreatment serum C-reactive protein （CRP,Group A）.Twelve of the 18 cases were symptomized with febrile episode.We also selected 49 cases ofccRCC with normal pretreatment CRP （Group B）.Using 22 microsatellite markers,we compared the incidence of loss of heterozygosity （LOH） between Group A and Group B.All statistical tests are two-sided.Results：The 3p LOH was common in both Group A （89%） and Group B （92%）.The frequency of 14q LOH in Group A （16 of 18） was higher than Group B （4 of 49,χ^2 =40.97 P 〈 0.0001）.The 3p and 14q LOH were the characteristics of ccRCC with elevated acute phase reactants,including PIS,regardless of the presence of metastasis.On the contrary,14q LOH was a rare genomic alternation in advanced-staged ccRCC without PIS.The overall survival of patients with elevated CRP （33.3%） was lower than its counterparts （6.1%,hazard ratio=1.852,P 〈 0.0001） in Kaplan-Meier curve.Conclusions：The results imply that the disruption ofa 14q gene（s） might result in not only the inflammatory manifestations in the tumor host but also the poor survival rate as well.The isolation of the gene（s） on 14q might be a vital goal in the treatment of PIS-associated RCC.

Loss of heterozygosity on chromosome 22 in sporadic schwannoma and its relation to the proliferation of tumor cells

Background Schwannoma is the tumor arising mainly from the cranial and spinal nerves. Bilateral vestibular schwannoma is the hallmark of neurofibromatosis type 2 （NF2）. The NF2 gene has been cloned with comprehensive analysis of its mutations in schwannoma. However, most studies focused on vestibular schwannoma. There are differences in proliferation of tumor cell and uhrastructure between vestibular and spinal schwannomas. It is unknown whether genetic alterations in vestibular schwannoma are different from those in non-vestibular schwannoma. We analyzed the loss of heterozygosity （LOH） on chromosome 22 in patients with sporadic schwannoma including vestibular and spinal schwannomas and correlated this genetic alteration with tumor proliferation. Methods In 54 unrelated patients without clinical NF1 or NF2, 36 patients had sporadic vestibular schwannoma, and 18 dorsal spinal root schwannoma. Four highly polymorphic linkage to NF2 gene microsatellite DNA markers （D22S264, D22S268, D22S280, CRYB2） were used to analyze LOH. The proliferative index was evaluated by Ki-67 and proliferative cell nuclear antigen （PCNA） immunostaining. Student＇s t test was used to analyze the difference of the proliferative index between schwannoma with LOH and that without LOH. The difference of the frequency of LOH in vestibular and spinal schwannomas was investigated by the chi-square test. Results Twenty-three schwannomas （42. 6% , 23/54） showed allele loss. The frequency of LOH in vestibular schwannoma was significantly higher than that in spinal schwannoma （ X^2 = 5.14, P 〈 0.05 ）. The proliferative index of schwannoma with LOH was significantly higher than that without LOH （tki-67 = 2. 97, P= 0. 0045 ; tPCNA =2.93, P =0. 0051）. Conclusions LOH on chromosome 22 is a frequent there is a correlation between LOH on chromosome 22 event in the tumorigenesis of sporadic schwannoma. And, and proliferative activity in schwannoma. The frequency of LOH in vestibular schwannoma is significantly different from that in spinal schwannoma.

Effects of age on segregation of the X and Y chromosomes in cultured lymphocytes from Chinese men

Chromosome malsegregation in binucleated lymphocytes is a useful endpoint to evaluate age effect on genetic stability. However, the investigations on chromosome malsegregation in binucleated lymphocytes from Chinese are scarce. In this study, peripheral blood lym- phocytes were collected from 14 old （60-70 years） and 10 young （22-26 years） healthy Chinese men. To detect malsegregation of the sex chromosomes, multi-color fluorescence in situ hybridization （FISH） was performed on binucleated lymphocytes, cytokinesis-blocked by cytochalasin B at the first mitosis after phytohaemagglutinin stimulation. Compared with that in young men, a significant increase in frequencies of loss of chromosome X （9.2± 3.2‰ vs. 1.1 ± 0.9‰, P 〈 0.001） and Y （2.5 ± 1.9‰ vs. 0.2± 0.3‰, P 〈 0.001） was found in old men. Similarly, nondisjunction of chromosome X （16.5± 3.4‰ vs. 3.5 ± 1.1‰, P 〈 0.001） and Y （7.2 ± 2.6‰ vs. 2.4 ± 1.3‰, P 〈 0.001） occurred more frequently in old men than in young men. Regardless of donor＇s age, nondisjunction is more prevalent than loss for both chromosome X and Y. The frequencies of observed simultaneous malsegregation were relatively higher than the expected, suggest- ing an association between malsegregation. These results indicated that in Chinese men, malsegregation of the sex chromosomes increases with age in an associated fashion, and nondisjunction accounts for the majority of spontaneous chromosome malsegregation.

Dual role of lipids for genome stability and pluripotency facilitates full potency of mouse embryonic stem cells

While Mek1/2 and Gsk3βinhibition("2i")supports the maintenance of murine embryonic stem cells(EsCs)in a homogenous naive state,prolonged culture in 2i results in aneuploidy and DNA hypomethylation that impairs developmental potential.Additionally,2i fails to support derivation and culture of fully potent female ESCs.Here we find that mouse ESCs cultured in 2i/LIF supplemented with lipid-rich albumin(AlbuMAx)undergo pluripotency transition yet maintain genomic stability and full potency over long-term culture.Mechanisticaily,lipids in AlbuMAx impact intracellular metabolism including nucleotide biosynthesis,lipid biogenesis,and TCA cycle intermediates,with enhanced expression of DNMT3s that prevent DNA hypomethylation.Lipids induce a formative-like pluripotent state through direct stimulation of Erk2 phosphorylation,which also alleviates X chromosome loss in female ESCs.Importantly,both male and female"all-ESc"mice can be generated from de novo derived ESCs using AlbuMAXbased media.Our findings underscore the importance of lipids to pluripotency and link nutrient cues to genome integrity in early development.

Dentromere Size and Its Relationship to Haploid Formation in Plants

Wide species crosses often result in uniparental genome elimination and visible failures in centromere func- tion. Crosses involving lines with mutated forms of the CENH3 histone variant that organizes the centromere/ kinetochore interface have been shown to have similar effects, inducing haploids at high frequencies. Here, we propose a simple centromere size model that endeavors to explain both observations. It is based on the idea of a quantitative centromere architecture where each centromere in an individual is the same size, and the average size is dictated by a natural equilibrium between bound and unbound CENH3 （and its chaperones or binding proteins）. While centromere size is determined by the cellular milieu, centromere positions are heritable and defined by the interactions of a small set of proteins that bind to both DNA and CENH3. Lines with defective or mutated CENH3 have a lower loading capacity and support smaller centromeres. In cases where a line with small or defective centromeres is crossed to a line with larger or normal centromeres, the smaller/defective centromeres are selectively degraded or not maintained, resulting in chromosome loss from the small-centromere parent. The model is testable and generalizable, and helps to explain the coun- terintuitive observation that inducer lines do not induce haploids when crossed to themselves.