Nuclear–cytoplasmic balance: whole genome duplications induce elevated organellar genome copy number

The plant genome is partitioned across three distinct subcellular compartments: the nucleus, mitochondria, and plastids. Successful coordination of gene expression among these organellar genomes and the nuclear genome is critical for plant function and fitness. Whole genome duplication (WGD) events in the nucleus have played a major role in the diversification of land plants and are expected to perturb the relative copy number (stoichiometry) of nuclear, mitochondrial, and plastid genomes. Thus, elucidating the mechanisms whereby plant cells respond to the cytonuclear stoichiometric imbalance that follows WGDs represents an important yet underexplored question in understanding the evolutionary consequences of genome doubling. We used droplet digital PCR to investigate the relationship between nuclear and organellar genome copy numbers in allopolyploids and their diploid progenitors in both wheat and Arabidopsis. Polyploids exhibit elevated organellar genome copy numbers per cell, largely preserving the cytonuclear stoichiometry observed in diploids despite the change in nuclear genome copy number. To investigate the timescale over which cytonuclear stoichiometry may respond to WGD, we also estimated the organellar genome copy number in Arabidopsis synthetic autopolyploids and in a haploid-induced diploid line. We observed corresponding changes in organellar genome copy number in these laboratory-generated lines, indicating that at least some of the cellular response to cytonuclear stoichiometric imbalance is immediate following WGD. We conclude that increases in organellar genome copy numbers represent a common response to polyploidization, suggesting that maintenance of cytonuclear stoichiometry is an important component in establishing polyploid lineages.     

Rare chromosomal aberrations in the Shereshevski?-Turner syndrome

Among 106 females with the Turner syndrome phenotype, two displayed rare chromosomal anomalies. In one patient, in addition to X-chromosome monosomy, among cultured lymphocytes cells with two isochromosomes made by long arms of X-chromosome were detected. Their frequency was 25%, and this value was the same in cultures obtained repeatedly after 3 and 5 months, which may suggest a certain stability of this clone. The other patient had a combination of two aberrations never reported before: the combination of isochromosome Xq and the Robertsonian translocation 13; 14. By their phenotype, these two women did not change from other patients with isochromosome Xq.     

Designing a simple multiplex ligation-dependent probe amplification （MLPA） assay for rapid detection of copy number variants in the genome

Copy number variants （CNVs） are pervasive in the human genome and are responsible for many Mendelian diseases and genomic disorders. The detection of CNVs is an essential element of a complete mutation screening strategy. Many techniques have been developed for gene dosage testing. Multiplex ligation-dependent probe amplification （MLPA） is a robust, easy and flexible technique that can detect both deletions and duplications for more than 40 loci in one assay. It has been widely used in research and diagnostic laboratories. We routinely develop our own MLPA assays for quick validation of array comparative genomic hybridization （CGH） findings. Here we discuss the general principles and critical aspects of MLPA assay development and validation using all synthetic MLPA probes. We believe that MLPA will play important roles in the rapid detection of genomic disorders associated with genomic imbalances, the confirmation of pathogenic mutations involving exonic deletions/duplications, CNV genotyping and population frequency analysis of CNVs.     

A genome wide association study between copy number variation （CNV） and human height in Chinese population

Copy number variation (CNV) is a type of genetic variation which may have important roles in phenotypic variability and disease susceptibility. To hunt for genetic variants underlying human height variation, we performed a genome wide CNV association study for human height in 618 Chinese unrelated subjects using Affymetrix 500K array set. After adjusting for age and sex, we found that four CNVs at 6p21.3, 8p23.3-23.2, 9p23 and 16p12.1 were associated with human height (with borderline significant p value: 0.013, 0.011, 0.024, 0.049; respectively). However, after multiple tests correction, none of them was associated with human height. We observed that the gain of copy number (more than 2 copies) at 8p23.3-23.2 was associated with lower height (normal copy number vs. gain of copy number; 161.2 cm vs. 153.7 cm, p = 0.011), which accounted for 0.9% of height variation. Loss of copy number (less than 2 copies) at 6p21.3 was associated with 0.8% lower height (loss of copy number vs. normal copy number: 154.5 cm vs. 161.1 cm, p = 0.013). Since no important genes influencing height located in CNVs at loci of 8p23.3-23.2 and 6p21.3, the two CNVs may cause the structural rearrangements of neighbored important candidate genes, thus regulates the variation of height. Our results expand our knowledge of the genetic factors underlying height variation and the biological regulation of human height.     

Assessing structural variation in a personal genome—towards a human reference diploid genome

Background

Characterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and methods are available to detect these structural variants (SVs), they remain less characterized than smaller variants because of SV diversity, complexity, and size. These challenges are exacerbated by the experimental and computational demands of SV analysis. Here, we characterize the SV content of a personal genome with Parliament, a publicly available consensus SV-calling infrastructure that merges multiple data types and SV detection methods.

Results

We demonstrate Parliament’s efficacy via integrated analyses of data from whole-genome array comparative genomic hybridization, short-read next-generation sequencing, long-read (Pacific BioSciences RSII), long-insert (Illumina Nextera), and whole-genome architecture (BioNano Irys) data from the personal genome of a single subject (HS1011). From this genome, Parliament identified 31,007 genomic loci between 100 bp and 1 Mbp that are inconsistent with the hg19 reference assembly. Of these loci, 9,777 are supported as putative SVs by hybrid local assembly, long-read PacBio data, or multi-source heuristics. These SVs span 59 Mbp of the reference genome (1.8%) and include 3,801 events identified only with long-read data. The HS1011 data and complete Parliament infrastructure, including a BAM-to-SV workflow, are available on the cloud-based service DNAnexus.

Conclusions

HS1011 SV analysis reveals the limits and advantages of multiple sequencing technologies, specifically the impact of long-read SV discovery. With the full Parliament infrastructure, the HS1011 data constitute a public resource for novel SV discovery, software calibration, and personal genome structural variation analysis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1479-3) contains supplementary material, which is available to authorized users.     

What regulates mitochondrial DNA copy number in animal cells?

The study of the control of mitochondrial DNA copy number spans several decades and has identified many factors involved in the replication of the mitochondrial genome. However, the mechanisms involved in the regulation of this process are still obscure, particularly in animal cells. During the past decade, however, the identification of human diseases associated with drastically reduced levels of mtDNA caused renewed interest in this topic. Here, I will discuss recent work that sheds some light on how animal cells might maintain and control mtDNA levels.     

Ploidy-specific interactions of three host plants with arbuscular mycorrhizal fungi: Does genome copy number matter?

? Premise of the study: Polyploidy has been shown to affect different plant traits and modulate interactions between plants and other organisms, such as pollinators and herbivores. However, no information is available on whether it can also shape the functioning of mycorrhizal symbiosis. ? Methods: The mycorrhizal growth response was assessed for three angiosperms with intraspecific ploidy variation. Different cytotypes of Aster amellus, Campanula gentilis, and Pimpinella saxifraga were either left uninoculated or were inoculated with arbuscular mycorrhizal (AM) fungi in a pot experiment. After 3 mo of cultivation in a greenhouse, plant growth, phosphorus concentration in the shoot biomass, and development of the AM symbiosis were evaluated. ? Key results: No significant ploidy-specific differences in AM development were recorded. The inoculation led to consistently greater phosphorus uptake; however, the effect on plant growth differed considerably among plant species, populations, ploidy levels, and AM species. A salient ploidy-specific response was observed in A. amellus. Whereas diploid plants benefited from AM inoculation, the hexaploids consistently showed negative or no-growth responses (depending on the AM species). In contrast to A. amellus, no interactions between inoculation and ploidy were observed in C. gentilis and P. saxifraga. ? Conclusions: The first evidence is provided of a ploidy-specific response of a mycotrophic plant to AM fungi. Our results demonstrate the complexity of interaction between plants and associated AM fungi, with the ploidy level of the host plant being one component that may modulate the functioning of the symbiosis.     

On the origins of tandemly repeated genes: Does histone gene copy number inDrosophila reflect chromosomal location?

Widely regarded beliefs aboutDrosophila histone gene copy numbers and developmental requirements have been generalized from fairly limited data since studies on histone gene arrangements and copy numbers have been largely confined to a single species,D. melanogaster. Histone gene copy numbers and chromosomal locations were examined in three species:D. melanogaster, D. hydei andD. hawaiiensis. Quantitative whole genome blot analysis of DNA from diploid tissues revealed a tenfold variability in histone gene copy numbers for these three species. In situ hybridization to polytene chromosomes showed that the histone DNA (hDNA) chromosomal location is different in all three species. These observations lead us to propose a relationship between histone gene reiteration and chromosomal position.     

Effects of α-particles on survial and chromosomal aberrations in human mammary epithelial cells

We have studied the radiation responses of a human mammary epithelial cell line, H184B5 F5-1 M/10. This cell line was derived from primary mammary cells after treatment with chemicals and heavy ions. The F5-1 M/10 cells are immortal, density-inhibited in growth, and non-tumorigenic in athymic nude mice and represent an in vitro model of the human epithelium for radiation studies. Because epithelial cells are the target of -particles emitted from radon daughters, we concentrated our studies on the efficiency of -particles. Confluent cultures of M/10 cells were exposed to accelerated -particles [beam energy incident at the cell monolayer=3.85 MeV, incident linear energy transfer (LET) in cell= 109 keV/µm] and, for comparison, to 80 kVp x-rays. The following endpoints were studied: (1) survival, (2) chromosome aberrations at the first postirradiation mitosis, and (3) chromosome alterations at later passages following irradiation. The survival curve was exponential for -particles (D₀ = 0.73± 0.04 Gy), while a shoulder was observed for x-rays (/ = 2.9 Gy; D₀ = 2.5 Gy, extrapolation number 1.6). The relative biological effectiveness (RBE) of high-LET -particles for human epithelial cell killing was 3.3 at 37% survival. Dose-response curves for the induction of chromosome aberrations were linear for cc-particles and linear-quadratic for x-rays. The RBE for the induction of chromosome aberrations varied with the type of aberration scored and was high (about 5) for chromosome breaks and low (about 2) for chromosome exchanges. The RBE for the induction of total chromosome aberrations (2.3 at 37% cell survival) was lower than that for cell survival, suggesting that chromosome damage at the first postirradiation mitosis is not sufficient to account for the increased efficiency of -particles in the induction of lethal effects. However, measured cell survival after -particle irradiation can be predicted from chromosome damage when cells at different population doubling numbers after irradiation are considered. In fact, a high percentage of -irradiated cells carried unstable chromosomal aberrations up to population doubling number about 5. On the other hand, x-ray-induced damage disappeared rapidly. These results suggest that -particle-induced reproductive death of human mammary epithelial cells is caused by chromosome damage in the first 5 generations following exposure, whereas the in-activation produced by low-LET radiation is mostly related to the aberrations at the first post-irradiation mitosis.     

Quantitative real-time PCR as a screening tool for estimating transgene copy number in WHISKERS™-derived transgenic maize

. Quantitative real-time PCR (qRT-PCR) was adapted to estimate transgene copy number in transgenic maize callus and plants. WHISKERS™-derived transgenic callus lines and plants were generated using two different gene constructs. These transgenic materials represented a range of copy number. A 'standard curve' was established by mixing plasmid DNA with non-transgenic genomic maize DNA using a calculated ratio of target gene to host genome size. 'Estimated' copy number in the callus lines and plants using qRT-PCR was correlated with the 'actual' copy number based on Southern blot analysis. The results indicated that there was a significant correlation between the two methods with both gene constructs. Thus, qRT-PCR represents an efficient means of estimating copy number in transgenic maize.     

Evaluation of SHOX copy number variations in patients with Müllerian aplasia

Background

Thymic epithelial tumours (thymoma and carcinoma) are exceptionally rare in children. We describe a national multicentre series with a view to illustrating their clinical behaviour and the results of treatment.

Methods

From January 2000 all patients under 18 years of age diagnosed with "rare paediatric tumours" were centrally registered by the Italian centres participating in the TREP project (Tumori Rari in Età Pediatrica [Rare Tumours in Paediatric Age]). The clinical data of children with a thymic epithelial tumour registered as at December 2009 were analyzed for the purposes of the present study.

Results

Our series comprised 4 patients with thymoma and 5 with carcinoma (4 males, 5 females; median age 12.4 years). The tumour masses were mainly large, exceeding 5 cm in largest diameter. Based on the Masaoka staging system, 3 patients were stage I, 1 was stage III, 1 was stage IVa and 4 were stage IVb. All 3 patients with stage I thymoma underwent complete tumour resection at diagnosis and were alive 22, 35 and 93 months after surgery. One patient with a thymoma metastasizing to the kidneys died rapidly due to respiratory failure. Thymic carcinomas were much more aggressive, infiltrating nearby organs (in 4 cases) and regional nodes (in 5), and spreading to the bone (in 3) and liver (in 1). All patients received multidrug chemotherapy (platinum derivatives + etoposide or other drugs) with evidence of tumour reduction in 3 cases. Two patients underwent partial tumour resection (after chemo-radiotherapy in one case) and 4 patients were given radiotherapy (45-54 Gy). All patients died of their disease.

Conclusions

Children with thymomas completely resected at diagnosis have an excellent prognosis while thymic carcinomas behave aggressively and carry a poor prognosis despite multimodal treatment.     

How many genes in a genome?

Despite the current good level of annotation, the Drosophila genome still holds surprises. A recent study has added perhaps 2,000 genes to the predicted total, and raises a number of questions about how genome annotation data should be stored and presented.     

Whole genome sequencing of cotton—a new chapter in cotton genomics

<正>A Cotton Genome Consortium led by the Cotton Research Institute,Chinese Academy of Agricultural Sciences,with scientists from Peking University,Wuhan University,BGI and US Department of Agriculture Southern Plains Research Center has completed the genome sequence of the allotetraploid G.hirsutum(At Dt)by using the second-generation high-throughput sequencing technology     

N-Methyl-N′-nitro-N-nitrosoguanidine-induced light emission in Chinese hamster cell cultures: correlation with enhancement of chromosomal aberrations

N-Methyl-N′-nitro-N-nitrosoguanidine (MNNG) was found to induce an ultraweak photon emission in cultures of Chinese hamster fibroblasts (CHL). Measurements suggest that the light emission is due to a reaction between MNNG and cellular metabolites. The light emission depended on the concentration of MNNG and was oxygen-dependent, disappearing in a nitrogen atmosphere. Superoxide dismutase (SOD) or sodium azide decreased the emission intensity. The production of chromosomal aberrations in CHL by MNNG was correlated with the light emission intensity and was inhibited in the presence of SOD.