Showing papers on "Chromosome published in 2013"

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

Abstract: Large-scale chromosome structure and spatial nuclear arrangement have been linked to control of gene expression and DNA replication and repair Genomic techniques based on chromosome conformation capture (3C) assess contacts for millions of loci simultaneously, but do so by averaging chromosome conformations from millions of nuclei Here we introduce single-cell Hi-C, combined with genome-wide statistical analysis and structural modelling of single-copy X chromosomes, to show that individual chromosomes maintain domain organization at the megabase scale, but show variable cell-to-cell chromosome structures at larger scales Despite this structural stochasticity, localization of active gene domains to boundaries of chromosome territories is a hallmark of chromosomal conformation Single-cell Hi-C data bridge current gaps between genomics and microscopy studies of chromosomes, demonstrating how modular organization underlies dynamic chromosome structure, and how this structure is probabilistically linked with genome activity patterns

Replication stress links structural and numerical cancer chromosomal instability

Abstract: Cancer chromosomal instability (CIN) results in an increased rate of change of chromosome number and structure and generates intratumour heterogeneity. CIN is observed in most solid tumours and is associated with both poor prognosis and drug resistance. Understanding a mechanistic basis for CIN is therefore paramount. Here we find evidence for impaired replication fork progression and increased DNA replication stress in CIN(+) colorectal cancer (CRC) cells relative to CIN(-) CRC cells, with structural chromosome abnormalities precipitating chromosome missegregation in mitosis. We identify three new CIN-suppressor genes (PIGN (also known as MCD4), MEX3C (RKHD2) and ZNF516 (KIAA0222)) encoded on chromosome 18q that are subject to frequent copy number loss in CIN(+) CRC. Chromosome 18q loss was temporally associated with aneuploidy onset at the adenoma-carcinoma transition. CIN-suppressor gene silencing leads to DNA replication stress, structural chromosome abnormalities and chromosome missegregation. Supplementing cells with nucleosides, to alleviate replication-associated damage, reduces the frequency of chromosome segregation errors after CIN-suppressor gene silencing, and attenuates segregation errors and DNA damage in CIN(+) cells. These data implicate a central role for replication stress in the generation of structural and numerical CIN, which may inform new therapeutic approaches to limit intratumour heterogeneity.

High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

Abstract: Chromosomes must be highly compacted and organized within cells, but how this is achieved in vivo remains poorly understood. We report the use of Hi-C to map the structure of bacterial chromosomes. Analysis of Hi-C data and polymer modeling indicates that the Caulobacter crescentus chromosome consists of multiple, largely independent spatial domains likely comprised of supercoiled plectonemes arrayed into a bottlebrush-like fiber. These domains are stable throughout the cell cycle and re-established concomitantly with DNA replication. We provide evidence that domain boundaries are established by highly expressed genes and the formation of plectoneme-free regions, whereas the histone-like proteins HU and SMC promote short-range compaction and the cohesion of chromosomal arms, respectively. Collectively, our results reveal general principles for the organization and structure of chromosomes in vivo.

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

Abstract: Loss of sexual reproduction is considered an evolutionary dead end for metazoans, but bdelloid rotifers challenge this view as they appear to have persisted asexually for millions of years. Neither male sex organs nor meiosis have ever been observed in these microscopic animals: oocytes are formed through mitotic divisions, with no reduction of chromosome number and no indication of chromosome pairing. However, current evidence does not exclude that they may engage in sex on rare, cryptic occasions. Here we report the genome of a bdelloid rotifer, Adineta vaga (Davis, 1873), and show that its structure is incompatible with conventional meiosis. At gene scale, the genome of A. vaga is tetraploid and comprises both anciently duplicated segments and less divergent allelic regions. However, in contrast to sexual species, the allelic regions are rearranged and sometimes even found on the same chromosome. Such structure does not allow meiotic pairing; instead, we find abundant evidence of gene conversion, which may limit the accumulation of deleterious mutations in the absence of meiosis. Gene families involved in resistance to oxidation, carbohydrate metabolism and defence against transposons are significantly expanded, which may explain why transposable elements cover only 3% of the assembled sequence. Furthermore, 8% of the genes are likely to be of non-metazoan origin and were probably acquired horizontally. This apparent convergence between bdelloids and prokaryotes sheds new light on the evolutionary significance of sex.

Comparative sex chromosome genomics in snakes: differentiation, evolutionary strata, and lack of global dosage compensation.

Abstract: Snakes exhibit genetic sex determination, with female heterogametic sex chromosomes (ZZ males, ZW females). Extensive cytogenetic work has suggested that the level of sex chromosome heteromorphism varies among species, with Boidae having entirely homomorphic sex chromosomes, Viperidae having completely heteromorphic sex chromosomes, and Colubridae showing partial differentiation. Here, we take a genomic approach to compare sex chromosome differentiation in these three snake families. We identify homomorphic sex chromosomes in boas (Boidae), but completely heteromorphic sex chromosomes in both garter snakes (Colubridae) and pygmy rattlesnake (Viperidae). Detection of W-linked gametologs enables us to establish the presence of evolutionary strata on garter and pygmy rattlesnake sex chromosomes where recombination was abolished at different time points. Sequence analysis shows that all strata are shared between pygmy rattlesnake and garter snake, i.e., recombination was abolished between the sex chromosomes before the two lineages diverged. The sex-biased transmission of the Z and its hemizygosity in females can impact patterns of molecular evolution, and we show that rates of evolution for Z-linked genes are increased relative to their pseudoautosomal homologs, both at synonymous and amino acid sites (even after controlling for mutational biases). This demonstrates that mutation rates are male-biased in snakes (male-driven evolution), but also supports faster-Z evolution due to differential selective effects on the Z. Finally, we perform a transcriptome analysis in boa and pygmy rattlesnake to establish baseline levels of sex-biased expression in homomorphic sex chromosomes, and show that heteromorphic ZW chromosomes in rattlesnakes lack chromosome-wide dosage compensation. Our study provides the first full scale overview of the evolution of snake sex chromosomes at the genomic level, thus greatly expanding our knowledge of reptilian and vertebrate sex chromosomes evolution.

A two-step mechanism for epigenetic specification of centromere identity and function

Abstract: The basic determinant of chromosome inheritance, the centromere, is specified in many eukaryotes by an epigenetic mark. Using gene targeting in human cells and fission yeast, chromatin containing the centromere-specific histone H3 variant CENP-A is demonstrated to be the epigenetic mark that acts through a two-step mechanism to identify, maintain and propagate centromere function indefinitely. Initially, centromere position is replicated and maintained by chromatin assembled with the centromere-targeting domain (CATD) of CENP-A substituted into H3. Subsequently, nucleation of kinetochore assembly onto CATD-containing chromatin is shown to require either the amino- or carboxy-terminal tail of CENP-A for recruitment of inner kinetochore proteins, including stabilizing CENP-B binding to human centromeres or direct recruitment of CENP-C, respectively.

Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

Abstract: We report intron chromosomal expression FISH (iceFISH), a multiplex imaging method for measuring gene expression and chromosome structure simultaneously on single chromosomes. We find substantial differences in transcriptional frequency between genes on a translocated chromosome and the same genes in their normal chromosomal context in the same cell. Correlations between genes on a single chromosome pointed toward a cis chromosome-level transcriptional interaction spanning 14.3 megabases.

Sex-biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution

Abstract: Sex chromosomes originate from autosomes. The accumulation of sexually antagonistic mutations on protosex chromosomes selects for a loss of recombination and sets in motion the evolutionary processes generating heteromorphic sex chromosomes. Recombination suppression and differentiation are generally viewed as the default path of sex chromosome evolution, and the occurrence of old, homomorphic sex chromosomes, such as those of ratite birds, has remained a mystery. Here, we analyze the genome and transcriptome of emu (Dromaius novaehollandiae) and confirm that most genes on the sex chromosome are shared between the Z and W. Surprisingly, however, levels of gene expression are generally sex-biased for all sex-linked genes relative to autosomes, including those in the pseudoautosomal region, and the male-bias increases after gonad formation. This expression bias suggests that the emu sex chromosomes have become masculinized, even in the absence of ZW differentiation. Thus, birds may have taken different evolutionary solutions to minimize the deleterious effects imposed by sexually antagonistic mutations: some lineages eliminate recombination along the protosex chromosomes to physically restrict sexually antagonistic alleles to one sex, whereas ratites evolved sex-biased expression to confine the product of a sexually antagonistic allele to the sex it benefits. This difference in conflict resolution may explain the preservation of recombining, homomorphic sex chromosomes in other lineages and illustrates the importance of sexually antagonistic mutations driving the evolution of sex chromosomes.

Non-invasive prenatal testing of fetal whole chromosome aneuploidy by massively parallel sequencing.

Abstract: Objective To determine whether non-invasive prenatal testing by maternal plasma DNA sequencing can uncover all fetal chromosome aneuploidies in one simple sequencing event. Methods Plasma samples from 435 pregnant women at high risk for Down syndrome were collected prior to amniocentesis in three hospitals in China between March 2009 and June 2011. We sequenced the plasma DNA extracted from these samples at low coverage. We discovered that the genome representation of each of the 24 chromosomes obeyed a linear relationship to its GC content. Applying this relationship, we analysed the copy number of each of the 24 chromosomes. Full fetal karyotyping was compared with maternal plasma DNA sequencing results. Results Among the 435 samples, 412 samples (94.7%) have full karyotyping and sequencing results. Sixty-seven samples containing a fetal chromosome aneuploidy, including trisomy 21, trisomy 18, trisomy 13, trisomy 9, monosomy X or others, can be accurately identified with a detection sensitivity of 100% and a detection specificity of 99.71%. Normalization of the chromosome representation values against chromosomal guanine/cytosine base content is the key issue to ensure the accuracy. Conclusions Our results indicate that non-invasive detection of fetal chromosome aneuploidies for all 24 chromosomes in one single sequencing event is feasible. © 2013 John Wiley & Sons, Ltd.

Cancer cells preferentially lose small chromosomes.

Abstract: Genetic and genomic aberrations are the primary cause of cancer. Chromosome missegregation leads to aneuploidy and provides cancer cells with a mechanism to lose tumor suppressor loci and gain extra copies of oncogenes. Using cytogenetic and array-based comparative genomic hybridization data, we analyzed numerical chromosome aneuploidy in 43,205 human tumors and found that 68% of solid tumors are aneuploid. In solid tumors, almost all chromosomes are more frequently lost than gained with chromosomes 7, 12 and 20 being the only exceptions with more frequent gains. Strikingly, small chromosomes are lost more readily than large ones, but no such inverse size correlation is observed with chromosome gains. Because of increasing levels of proteotoxic stress, chromosome gains have been shown to slow cell proliferation in a manner proportional to the number of extra gene copies gained. However, we find that the extra chromosome in trisomic tumors does not preferentially have a low gene copy number, suggesting that a proteotoxicity-mediated proliferation barrier is not sustained during tumor progression. Paradoxically, despite a bias toward chromosome loss, gains of chromosomes are a poor prognostic marker in ovarian adenocarcinomas. In addition, we find that solid and non-solid cancers have markedly distinct whole-chromosome aneuploidy signatures, which may underlie their fundamentally different etiologies. Finally, preferential chromosome loss is observed in both early and late stages of astrocytoma. Our results open up new avenues of enquiry into the role and nature of whole-chromosome aneuploidy in human tumors and will redirect modeling and genetic targeting efforts in patients.

Report Meiotic Adaptation to Genome Duplication in Arabidopsis arenosa

Abstract: SchoolofBiosciences,UniversityofBirmingham,Edgbaston,Birmingham B15 2TT, UKSummaryWhole genome duplication (WGD) is a major factor in theevolution of multicellular eukaryotes, yet by doubling thenumber of homologs, WGD severely challenges reliablechromosomesegregation[1–3],aprocessconservedacrosskingdoms [4]. Despite this, numerous genome-duplicated(polyploid) species persist in nature, indicating early prob-lems can be overcome [1, 2]. Little is known about whichgenes are involved—only one has been molecularly charac-terized [5]. To gain new insights into the molecular basis ofadaptation to polyploidy, we investigated genome-widepatterns of differentiation between natural diploids andtetraploids of Arabidopsis arenosa, an outcrossing relativeof A. thaliana [6, 7]. We first show that diploids are notpreadapted to polyploid meiosis. We then use a genomescanning approach to show that although polymorphism isextensively shared across ploidy levels, there is strongploidy-specific differentiation in 39 regions spanning 44genes. These are discrete, mostly single-gene peaks ofsharply elevated differentiation. Among these peaks areeight meiosis genes whose encoded proteins coordinate aspecific subset of early meiotic functions, suggesting thesegenes comprise a polygenic solution to WGD-associatedchromosome segregation challenges. Our findings indicatethat even conserved meiotic processes can be capable ofnimble evolutionary shifts when required.Results and DiscussionMeiotic Chromosome Behavior in Tetraploid A. arenosaAtleastinitially,WGDiscommonlyassociatedwithdeleteriouschromosome missegregation arising from multivalent associ-ations among available homologs (e.g., [1–3, 8–11]). This isespecially challenging for autopolyploids, which arise fromwithin-species duplication and have multiple approximatelyequally homologous chromosomes. We asked if for autotetra-ploidA.arenosa(1)thetetraploidmaterialweareworkingwithhas diploid-like chromosome behavior, and (2) the diploidgenome we are comparing to is not preadapted for poly-ploid meiosis, as has been seen in some species [e.g., 12].Though bivalent formation among homologs appears to berandom and inheritance tetrasomic in natural autotetraploidA. arenosa [13], metaphase I chromosomes associatepredominantly as bivalents like in diploids ([14] and Fig-ure 1A). There are structural differences, however: tetraploidshavesignificantlymorerodbivalents(andfewerringbivalents)than diploids do, which indicates natural tetraploid A. arenosaaveragesfewerchiasmataperbivalentthandiploidA.arenosa(Table S1 available online). A reduction in chiasma numberto one per bivalent has previously been suggested as apossible mechanism for meiotic diploidization in autopoly-ploids because limiting crossovers to one per chromosomeprevents multivalent associations (e.g., [10, 11]).WeinducedWGDintwodiploidA.arenosagenotypesusingcolchicine and examined chromosome behavior of confirmedneotetraploids in diakinesis and metaphase I, when multiva-lents are readily discernable. Unlike natural autotetraploids,synthetic neotetraploids exhibit extensive multivalent forma-tion and ectopic connections between the chromosomes(Figure1A;TableS1).Thecytologicalabnormalitiesintheneo-tetraploid lines correlate with sharply reduced pollen viability:the two colchicine-doubled lines had only 3% and 5% pollenviability, in contrast to two natural autotetraploid lines thathad 91% and 92% pollen viability. Thus, diploid A. arenosaprovidesan‘‘unevolved’’comparisonforthenaturaltetraploid.Bivalent associations and reduced estimated chiasma fre-quency in natural autotetraploids, and the aberrant meiosisof neotetraploids, are consistent with data from many otherautopolyploids (e.g., [8–11]), suggesting A. arenosa is a repre-sentativemodelforstudyingthemolecularbasisofadaptationto autopolyploid meiosis.Evidence of Polygenic Selection in AutotetraploidA. arenosaBecauseofitsconnectiontofertility[1,2],selectionformeioticstability immediately following WGD should be intense. Thus,we reasoned that alleles contributing to stable chromosomesegregation in the autopolyploid should show reduced allelicdiversity and excess differentiation between autotetraploidsand diploids. High genetic diversity suggests A. arenosaautotetraploids did not undergo a severe recent bottleneckassociated with WGD [7, 13] and/or have ongoing gene flowwith diploids [15]. We have previously shown evidence thatautotetraploid A. arenosa has undergone selective sweeps[13], but because diploids were not included, it remained un-known whether top outliers reflect adaptation to polyploidyor species-wide patterns shared with diploids.We used a genome scanning approach to compare thegenomes of diploid and tetraploid A. arenosa. We short-readsequenced whole genomes from 16 natural autotetraploidand 8 diploid individuals from six natural populations (Fig-ure 1B; Table S2). We aligned reads to the closely relatedA. lyrata genome [16]. More than 46 million sites had coverageinall24individuals, ofwhichabout5.6millionarepolymorphicrelative to the A. lyrata reference (Table 1). There is extensiveshared variation between diploids and autotetraploids (>1.7millionsites)andremarkablyfewfixeddifferences(26genomewide; Table 1).We scanned for signatures suggestive of selective sweepsby analyzing consecutive windows of 100 polymorphic sites

How unfinished business from S‐phase affects mitosis and beyond

Abstract: The eukaryotic cell cycle is conventionally viewed as comprising several discrete steps, each of which must be completed before the next one is initiated. However, emerging evidence suggests that incompletely replicated, or unresolved, chromosomes from S-phase can persist into mitosis, where they present a potential threat to the faithful segregation of sister chromatids. In this review, we provide an overview of the different classes of loci where this ‘unfinished S-phase business' can lead to a variety of cytogenetically distinct DNA structures throughout the various steps of mitosis. Furthermore, we discuss the potential ways in which cells might not only tolerate this inevitable aspect of chromosome biology, but also exploit it to assist in the maintenance of genome stability.

Visualization of repetitive DNA sequences in human chromosomes with transcription activator-like effectors

Abstract: We describe a transcription activator-like effector (TALE)-based strategy, termed "TALEColor," for labeling specific repetitive DNA sequences in human chromosomes. We designed TALEs for the human telomeric repeat and fused them with any of numerous fluorescent proteins (FPs). Expression of these TALE-telomere-FP fusion proteins in human osteosarcoma's (U2OS) cells resulted in bright signals coincident with telomeres. We also designed TALEs for centromeric sequences unique to certain chromosomes, enabling us to localize specific human chromosomes in live cells. Meanwhile we generated TALE-FPs in vitro and used them as probes to detect telomeres in fixed cells. Using human cells with different average telomere lengths, we found that the TALEColor signals correlated positively with telomere length. In addition, suspension cells were followed by imaging flow cytometry to resolve cell populations with differing telomere lengths. These methods may have significant potential both for basic chromosome and genome research as well as in clinical applications.

Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription

Abstract: To fit within the confines of the cell, bacterial chromosomes are highly condensed into a structure called the nucleoid. Despite the high degree of compaction in the nucleoid, the genome remains accessible to essential biological processes, such as replication and transcription. Here, we present the first high-resolution chromosome conformation capture-based molecular analysis of the spatial organization of the Escherichia coli nucleoid during rapid growth in rich medium and following an induced amino acid starvation that promotes the stringent response. Our analyses identify the presence of origin and terminus domains in exponentially growing cells. Moreover, we observe an increased number of interactions within the origin domain and significant clustering of SeqA-binding sequences, suggesting a role for SeqA in clustering of newly replicated chromosomes. By contrast, ‘histone-like’ protein (i.e. Fis, IHF and H-NS) -binding sites did not cluster, and their role in global nucleoid organization does not manifest through the mediation of chromosomal contacts. Finally, genes that were downregulated after induction of the stringent response were spatially clustered, indicating that transcription in E. coli occurs at transcription foci.

Massively Parallel Sequencing Reveals the Complex Structure of an Irradiated Human Chromosome on a Mouse Background in the Tc1 Model of Down Syndrome

Abstract: Down syndrome (DS) is caused by trisomy of chromosome 21 (Hsa21) and presents a complex phenotype that arises from abnormal dosage of genes on this chromosome. However, the individual dosage-sensitive genes underlying each phenotype remain largely unknown. To help dissect genotype – phenotype correlations in this complex syndrome, the first fully transchromosomic mouse model, the Tc1 mouse, which carries a copy of human chromosome 21 was produced in 2005. The Tc1 strain is trisomic for the majority of genes that cause phenotypes associated with DS, and this freely available mouse strain has become used widely to study DS, the effects of gene dosage abnormalities, and the effect on the basic biology of cells when a mouse carries a freely segregating human chromosome. Tc1 mice were created by a process that included irradiation microcell-mediated chromosome transfer of Hsa21 into recipient mouse embryonic stem cells. Here, the combination of next generation sequencing, array-CGH and fluorescence in situ hybridization technologies has enabled us to identify unsuspected rearrangements of Hsa21 in this mouse model; revealing one deletion, six duplications and more than 25 de novo structural rearrangements. Our study is not only essential for informing functional studies of the Tc1 mouse but also (1) presents for the first time a detailed sequence analysis of the effects of gamma radiation on an entire human chromosome, which gives some mechanistic insight into the effects of radiation damage on DNA, and (2) overcomes specific technical difficulties of assaying a human chromosome on a mouse background where highly conserved sequences may confound the analysis. Sequence data generated in this study is deposited in the ENA database, Study Accession number: ERP000439.

Just how conserved is vertebrate sex determination

Abstract: Background: Sex determination in vertebrate embryos has long been equated with gonadal differentiation into testes or ovaries. This view has been challenged over the years by reports of somatic sexual dimorphisms pre-dating gonadal sex differentiation. The recent finding that sex determination in birds is likely to be partly cell autonomous has again called for a broader definition of sex determination. Inherent sexual differentiation in each and every cell may apply widely among vertebrates, and may involve more than one “master sex gene” on a sex chromosome. At the gonadal level, key genes required for proper sexual differentiation are conserved among vertebrates, but their relative positions in the ovarian and testicular cascades differ. Results: We illustrate these differences by comparing key sex genes in fishes versus birds and mammals, with emphasis on DM domain genes and the SOX9-AMH pathway in the testis and the FOXL2-Aromatase pathway in the ovary. Such comparisons facilitate the identification of ancient versus derived genes involved in gonadal sex determination. Conclusions: The data indicate that vertebrate sex-determining cascades are not as conserved as once thought. Developmental Dynamics 242:380–387, 2013. © 2013 Wiley Periodicals, Inc.

Fertilization and Uniparental Chromosome Elimination during Crosses with Maize Haploid Inducers

Abstract: Producing maternal haploids via a male inducer can greatly accelerate maize (Zea mays) breeding process. However, the mechanism underlying haploid formation remains unclear. In this study, we constructed two inducer lines containing cytogenetic marker B chromosome or alien centromeric histone H3 variant-yellow fluorescent protein vector to investigate the mechanism. The two inducer lines as the pollinators were crossed with a hybrid ZhengDan958. B chromosomes were detected in F1 haploids at a low frequency, which was direct evidence to support the occurrence of selective chromosome elimination during haploid formation. We found that most of the inducer chromosomes were eliminated in haploid embryonic cells during the first week after pollination. The gradual elimination of chromosomes was also detected in the endosperm of defective kernels, although it occurred only in some endosperm cells as late as 15 d after pollination. We also performed a genome-wide identification of single nucleotide polymorphism markers in the inducers, noninducer inbred lines, and 42 derived haploids using a 50K single nucleotide polymorphism array. We found that an approximately 44-Mb heterozygous fragment from the male parent was detected in a single haploid, which further supported the occurrence of paternal introgression. Our results suggest that selective elimination of uniparental chromosomes leads to the formation of haploid and possible defective kernels in maize as well, which is accompanied with unusual paternal introgression in haploid cells.

Karyotype Diversity and Evolutionary Trends in Angiosperms

Abstract: Karyotypic change constitutes an important evolutionary mechanism contributing to in angiosperm diversification and speciation. Comparative analyses of the karyotype usually include numerical features (chromosome number) and their changes (dysploidy, aneuploidy, polyploidy), as well as morphological features (chromosome size, karyotype length and genome size, centromere position and karyotype symmetry, secondary constrictions, supernumerary chromosomal material). More detailed characterization of angiosperm karyotypes involves also analyses of the abundance, distribution, and organization of specific molecular landmarks of different types (heterochromatin, ribosomal DNA, telomeric sequences, transposable elements, tandemly repeated DNA) and sizes (ranging from small genomic blocks to entire chromosome sets). This chapter describes the above mentioned karyotypic features and discusses their variation and evolutionary trends within angiosperms with respect to, for instance, their phylogenetic distribution and significance, directionality of chromosome number changes, or the nature and function of genetic elements involved in genome diploidization.

Analysis of plastid and mitochondrial DNA insertions in the nucleus (NUPTs and NUMTs) of six plant species: size, relative age and chromosomal localization

Abstract: We analysed the size, relative age and chromosomal localization of nuclear sequences of plastid and mitochondrial origin (NUPTs-nuclear plastid DNA and NUMTs-nuclear mitochondrial DNA) in six completely sequenced plant species. We found that the largest insertions showed lower divergence from organelle DNA than shorter insertions in all species, indicating their recent origin. The largest NUPT and NUMT insertions were localized in the vicinity of the centromeres in the small genomes of Arabidopsis and rice. They were also present in other chromosomal regions in the large genomes of soybean and maize. Localization of NUPTs and NUMTs correlated positively with distribution of transposable elements (TEs) in Arabidopsis and sorghum, negatively in grapevine and soybean, and did not correlate in rice or maize. We propose a model where new plastid and mitochondrial DNA sequences are inserted close to centromeres and are later fragmented by TE insertions and reshuffled away from the centromere or removed by ectopic recombination. The mode and tempo of TE dynamism determines the turnover of NUPTs and NUMTs resulting in their species-specific chromosomal distributions.

Multiple genetic origins of histidine-rich protein 2 gene deletion in Plasmodium falciparum parasites from Peru

Abstract: The majority of malaria rapid diagnostic tests (RDTs) detect Plasmodium falciparum histidine-rich protein 2 (PfHRP2), encoded by the pfhrp2 gene. Recently, P. falciparum isolates from Peru were found to lack pfhrp2 leading to false-negative RDT results. We hypothesized that pfhrp2-deleted parasites in Peru derived from a single genetic event. We evaluated the parasite population structure and pfhrp2 haplotype of samples collected between 1998 and 2005 using seven neutral and seven chromosome 8 microsatellite markers, respectively. Five distinct pfhrp2 haplotypes, corresponding to five neutral microsatellite-based clonal lineages, were detected in 1998-2001; pfhrp2 deletions occurred within four haplotypes. In 2003-2005, outcrossing among the parasite lineages resulted in eight population clusters that inherited the five pfhrp2 haplotypes seen previously and a new haplotype; pfhrp2 deletions occurred within four of these haplotypes. These findings indicate that the genetic origin of pfhrp2 deletion in Peru was not a single event, but likely occurred multiple times.

FISHIS: fluorescence in situ hybridization in suspension and chromosome flow sorting made easy.

Abstract: The large size and complex polyploid nature of many genomes has often hampered genomics development, as is the case for several plants of high agronomic value. Isolating single chromosomes or chromosome arms via flow sorting offers a clue to resolve such complexity by focusing sequencing to a discrete and self-consistent part of the whole genome. The occurrence of sufficient differences in the size and or base-pair composition of the individual chromosomes, which is uncommon in plants, is critical for the success of flow sorting. We overcome this limitation by developing a robust method for labeling isolated chromosomes, named Fluorescent In situ Hybridization In suspension (FISHIS). FISHIS employs fluorescently labeled synthetic repetitive DNA probes, which are hybridized, in a wash-less procedure, to chromosomes in suspension following DNA alkaline denaturation. All typical A, B and D genomes of wheat, as well as individual chromosomes from pasta (T. durum L.) and bread (T. aestivum L.) wheat, were flow-sorted, after FISHIS, at high purity. For the first time in eukaryotes, each individual chromosome of a diploid organism, Dasypyrum villosum (L.) Candargy, was flow-sorted regardless of its size or base-pair related content. FISHIS-based chromosome sorting is a powerful and innovative flow cytogenetic tool which can develop new genomic resources from each plant species, where microsatellite DNA probes are available and high quality chromosome suspensions could be produced. The joining of FISHIS labeling and flow sorting with the Next Generation Sequencing methodology will enforce genomics for more species, and by this mightier chromosome approach it will be possible to increase our knowledge about structure, evolution and function of plant genome to be used for crop improvement. It is also anticipated that this technique could contribute to analyze and sort animal chromosomes with peculiar cytogenetic abnormalities, such as copy number variations or cytogenetic aberrations.

X and Y Chromosome Complement Influence Adiposity and Metabolism in Mice

Abstract: Three different models of MF1 strain mice were studied to measure the effects of gonadal secretions and sex chromosome type and number on body weight and composition, and on related metabolic variables such as glucose homeostasis, feeding, and activity. The 3 genetic models varied sex chromosome complement in different ways, as follows: 1) "four core genotypes" mice, comprising XX and XY gonadal males, and XX and XY gonadal females; 2) the XY* model comprising groups similar to XO, XX, XY, and XXY; and 3) a novel model comprising 6 groups having XO, XX, and XY chromosomes with either testes or ovaries. In gonadally intact mice, gonadal males were heavier than gonadal females, but sex chromosome complement also influenced weight. The male/female difference was abolished by adult gonadectomy, after which mice with 2 sex chromosomes (XX or XY) had greater body weight and percentage of body fat than mice with 1 X chromosome. A second sex chromosome of either type, X or Y, had similar effects, indicating that the 2 sex chromosomes each possess factors that influence body weight and composition in the MF1 genetic background. Sex chromosome complement also influenced metabolic variables such as food intake and glucose tolerance. The results reveal a role for the Y chromosome in metabolism independent of testes and gonadal hormones and point to a small number of X-Y gene pairs with similar coding sequences as candidates for causing these effects.

Efficient neocentromere formation is suppressed by gene conversion to maintain centromere function at native physical chromosomal loci in Candida albicans

Abstract: CENPA/Cse4 assembles centromeric chromatin on diverse DNA. CENPA chromatin is epigenetically propagated on unique and different centromere DNA sequences in a pathogenic yeast Candida albicans. Formation of neocentromeres on DNA, nonhomologous to native centromeres, indicates a role of non-DNA sequence determinants in CENPA deposition. Neocentromeres have been shown to form at multiple loci in C. albicans when a native centromere was deleted. However, the process of site selection for CENPA deposition on native or neocentromeres in the absence of defined DNA sequences remains elusive. By systematic deletion of CENPA chromatin-containing regions of variable length of different chromosomes, followed by mapping of neocentromere loci in C. albicans and its related species Candida dubliniensis, which share similar centromere properties, we demonstrate that the chromosomal location is an evolutionarily conserved primary determinant of CENPA deposition. Neocentromeres on the altered chromosome are always formed close to the site which was once occupied by the native centromere. Interestingly, repositioning of CENPA chromatin from the neocentromere to the native centromere occurs by gene conversion in C. albicans.

The Epigenome of Evolving Drosophila Neo-Sex Chromosomes: Dosage Compensation and Heterochromatin Formation

Abstract: Sex chromosomes originated from autosomes but have evolved a highly specialized chromatin structure. Drosophila Y chromosomes are composed entirely of silent heterochromatin, while male X chromosomes have highly accessible chromatin and are hypertranscribed as a result of dosage compensation. Here, we dissect the molecular mechanisms and functional pressures driving heterochromatin formation and dosage compensation of the recently formed neo-sex chromosomes of Drosophila miranda. We show that the onset of heterochromatin formation on the neo-Y is triggered by an accumulation of repetitive DNA. The neo-X has evolved partial dosage compensation and we find that diverse mutational paths have been utilized to establish several dozen novel binding consensus motifs for the dosage compensation complex on the neo-X, including simple point mutations at pre-binding sites, insertion and deletion mutations, microsatellite expansions, or tandem amplification of weak binding sites. Spreading of these silencing or activating chromatin modifications to adjacent regions results in massive mis-expression of neo-sex linked genes, and little correspondence between functionality of genes and their silencing on the neo-Y or dosage compensation on the neo-X. Intriguingly, the genomic regions being targeted by the dosage compensation complex on the neo-X and those becoming heterochromatic on the neo-Y show little overlap, possibly reflecting different propensities along the ancestral chromosome that formed the sex chromosome to adopt active or repressive chromatin configurations. Our findings have broad implications for current models of sex chromosome evolution, and demonstrate how mechanistic constraints can limit evolutionary adaptations. Our study also highlights how evolution can follow predictable genetic trajectories, by repeatedly acquiring the same 21-bp consensus motif for recruitment of the dosage compensation complex, yet utilizing a diverse array of random mutational changes to attain the same phenotypic outcome.

Metabolic impact of sex chromosomes.

Abstract: Obesity and associated metabolic diseases are sexually dimorphic. To provide better diagnosis and treatment for both sexes, it is of interest to identify the factors that underlie male/female differences in obesity. Traditionally, sexual dimorphism has been attributed to effects of gonadal hormones, which influence numerous metabolic processes. However, the XX/XY sex chromosome complement is an additional factor that may play a role. Recent data using the four core genotypes mouse model have revealed that sex chromosome complement—independently from gonadal sex—plays a role in adiposity, feeding behavior, fatty liver and glucose homeostasis. Potential mechanisms for the effects of sex chromosome complement include differential gene dosage from X chromosome genes that escape inactivation, and distinct genomic imprints on X chromosomes inherited from maternal or paternal parents. Here we review recent data in mice and humans concerning the potential impact of sex chromosome complement on obesity and metabolic disease.

The holocentric species Luzula elegans shows interplay between centromere and large-scale genome organization.

Abstract: SUMMARYIn higher plants, the large-scale structure of monocentric chromosomes consists of distinguishable eu- andheterochromatic regions, the proportions and organization of which depend on a species’ genome size. Todetermine whether the same interplay is maintained for holocentric chromosomes, we investigated the distri-bution of repetitive sequences and epigenetic marks in the woodrush Luzula elegans (3.81 Gbp/1C). Sixty-one per cent of the L. elegans genome is characterized by highly repetitive DNA, with over 30 distinctsequence families encoding an exceptionally high diversity of satellite repeats. Over 33% of the genome iscomposed of the Angela clade of Ty1/copia LTR retrotransposons, which are uniformly dispersed along thechromosomes, while the satellite repeats occur as bands whose distribution appears to be biased towardsthe chromosome termini. No satellite showed an almost chromosome-wide distribution pattern as expectedfor a holocentric chromosome and no typical centromere-associated LTR retrotransposons were found either.No distinguishable large-scale patterns of eu- and heterochromatin-typical epigenetic marks or early/lateDNA replicating domains were found along mitotic chromosomes, although super-high-resolution lightmicroscopy revealed distinguishable interspersed units of various chromatin types. Our data suggest a corre-lation between the centromere and overall genome organization in species with holocentric chromosomes.Keywords: holocentric genome organization, holokinetic chromosome, centromere, histone marks, repeti-tive DNA, Luzula elegans.INTRODUCTIONMost studied organisms feature one single size-restrictedcentromere per chromosome (monocentric chromosomes),but in certain independent eukaryotic lineages, holocentricchromosomes occur (Melters et al., 2012). These holocentricchromosomes lack a primary constriction, and, in contrastto monocentric chromosomes, they form holokinetic kinet-ochores (also called diffuse or non-localized kinetochores)that are distributed along almost the entire poleward sur-face of the chromatids, to which the spindle fibers attach(Guerra et al., 2010; Heckmann and Houben, 2012).Centromere functions are highly conserved betweenmono- and holocentric chromosome species, and similarkinetochore components have been found in the activecentromeres of both types (Maddox et al., 2004; Nagakiet al., 2005; d’Alencon et al., 2011). However, structuralanalysis of mitotic chromosomes in the holocentric plantgenus Luzula challenged the notion of a ‘diffuse’ centro-mere organization along holocentric chromosomes (Nagakiet al., 2005; Heckmann et al., 2011). Instead, a longitudinalcentromere-like groove that was positive for CENH3[a mark for active centromeres (Kalitsis and Choo, 2012)]was found along each sister chromatid, discontinued ateach sub-terminal end. Consistently, entire mitotic chromo-somes of Luzula (Gernand et al., 2003; Nagaki et al., 2005)and Rhynchospora tenuis (Guerra et al., 2006) displayed acell cycle-dependent uniform histone H3S10/S28 phosphor-ylation mark, illustrating a chromosome-wide ‘pericentro-meric-like’ structure (Houben et al., 2007a).The DNA of centromeres is highly variable, and, exceptfor budding yeast (Clarke and Carbon, 1985), thesequences are neither necessary nor sufficient for centro-mere formation. However, satellite DNA repeats and

Intrinsic karyotype stability and gene copy number variations may have laid the foundation for tetraploid wheat formation

Abstract: Polyploidy or whole-genome duplication is recurrent in plant evolution, yet only a small fraction of whole-genome duplications has led to successful speciation. A major challenge in the establishment of nascent polyploids is sustained karyotype instability, which compromises fitness. The three putative diploid progenitors of bread wheat, with AA, SS (S ∼ B), and DD genomes occurred sympatrically, and their cross-fertilization in different combinations may have resulted in fertile allotetraploids with various genomic constitutions. However, only SSAA or closely related genome combinations have led to the speciation of tetraploid wheats like Triticum turgidum and Triticum timopheevii. We analyzed early generations of four newly synthesized allotetraploid wheats with genome compositions SshSshAmAm, SlSlAA, SbSbDD, and AADD by combined fluorescence and genomic in situ hybridization-based karyotyping. Results of karyotype analyses showed that although SshSshAmAm and SlSlAA are characterized by immediate and persistent karyotype stability, massive aneuploidy and extensive chromosome restructuring are associated with SbSbDD and AADD in which parental subgenomes showed markedly different propensities for chromosome gain/loss and rearrangements. Although compensating aneuploidy and reciprocal translocation between homeologs prevailed, reproductive fitness was substantially compromised due to chromosome instability. Strikingly, localized genomic changes in repetitive DNA and copy-number variations in gene homologs occurred in both chromosome stable lines, SshSshAmAm and SlSlAA. Our data demonstrated that immediate and persistent karyotype stability is intrinsic to newly formed allotetraploid wheat with genome combinations analogous to natural tetraploid wheats. This property, coupled with rapid gene copy-number variations, may have laid the foundation of tetraploid wheat establishment.

Homoeologous chromosomes of Xenopus laevis are highly conserved after whole-genome duplication.

Abstract: It has been suggested that whole-genome duplication (WGD) occurred twice during the evolutionary process of vertebrates around 450 and 500 million years ago, which contributed to an increase in the genomic and phenotypic complexities of vertebrates. However, little is still known about the evolutionary process of homoeologous chromosomes after WGD because many duplicate genes have been lost. Therefore, Xenopus laevis (2n=36) and Xenopus (Silurana) tropicalis (2n=20) are good animal models for studying the process of genomic and chromosomal reorganization after WGD because X. laevis is an allotetraploid species that resulted from WGD after the interspecific hybridization of diploid species closely related to X. tropicalis. We constructed a comparative cytogenetic map of X. laevis using 60 complimentary DNA clones that covered the entire chromosomal regions of 10 pairs of X. tropicalis chromosomes. We consequently identified all nine homoeologous chromosome groups of X. laevis. Hybridization signals on two pairs of X. laevis homoeologous chromosomes were detected for 50 of 60 (83%) genes, and the genetic linkage is highly conserved between X. tropicalis and X. laevis chromosomes except for one fusion and one inversion and also between X. laevis homoeologous chromosomes except for two inversions. These results indicate that the loss of duplicated genes and inter- and/or intrachromosomal rearrangements occurred much less frequently in this lineage, suggesting that these events were not essential for diploidization of the allotetraploid genome in X. laevis after WGD.

Homologous sex chromosomes in three deeply divergent anuran species

Abstract: Comparative genomic studies are revealing that, in sharp contrast with the strong stability found in birds and mammals, sex determination mechanisms are surprisingly labile in cold-blooded vertebrates, with frequent transitions between different pairs of sex chromosomes. It was recently suggested that, in context of this high turnover, some chromosome pairs might be more likely than others to be co-opted as sex chromosomes. Empirical support, however, is still very limited. Here we show that sex-linked markers from three highly divergent groups of anurans map to Xenopus tropicalis scaffold 1, a large part of which is homologous to the avian sex chromosome. Accordingly, the bird sex determination gene DMRT1, known to play a key role in sex differentiation across many animal lineages, is sex linked in all three groups. Our data provide strong support for the idea that some chromosome pairs are more likely than others to be co-opted as sex chromosomes because they harbor key genes from the sex determination pathway.