Changes In Genome Structure Research Articles

DNA copy number evolution in Drosophila cell lines.

BackgroundStructural rearrangements of the genome resulting in genic imbalance due to copy number change are often deleterious at the organismal level, but are common in immortalized cell lines and tumors, where they may be an advantage to cells. In order to explore the biological consequences of copy number changes in the Drosophila genome, we resequenced the genomes of 19 tissue-culture cell lines and generated RNA-Seq profiles.ResultsOur work revealed dramatic duplications and deletions in all cell lines. We found three lines of evidence indicating that copy number changes were due to selection during tissue culture. First, we found that copy numbers correlated to maintain stoichiometric balance in protein complexes and biochemical pathways, consistent with the gene balance hypothesis. Second, while most copy number changes were cell line-specific, we identified some copy number changes shared by many of the independent cell lines. These included dramatic recurrence of increased copy number of the PDGF/VEGF receptor, which is also over-expressed in many cancer cells, and of bantam, an anti-apoptosis miRNA. Third, even when copy number changes seemed distinct between lines, there was strong evidence that they supported a common phenotypic outcome. For example, we found that proto-oncogenes were over-represented in one cell line (S2-DRSC), whereas tumor suppressor genes were under-represented in another (Kc167).ConclusionOur study illustrates how genome structure changes may contribute to selection of cell lines in vitro. This has implications for other cell-level natural selection progressions, including tumorigenesis.Electronic supplementary materialThe online version of this article (doi:10.1186/gb-2014-15-8-r70) contains supplementary material, which is available to authorized users.

Unraveling the effect of genomic structural changes in the rhesus macaque - implications for the adaptive role of inversions.

BackgroundBy reshuffling genomes, structural genomic reorganizations provide genetic variation on which natural selection can work. Understanding the mechanisms underlying this process has been a long-standing question in evolutionary biology. In this context, our purpose in this study is to characterize the genomic regions involved in structural rearrangements between human and macaque genomes and determine their influence on meiotic recombination as a way to explore the adaptive role of genome shuffling in mammalian evolution.ResultsWe first constructed a highly refined map of the structural rearrangements and evolutionary breakpoint regions in the human and rhesus macaque genomes based on orthologous genes and whole-genome sequence alignments. Using two different algorithms, we refined the genomic position of known rearrangements previously reported by cytogenetic approaches and described new putative micro-rearrangements (inversions and indels) in both genomes. A detailed analysis of the rhesus macaque genome showed that evolutionary breakpoints are in gene-rich regions, being enriched in GO terms related to immune system. We also identified defense-response genes within a chromosome inversion fixed in the macaque lineage, underlying the relevance of structural genomic changes in evolutionary and/or adaptation processes. Moreover, by combining in silico and experimental approaches, we studied the recombination pattern of specific chromosomes that have suffered rearrangements between human and macaque lineages.ConclusionsOur data suggest that adaptive alleles – in this case, genes involved in the immune response – might have been favored by genome rearrangements in the macaque lineage.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-530) contains supplementary material, which is available to authorized users.

Genomic regions involved in yield potential detected by genome-wide association analysis in Japanese high-yielding rice cultivars.

BackgroundHigh-yielding cultivars of rice (Oryza sativa L.) have been developed in Japan from crosses between overseas indica and domestic japonica cultivars. Recently, next-generation sequencing technology and high-throughput genotyping systems have shown many single-nucleotide polymorphisms (SNPs) that are proving useful for detailed analysis of genome composition. These SNPs can be used in genome-wide association studies to detect candidate genome regions associated with economically important traits. In this study, we used a custom SNP set to identify introgressed chromosomal regions in a set of high-yielding Japanese rice cultivars, and we performed an association study to identify genome regions associated with yield.ResultsAn informative set of 1152 SNPs was established by screening 14 high-yielding or primary ancestral cultivars for 5760 validated SNPs. Analysis of the population structure of high-yielding cultivars showed three genome types: japonica-type, indica-type and a mixture of the two. SNP allele frequencies showed several regions derived predominantly from one of the two parental genome types. Distinct regions skewed for the presence of parental alleles were observed on chromosomes 1, 2, 7, 8, 11 and 12 (indica) and on chromosomes 1, 2 and 6 (japonica). A possible relationship between these introgressed regions and six yield traits (blast susceptibility, heading date, length of unhusked seeds, number of panicles, surface area of unhusked seeds and 1000-grain weight) was detected in eight genome regions dominated by alleles of one parental origin. Two of these regions were near Ghd7, a heading date locus, and Pi-ta, a blast resistance locus. The allele types (i.e., japonica or indica) of significant SNPs coincided with those previously reported for candidate genes Ghd7 and Pi-ta.ConclusionsIntrogression breeding is an established strategy for the accumulation of QTLs and genes controlling high yield. Our custom SNP set is an effective tool for the identification of introgressed genome regions from a particular genetic background. This study demonstrates that changes in genome structure occurred during artificial selection for high yield, and provides information on several genomic regions associated with yield performance.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-346) contains supplementary material, which is available to authorized users.

Genomic Stability of Palmer amaranth Plants Derived by Macro-Vegetative Propagation

qPCR (quantitative polymerase chain reaction) and random amplified polymorphic DNA (RAPD) were utilized to investigate genetic stability of Palmer amaranth cloned plants over 10 generations. DNA from original parent Palmer amaranth plants (grown from seeds) was re-analyzed using qPCR, and confidence levels for determining ΔΔCt (threshold crossing) values were established. ANOVA was used to determine variation (margin of error) of these ΔΔCt values. This margin of error was applied to qPCR analysis of DNA from eight individual parent plants and their descendants (10th generation) so that possible differences in EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) gene copy number could be ascertained. This method (and the associated error) indicated a lack of agreement in ΔΔCt values of DNA from plants of these two generations. qPCR analysis showed that in five out of eight clones, EPSPS gene copy number varied more than the calculated error (P = 0.05). A second technique to monitor genetic stability, RAPD was used to determine possible changes in genomic DNA due to extended cloning of these regenerated plants. RAPD analysis showed that four out of the eight clones differed when the profiles of the two generations were compared. Results show that qPCR and RAPD analysis point to the fact that several Palmer amaranth clones experienced changes in genome structure over 10 generations. Although the glyphosate resistance trait was retained, results suggest that during cloning studies, the genetic stability of macro-vegetatively propagated lines should be monitored.

A recurring syndrome of accelerated plastid genome evolution in the angiosperm tribe Sileneae (Caryophyllaceae)

In flowering plants, plastid genomes are generally conserved, exhibiting slower rates of sequence evolution than the nucleus and little or no change in structural organization. However, accelerated plastid genome evolution has occurred in scattered angiosperm lineages. For example, some species within the genus Silene have experienced a suite of recent changes to their plastid genomes, including inversions, shifts in inverted repeat boundaries, large indels, intron losses, and rapid rates of amino acid sequence evolution in a subset of protein genes, with the most extreme divergence occurring in the protease gene clpP. To investigate the relationship between the rates of sequence and structural evolution, we sequenced complete plastid genomes from three species (Silene conoidea, S. paradoxa, and Lychnis chalcedonica), representing independent lineages within the tribe Sileneae that were previously shown to have accelerated rates of clpP evolution. We found a high degree of parallel evolution. Elevated rates of amino acid substitution have occurred repeatedly in the same subset of plastid genes and have been accompanied by a recurring pattern of structural change, including cases of identical inversions and intron loss. This “syndrome” of changes was not observed in the closely related outgroup Agrostemma githago or in the more slowly evolving Silene species that were sequenced previously. Although no single mechanism has yet been identified to explain the correlated suite of changes in plastid genome sequence and structure that has occurred repeatedly in angiosperm evolution, we discuss a possible mixture of adaptive and non-adaptive forces that may be responsible.

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes

Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform transcriptome analysis to gain insights into the extreme phenotypes of the python. We discovered rapid and massive transcriptional responses in multiple organ systems that occur on feeding and coordinate major changes in organ size and function. Intriguingly, the homologs of these genes in humans are associated with metabolism, development, and pathology. We also found that many snake metabolic genes have undergone positive selection, which together with the rapid evolution of mitochondrial proteins, provides evidence for extensive adaptive redesign of snake metabolic pathways. Additional evidence for molecular adaptation and gene family expansions and contractions is associated with major physiological and phenotypic adaptations in snakes; genes involved are related to cell cycle, development, lungs, eyes, heart, intestine, and skeletal structure, including GRB2-associated binding protein 1, SSH, WNT16, and bone morphogenetic protein 7. Finally, changes in repetitive DNA content, guanine-cytosine isochore structure, and nucleotide substitution rates indicate major shifts in the structure and evolution of snake genomes compared with other amniotes. Phenotypic and physiological novelty in snakes seems to be driven by system-wide coordination of protein adaptation, gene expression, and changes in the structure of the genome.

Karyotypes in Ethiopian Aloe species (Xanthorrhoeaceae: Asphodeloideae)

A cytogenetic survey of 17 species in the succulent-leaved genus Aloe L. (Xanthorrhoeaceae subfamily Asphodeloideae) in Ethiopia was undertaken towards a more complete genetic characterisation of the genus throughout its distribution in Africa, Arabia and Madagascar. Somatic metaphase chromosomes of all species studied showed the same diploid chromosome number of 2n = 14, consisting of four pairs of long and three pairs of short chromosomes. Symmetry was characterised as Stebbins type 2B and the asymmetry indices AsK%, TF%, A1 and A2 revealed minor karyotypic variation common in closely related species. The metrics showed that A. benishangulana has a marginally higher degree of asymmetry than is typical, and the pubescent-flowered A. trichosantha has a more symmetrical karyotype than most other species. We suggest that the stable karyotype morphology in Aloe indicates that structural genome changes and ecological factors play a more prominent role in speciation in Aloe.

Aluminum tolerance in maize is associated with higherMATE1gene copy number

Genome structure variation, including copy number variation and presence/absence variation, comprises a large extent of maize genetic diversity; however, its effect on phenotypes remains largely unexplored. Here, we describe how copy number variation underlies a rare allele that contributes to maize aluminum (Al) tolerance. Al toxicity is the primary limitation for crop production on acid soils, which make up 50% of the world's potentially arable lands. In a recombinant inbred line mapping population, copy number variation of the Al tolerance gene multidrug and toxic compound extrusion 1 (MATE1) is the basis for the quantitative trait locus of largest effect on phenotypic variation. This expansion in MATE1 copy number is associated with higher MATE1 expression, which in turn results in superior Al tolerance. The three MATE1 copies are identical and are part of a tandem triplication. Only three maize inbred lines carrying the three-copy allele were identified from maize and teosinte diversity panels, indicating that copy number variation for MATE1 is a rare, and quite likely recent, event. These maize lines with higher MATE1 copy number are also Al-tolerant, have high MATE1 expression, and originate from regions of highly acidic soils. Our findings show a role for copy number variation in the adaptation of maize to acidic soils in the tropics and suggest that genome structural changes may be a rapid evolutionary response to new environments.

Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes.

BackgroundPlastid genome structure and content is remarkably conserved in land plants. This widespread conservation has facilitated taxon-rich phylogenetic analyses that have resolved organismal relationships among many land plant groups. However, the relationships among major fern lineages, especially the placement of Equisetales, remain enigmatic.ResultsIn order to understand the evolution of plastid genomes and to establish phylogenetic relationships among ferns, we sequenced the plastid genomes from three early diverging species: Equisetum hyemale (Equisetales), Ophioglossum californicum (Ophioglossales), and Psilotum nudum (Psilotales). A comparison of fern plastid genomes showed that some lineages have retained inverted repeat (IR) boundaries originating from the common ancestor of land plants, while other lineages have experienced multiple IR changes including expansions and inversions. Genome content has remained stable throughout ferns, except for a few lineage-specific losses of genes and introns. Notably, the losses of the rps16 gene and the rps12i346 intron are shared among Psilotales, Ophioglossales, and Equisetales, while the gain of a mitochondrial atp1 intron is shared between Marattiales and Polypodiopsida. These genomic structural changes support the placement of Equisetales as sister to Ophioglossales + Psilotales and Marattiales as sister to Polypodiopsida. This result is augmented by some molecular phylogenetic analyses that recover the same relationships, whereas others suggest a relationship between Equisetales and Polypodiopsida.ConclusionsAlthough molecular analyses were inconsistent with respect to the position of Marattiales and Equisetales, several genomic structural changes have for the first time provided a clear placement of these lineages within the ferns. These results further demonstrate the power of using rare genomic structural changes in cases where molecular data fail to provide strong phylogenetic resolution.

Black Swans and Bell Curves

Two hundred terabytes of data from the Thousand Genomes project is now publicly available through an Amazon Web Services cloud. But the data describing human genetic variation will only be useful when we know how to translate it to improve human health. This partly depends on a comprehensive understanding of the relationship between our genomes and a vast range of phenotypes, be they rare mendelian or common quantitative traits. Moyra Smith helps us in this endeavour; she begins her book on phenotypic variation with cautious words from Lewis Thomas ‘Now that we have begun exploring in earnest, doing serious science, we are getting glimpses of how huge the questions are and how far from being answered'. This is an apt quotation for Smith's book, which painstakingly curates an impressive swath of very serious science published in her field of functional genomics up until 2009, and is modest in its claims about how we can currently apply the findings to medicine. The early chapters provide a detailed context for issues that are subsequently explored with increasing complexity. Genome architecture and structural DNA changes are described that have a functional influence on protein expression and in some cases may mark evolutionarily important stages for humans. For example, comparative genomic studies in humans and primates have identified loci that influence brain function (FOXP2, ASPM) and that have undergone rapid evolution. The influence of alleles under positive natural selection on the human genome is also considered with the concomitant reduction in genetic diversity for specific haplotypes. Chapter 4, Linkage, Association, and Linkage Disequilibrium, presents data from GWAS (genome-wide association studies) and explores both the rapid progress made and factors that can impede our understanding of associations between genotype and complex phenotypes. Some of the factors are technical; the limitations of data generated from microarrays that were constructed before large-scale mRNA sequencing had revealed the complexity of the transcriptome. Other confounding factors are biological; functional studies reveal a good deal of redundancy because evolutionary processes result in chaotic complex systems, and the co-segregation of some SNPs with disease phenotypes is because of linkage disequilibrium with the causal structural variants within the genome. Further complexity that necessitates the functional plasticity of the human genome is elaborated on in chapters 5–7, which consider transcriptional control; the spliceosome; protein turnover; and the heteroplasmy and mutations that affect the expression of the mitochondrial genome. Aberrant protein folding and impaired autophagy are phenotypic changes associated with ageing and neurodegenerative disease, as are somatic mutations in the mitochondrial genome. The later chapters consider complex disease phenotypes, including neurobehavioural disorders, malformation syndromes, and late-onset conditions such as Parkinson's disease. Some overarching themes emerge from Smith's detailed review of the results of familial, population genetic, and experimental studies. For psychiatric diseases, the diagnostic categorisation may need to change in the light of genetic findings and an understanding of molecular pathophysiology; a paradigm shift that is already underway in other fields such as oncology. In considering the molecular basis of schizophrenia Matt Ridley's maxim of nature via nurture came to mind because of the putative role of infectious agents in the disease aetiology (schizophrenia-associated markers identified in the MHC region) and the effects of cannabis in its associated cognitive impairment (cannabis sensitivity associated COMT genotypes). By reviewing the common clinical features of Noonan, Costello, and cardio-facial cutaneous syndromes, caused by perturbation of the RAS MAP kinase signalling pathway, we are reminded that we can't understand complex phenotypes without considering how individual proteins function in (networks of) biochemical pathways. This book provided a deeply satisfying read for the human genetics geek who does not get out of her own narrow research niche nearly often enough. But it is quite dry in places and would be a challenge for the novice. The book has a narrative within and between chapters but the story is far from explicit and may have benefited from more signposting and figures with detailed legends; for example, a diagram of the RAS MAP kinase pathway would have been helpful in chapter 10. Perhaps the paucity of emphatic conclusions in this book was deliberate, to illustrate the fact that functional genomics has not yet come of age? The new generation of GWAS, the rapid pace of eQTL (expression quantitative trait loci) mapping and metabolomics, together with the launch of the Human Proteome Project all suggest that a detailed understanding of the relationships between our genomes, intermediate phenotypes, and disease aetiology is finally within sight▪

918 Genetic and Phylogenetic Characterization of Staphylococcus Aureus Strains Isolated from Atopic Dermatitis Pediatric Patients and Their Cohabitants

Atopic dermatitis (AD) is characterized by dysfunctional skin susceptible to Staphylococcus aureus colonization, which can exacerbate the symptoms. Recent studies indicate that the S. aureus’s great versatility is direct consequence...

Radiation-Induced Human Endogenous Retrovirus (HERV)-R env Gene Expression by Epigenetic Control

It is commonly accepted that ionizing radiation induces genomic instability by changes in genomic structure, epigenetic regulation and gene expression. Human endogenous retroviruses (HERV)-R also are often differentially expressed between normal and disease tissues under unstable genomic conditions and are implicated in the pathogenesis of several human diseases. To understand the influence of ionizing radiation on HERV-R expression, we performed quantitative reverse transcription-polymerase chain reaction (RT-PCR) analyses using γ-irradiated normal human cells. Compared to nonirradiated cells, HERV-R expression was up-regulated in γ-irradiated cells. The regulatory mechanism of HERV-R expression in irradiated cells was investigated by methylation analyses of HERV-R 5'LTRs and treatment with garcinol. These data indicated that the up-regulated transcription of HERV-R may be regulated by radiation-induced epigenetic changes induced by histone modification, and thus could be of great importance for understanding the relationship between radiation-induced biological effects and transposable elements.

Radiation-induced retroelement-mediated genomic instability

Ionizing radiation induces numerous biological events in mammalian cells, including cell death, mutagenesis, and genomic instability via changes in genomic structure, epigenetic regulation, and gene expression. Retroelements can also alter genomic structure based on their ability to mobilize, and their abundance and sequence similarity have been implicated in the pathogenesis of several human diseases. Here, we summarize the current knowledge on the mobilization, genomic rearrangement, epigenetic state, and transcriptional activation of retroelements in response to radiation. We further discuss the potential effects of their activation in radiation-induced genomic instability.

Allopolyploidization Lays the Foundation for Evolution of Distinct Populations: Evidence From Analysis of SyntheticArabidopsisAllohexaploids

Polyploidization is an important mechanism for introducing diversity into a population and promoting evolutionary change. It is believed that most, if not all, angiosperms have undergone whole genome duplication events in their evolutionary history, which has led to changes in genome structure, gene regulation, and chromosome maintenance. Previous studies have shown that polyploidy can coincide with meiotic abnormalities and somatic cytogenetic mosaics in Arabidopsis allotetraploids, but it is unclear whether this phenomenon can contribute to novel diversity or act as a mechanism for speciation. In this study we tested the hypothesis that mosaic aneuploidy contributes to the formation of incipient diversity in neoallopolyploids. We generated a population of synthesized Arabidopsis allohexaploids and monitored karyotypic and phenotypic variation in this population over the first seven generations. We found evidence of sibling line-specific chromosome number variations and rapidly diverging phenotypes between lines, including flowering time, leaf shape, and pollen viability. Karyotypes varied between sibling lines and between cells within the same tissues. Cytotypic variation correlates with phenotypic novelty, and, unlike in allotetraploids, remains a major genomic destabilizing factor for at least the first seven generations. While it is still unclear whether new stable aneuploid lines will arise from these populations, our data are consistent with the notion that somatic aneuploidy, especially in higher level allopolyploids, can act as an evolutionary relevant mechanism to induce rapid variation not only during the initial allopolyploidization process but also for several subsequent generations. This process may lay the genetic foundation for multiple, rather than just a single, new species.

Abstract 3240: The Wnt secretion factor Evi/Wls/Gpr177 promotes glioma tumorigenesis

Abstract Malignant astrocytomas are highly aggressive brain tumors with poor prognosis. Despite multimodal therapy, including surgical resection followed by combined radio- and chemotherapy, the median survival of glioblastoma patients has remained as low as 12-14 months throughout the past decade. While a number of structural genomic changes and dysregulation of signaling pathways in gliomas have been described, the identification of biomarkers and druggable targets remains an important task for novel diagnostic and therapeutic approaches. Recent evidence supports the involvement of canonical and non-canonical Wnt signaling in glioma development and malignant progression. Here, we show that the Wnt-specific secretory protein Evi (also known as GPR177/Wntless/Sprinter) is overexpressed in astrocytic gliomas. Evi/Wls is a core Wnt signaling component and a specific regulator of pan-Wnt protein secretion, affecting both canonical and non-canonical signaling. We demonstrate that its depletion in glioma and glioma-derived stem-like cells led to decreased cell proliferation and apoptosis. Furthermore, Evi/Wls silencing in glioma cells reduced cell migration and the capacity to form tumors in vivo. We further show that Evi/Wls overexpression is sufficient to promote downstream Wnt signaling. Taken together, our study identifies Evi/Wls as an essential regulator of glioma tumorigenesis, identifying a pathway- specific protein trafficking factor as an oncogene and offering novel therapeutic options to interfere with the aberrant regulation of growth factors at the site of production. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3240. doi:1538-7445.AM2012-3240

Abstract 5066: Genome sequence and epigenome map of bladder cancer development from occult field effects

Abstract We are pursuing a unique strategy to identify early events in bladder cancer development by the genome-wide analysis of somatic changes in tissues from resected bladders and characterized pathologically as urothelial carcinoma. We then extend this analysis into precursor intraurothelial lesions and normal tissue. Here we report on the construction of a high resolution whole-organ histologic and genetic map of bladder cancer development that tracks its progression from in situ precursor conditions to invasive clinically aggressive cancer using total genome and exome sequencing and complemented with HumanOmni 2.5-8 v1 SNP-based Illumina genotyping, combined with CpG island methylation and cDNA microarray platforms derived from 12 whole-organ cystectomy specimens with invasive urothelial carcinoma. This approach provided a high resolution integrated map of structural genome, epigenome, and transcriptome alterations that parallel the development of bladder cancer from early field effects to invasive disease. By analyzing genome-wide patterns of structural genomic, epigenomic, and transcriptome changes, we found three major waves of alterations associated with growth advantage of successive clones reflecting a stepwise conversion of normal urothelial cells into cancer cells. This approach is significant for the identification of specific chromosomal regions as well as epigenetically and transcriptionally modified gene ontologies involved in early clonal expansion of intraurothelial neoplasia and their clonal evolution to carcinoma in situ progressing to invasive cancer. These studies suggest involvement of specific gene networks in early clonal expansion of intraurothelial neoplasia antecedent to microscopically recognizable precursor lesions such as dysplasia and carcinoma in situ. This map represents a prerequisite for specific studies on the mechanisms of incipient phases of bladder cancer development and should have a significant impact on the understanding of human carcinogenesis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5066. doi:1538-7445.AM2012-5066

Structural Genomic Changes During Mammalian Ontogeny: A New Dimension

mutations, happening spontaneously or from environmental insult. Mammalian brains are somatic mosaics, due to aneuploidy and genomic copy number variations. Recently, it also has been found that active transposable elements, long interspersed nuclear elements 1 (LINE-1) in neuronal tissue, contribute to the mosaicism, with tissue specificity [4,5]. LINE-1 elements influence chromosome integrity and gene expression. Retrotransposition activity for the LINE-1 elements was strong during neuronal different iation and occurred with high frequency. Activity was also found in the adult brain. Regulatory events leading to LINE-1 activation were elucidated [6]. These observations led to the proposition that LINE-1 element transposition has a purpose: adaptive increase in neuronal variation and plasticity and in brain-controlled phenotypes [7]. However, specific sites of insertion will need to be located to confirm this idea. Another line of evidence, implicating the occurrence of developmentally-programmed genomic structural changes, comes from a recent study of the gene for ribosomal DNA (rDNA) during ontogeny in the mouse [8]. There are hundreds of copies of rDNA in each cell on several chromosomes. The rDNA of the mice was found to present several SNPs in promoter regions of the gene. The relative percentages of these variant SNPs, indicative of rDNA structural status, were determined in sperm, embryos and two differentiated tissues, lung and liver, using a highthroughput quantitative pyrosequencing technique. The percentage of the variants changed in the differentiated tissues: in the males they differed significantly in lung and liver compared with sperm, and in the females they differed in lung compared with liver. Second, within-litter Differentiated tissues are elaborated during mammalian ontogeny by the coordinated sequential execution of cell type-specific gene expression programs. A common supposition is that basic inherited genomic structure remains constant during this process. This supposition is critically important for the recently developed procedures for obtaining induced pluripotent stem cells from somatic tissues, with great potential for clinical applications. Is this supposition comprehensively true? Would it not make sense, in terms of energy conservation, to program the necessary changes permanently through alterations in genome structure? Several special-case examples of such purposeful, site-specific manipulation of primary genome structure have long been known to exist [1,2] and have obvious functional consequences during a specific life-cycle stage. These are most common in unicellular organisms but also occur in higher organisms, for example, amplification of specific genes for rapid production of proteins, such as those of the chorion of insect eggs, and rearrangements to produce diversification of variant surface glycoprotein in trypanosomes. Vertebrates also utilize genomic re arrangement to enhance diversity of antigen receptors, through the action of the DNA sequence-specific V(D)J recombinases. Evidence is emerging that programmatic modification of the primary structure of the inherited genome may in fact be common, during development and in adult tissues. Structural genetic differences are known to occur between cell populations within an individual, including individual humans, constituting somatic mosaicism [3]. These differences, though frequent, have been interpreted as abnormalities, resulting from uncorrected somatic

Looking back at genomic medicine in 2011

Genomic medicine, in its broadest sense of being medical developments informed by ‘omic’ advances, has con­ tinued to move towards the clinic in 2011. To mark the end of the year and the beginning of 2012, the editors of the six sections within Genome Medicine were invited to provide their highlights of the past year and to hint at the developments that we are likely to see in the near future. Six different areas of progress are covered here, but the core of genomic medicine continues to be intrinsically linked to improvements in the underlying technology, and two obvious examples are sequencing and mass spec trometry. Technological advances have enabled larger studies and more complex analyses, allowing researchers and clinicians to track changes within a single cell and yet spot patterns across a whole population and within an entire physiological system. The foundations laid in 2011 should help the field to tackle the challenges of translating genomic medicine to the clinic in 2012. Complex genomic rearrangements and disease The past year has been marked by advances in the speed, accuracy and scale of genome sequencing. These improve­ ments have led to the first population­ scale genome sequencing study to provide information on structural variants [1]. Over 15,000 novel structural variants were identified from 185 individuals. Analysis of breakpoint junctions revealed that 70% of deletions and almost 90% of insertions showed microhomology ranging from 2 bp to 376 bp at the junctions. This suggests that nonhomolo­ gous recombination mechanisms are predominant in copy number variation, and that microhomology­mediated DNA replication mechanisms, such as microhomology­ mediated break­induced replication, might have a major role in human genome structural variation. Genome sequencing also revealed the extent of complex genomic rearrangements (CGRs) in disease. Over 700 genomes from different cancers were studied, and ‘chromosome catastrophes’ were identified in 2 to 3% of all cancers and in up to 25% of bone cancers [2]. This phenomenon, also termed ‘chromothripsis’ (shattering and regluing of chromosomes), is primarily localized to single chromosomes, but includes multiple structural genomic changes, such as gains, losses and inversions. As a result, chromothripsis can lead to the simultaneous occurrence of mutations in a number of different cancer ­ causing genes. Cancer is known to be driven by somati­ cally acquired point mutations and chromosomal re­ arrangements, conventionally thought to accumulate gradually over time. However, chromothripsis is a one­off event resulting in multigenic changes [2]. It remains to be shown whether chromothripsis is a major driver of cancer. Intriguingly, a similar chromosome catastrophe event that resulted in CGRs was found to be associated with a small fraction of genomic disorders [3]. This involved a germline or constitutional rearrangement event early in

The Wnt secretion protein Evi/Gpr177 promotes glioma tumourigenesis

Malignant astrocytomas are highly aggressive brain tumours with poor prognosis. While a number of structural genomic changes and dysregulation of signalling pathways in gliomas have been described, the identification of biomarkers and druggable targets remains an important task for novel diagnostic and therapeutic approaches. Here, we show that the Wnt-specific secretory protein Evi (also known as GPR177/Wntless/Sprinter) is overexpressed in astrocytic gliomas. Evi/Wls is a core Wnt signalling component and a specific regulator of pan-Wnt protein secretion, affecting both canonical and non-canonical signalling. We demonstrate that its depletion in glioma and glioma-derived stem-like cells led to decreased cell proliferation and apoptosis. Furthermore, Evi/Wls silencing in glioma cells reduced cell migration and the capacity to form tumours in vivo. We further show that Evi/Wls overexpression is sufficient to promote downstream Wnt signalling. Taken together, our study identifies Evi/Wls as an essential regulator of glioma tumourigenesis, identifying a pathway-specific protein trafficking factor as an oncogene and offering novel therapeutic options to interfere with the aberrant regulation of growth factors at the site of production.

Adaptation to P Element Transposon Invasion in Drosophila melanogaster

Transposons evolve rapidly and can mobilize and trigger genetic instability. Piwi-interacting RNAs (piRNAs) silence these genome pathogens, but it is unclear how the piRNA pathway adapts to invasion of new transposons. In Drosophila, piRNAs are encoded by heterochromatic clusters and maternally deposited in the embryo. Paternally inherited P element transposons thus escape silencing and trigger a hybrid sterility syndrome termed P-M hybrid dysgenesis. We show that P-M hybrid dysgenesis activates both P elements and resident transposons and disrupts the piRNA biogenesis machinery. As dysgenic hybrids age, however, fertility is restored, P elements are silenced, and P element piRNAs are produced de novo. In addition, the piRNA biogenesis machinery assembles, and resident elements are silenced. Significantly, resident transposons insert into piRNA clusters, and these new insertions are transmitted to progeny, produce novel piRNAs, and are associated with reduced transposition. P element invasion thus triggers heritable changes in genome structure that appear to enhance transposon silencing.