Trends in Genetics : TIGThis is an RSS file. You can use it to subscribe to this data in your favourite RSS reader, such as GoogleReader, or to display this data on your own website or blog. Subscribe to this data using MyMedWorm.Subscribe to this data using GoogleReader.Subscribe to this data using Bloglines.Subscribe to this data using MyYahoo.

This page shows you the latest items in this publication.

Pages: 1 2 3 4 5 6

295 records returned

Copy-number variants in neurodevelopmental disorders: promises and challenges.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Copy-number variation (CNV) is the most prevalent type of structural variation in the human genome. There is emerging evidence that copy-number variants (CNVs) provide a new vista on understanding susceptibility to neuropsychiatric disorders. Some challenges in the interpretation of current CNV studies include the use of overlapping samples, differing phenotypic definitions, an absence of population norms for CNVs and a lack of consensus in methods for CNV detection and analysis. Here, we review current CNV association study methods and results in autism spectrum disorders (ASD) and schizophrenia, and provide suggestio...
Source: Trends in Genetics : TIG - November 10, 2009 Category: Genetics & Stem Cells Authors: Merikangas AK, Corvin AP, Gallagher L Tags: Trends Genet Source Type: journals

Rare structural variants in schizophrenia: one disorder, multiple mutations; one mutation, multiple disorders.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recent studies have established an important role for rare genomic deletions and duplications in the etiology of schizophrenia. This research suggests that the genetic architecture of neuropsychiatric disorders includes a constellation of rare mutations in many different genes. Mutations that confer substantial risk for schizophrenia have been identified at several loci, most of which have also been implicated in other neurodevelopmental disorders, including autism. Genetic heterogeneity is a characteristic of schizophrenia; conversely, phenotypic heterogeneity is a characteristic of all schizophrenia-associated mutati...
Source: Trends in Genetics : TIG - October 31, 2009 Category: Genetics & Stem Cells Authors: Sebat J, Levy DL, McCarthy SE Tags: Trends Genet Source Type: journals

Double duty for nuclear proteins - the price of more open forms of mitosis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
During cell division, eukaryotic cells pass on their genetic material to the next generation by undergoing mitosis, which segregates their chromosomes. During mitosis, the nuclear envelope, nuclear pore complexes and nucleolus must also be segregated. Cells achieve this in a range of different forms of mitosis, from closed, in which these nuclear structures remain intact, to open, in which these nuclear structures are disassembled. In between lies a smorgasbord of intermediate forms of mitosis, displaying varying degrees of nuclear disassembly. Gathering evidence is revealing links between the extent of nuclear disasse...
Source: Trends in Genetics : TIG - October 28, 2009 Category: Genetics & Stem Cells Authors: De Souza CP, Osmani SA Tags: Trends Genet Source Type: journals

Tubulin-related cortical dysgeneses: microtubule dysfunction underlying neuronal migration defects.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The fine tuning of proliferation and neurogenesis, neuronal migration and differentiation and connectivity underlies the proper development of the cerebral cortex. Mutations in genes involved in these processes are responsible for neurodevelopmental disorders, such as cortical dysgeneses, which are usually associated with severe mental retardation and epilepsy. Over the past few years, the importance of cytoskeleton components in cellular processes crucial for cortical development has emerged from a body of functional data. This was reinforced by the association of mutations in the LIS1 and DCX genes, which both encode...
Source: Trends in Genetics : TIG - October 26, 2009 Category: Genetics & Stem Cells Authors: Jaglin XH, Chelly J Tags: Trends Genet Source Type: journals

Increased rate of human mutations where DNA and RNA polymerases collide.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Gene density and orientation of genes in eukaryotes seem to be correlated with the replication origin and the mutation rate is greater in late replicating regions; however, the reason for these patterns is unknown. Here, we investigate predicted replication origins in the human genome and find that levels of polymorphism as well as divergence from the chimpanzee genome are greater in genes transcribed on the lagging strand than those on the leading strand. This might be caused by interference between RNA and DNA polymerases, and avoidance of collisions between these enzymes might be an evolutionary force shaping gene o...
Source: Trends in Genetics : TIG - October 22, 2009 Category: Genetics & Stem Cells Authors: Jørgensen FG, Schierup MH Tags: Trends Genet Source Type: journals

Monoallelic expression and tissue specificity are associated with high crossover rates.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
What determines the recombination rate of a gene? Following the observation that, in humans, imprinted genes have unusually high recombination levels, we ask whether increased recombination is seen for other monoallelically expressed genes and, more generally, how transcriptional properties relate to recombination. We find that monoallelically expressed genes do have high crossover rates and discover a striking negative correlation between within-gene crossover rate and expression breadth. We hypothesise that these findings are possibly symptomatic of a more general, adverse relationship between recombination and trans...
Source: Trends in Genetics : TIG - October 19, 2009 Category: Genetics & Stem Cells Authors: Necsulea A, Sémon M, Duret L, Hurst LD Tags: Trends Genet Source Type: journals

Primary microcephaly: do all roads lead to Rome?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The relatively large brain and expanded cerebral cortex of humans is unusual in the animal kingdom and is thought to have promoted our adaptability and success as a species. One approach for investigating neurogenesis is the study of autosomal recessive primary microcephaly (MCPH), in which prenatal brain growth is significantly reduced without an effect on brain structure. To date, eight MCPH loci and five genes have been identified. Unexpectedly, all MCPH proteins are ubiquitous and localise to centrosomes for at least part of the cell cycle. Here, we focus on recent functional studies of MCPH proteins that reveal th...
Source: Trends in Genetics : TIG - October 19, 2009 Category: Genetics & Stem Cells Authors: Thornton GK, Woods CG Tags: Trends Genet Source Type: journals

Chromatin indexing in Arabidopsis: an epigenomic tale of tails and more.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Packaging DNA into chromatin is pivotal for the regulation of genome activity in eukaryotes. This chromatin-level control relies on a range of histone modifications and variants, chromatin-remodeling proteins and DNA methylation in plants and mammals. High-resolution maps have recently been obtained for several chromatin modifications in Arabidopsis, which provide a first glimpse at the organization of plant epigenomes. These maps suggest a pervasive involvement of transcriptional activity in indexing chromatin with reference to the underlying DNA sequence. However, to assess the contribution of chromatin dynamics to p...
Source: Trends in Genetics : TIG - October 19, 2009 Category: Genetics & Stem Cells Authors: Roudier F, Teixeira FK, Colot V Tags: Trends Genet Source Type: journals

Reading between the LINEs to see into the past.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Transposable elements (TEs) are an important source of genome diversity and play a crucial role in genome evolution. A recent study by Zhao et al. describes novel patterns of TE diversification in the genome of the extinct mammoth Mammuthus primigenius. Analysis of Mammuthus has provided a unique genome landscape, a pivotal species for understanding TEs and genome evolution and hints at the diversity we verge on discovering by expanding our taxonomic sampling among genomes. Strategies based on this work might also revolutionize investigations of the interface between TE dynamics and genome diversity. PMID: 19837475...
Source: Trends in Genetics : TIG - October 15, 2009 Category: Genetics & Stem Cells Authors: Ray DA, Platt RN, Batzer MA Tags: Trends Genet Source Type: journals

Next generation disparities in human genomics: concerns and remedies.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Studies of human genetics, particularly genome-wide association studies (GWAS), have concentrated heavily on European populations, with individuals of African ancestry rarely represented. Reasons for this include the distribution of biomedical funding and the increased population structure and reduced linkage disequilibrium in African populations. Currently, few GWAS findings have clinical utility and, therefore, the field has not yet contributed to health-care disparities. As human genomics research progresses towards the whole-genome sequencing era, however, more clinically relevant results are likely to be discovere...
Source: Trends in Genetics : TIG - October 14, 2009 Category: Genetics & Stem Cells Authors: Need AC, Goldstein DB Tags: Trends Genet Source Type: journals

High mitogenomic evolutionary rates and time dependency.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Using entire modern and ancient mitochondrial genomes of Adélie penguins (Pygoscelis adeliae) that are up to 44000 years old, we show that the rates of evolution of the mitochondrial genome are two to six times greater than those estimated from phylogenetic comparisons. Although the rate of evolution at constrained sites, including nonsynonymous positions and RNAs, varies more than twofold with time (between shallow and deep nodes), the rate of evolution at synonymous sites remains the same. The time-independent neutral evolutionary rates reported here would be useful for the study of recent evolutionary events. ...
Source: Trends in Genetics : TIG - October 13, 2009 Category: Genetics & Stem Cells Authors: Subramanian S, Denver DR, Millar CD, Heupink T, Aschrafi A, Emslie SD, Baroni C, Lambert DM Tags: Trends Genet Source Type: journals

Evolution of genomic imprinting in humans: does bipedalism have a role?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recent studies have indicated that genomic imprinting is less conserved in human placenta and fetuses than in mice. Studies in mice confirm evolutionary predictions that imprinted genes have an important role in fetal growth via their effects on placental function, nutrient demand and transfer. Here, I argue that the development of bipedalism in humans might have contributed to a reduced role for imprinted genes in fetal growth. As a consequence of bipedalism, the shape of the human pelvis has changed, leading to a reduced gestation period and smaller 'premature' babies. This overarching selective pressure could, in tu...
Source: Trends in Genetics : TIG - October 13, 2009 Category: Genetics & Stem Cells Authors: Isles AR Tags: Trends Genet Source Type: journals

The Origin at 150: is a new evolutionary synthesis in sight?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The 200th anniversary of Charles Darwin and the 150th jubilee of the On theOrigin of Species could prompt a new look at evolutionary biology. The 1959 Origin centennial was marked by the consolidation of the modern synthesis. The edifice of the modern synthesis has crumbled, apparently, beyond repair. The hallmark of the Darwinian discourse of 2009 is the plurality of evolutionary processes and patterns. Nevertheless, glimpses of a new synthesis might be discernible in emerging universals of evolution. PMID: 19836100 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - October 13, 2009 Category: Genetics & Stem Cells Authors: Koonin EV Tags: Trends Genet Source Type: journals

Detecting new neurodegenerative disease genes: does phenotype accuracy limit the horizon?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19819581 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - October 8, 2009 Category: Genetics & Stem Cells Authors: Samuels DC, Burn DJ, Chinnery PF Tags: Trends Genet Source Type: journals

Sex determination: the power of DMRT1.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
DMRT1, a mammalian gene related to sex-determining genes in flies and nematodes, is located in a region of the human genome that is important for sex development. This suggests that a common thread might run through the evolution of sex-determining mechanisms from worms to humans. New data show that DMRT1 can cause sex reversal in chickens, adding support to this hypothesis. PMID: 19819582 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - October 8, 2009 Category: Genetics & Stem Cells Authors: Koopman P Tags: Trends Genet Source Type: journals

Deciphering the genetic landscape of cancer - from genes to pathways.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Advances in genomic technologies have made it possible to screen the entire cancer genome for mutations, leading to a better understanding of the genetic landscape of cancer. Emerging results suggest that the cancer genome is composed of a few commonly mutated genes and many infrequently mutated genes. Although the number of mutated genes in any one tumor is limited, there is much heterogeneity in the genes mutated in two tumors of even the same class because of the large number of infrequently mutated genes. This could explain the wide variation in tumor behavior to chemotherapeutic intervention. Pathway analysis sugg...
Source: Trends in Genetics : TIG - October 6, 2009 Category: Genetics & Stem Cells Authors: Copeland NG, Jenkins NA Tags: Trends Genet Source Type: journals

Different gene regulation strategies revealed by analysis of binding motifs.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Coordinated regulation of gene expression relies on transcription factors (TFs) binding to specific DNA sites. Our large-scale information-theoretical analysis of >950 TF-binding motifs demonstrates that prokaryotes and eukaryotes use strikingly different strategies to target TFs to specific genome locations. Although bacterial TFs can recognize a specific DNA site in the genomic background, eukaryotic TFs exhibit widespread, nonfunctional binding and require clustering of sites to achieve specificity. We find support for this mechanism in a range of experimental studies and in our evolutionary analysis of DNA-bindi...
Source: Trends in Genetics : TIG - October 5, 2009 Category: Genetics & Stem Cells Authors: Wunderlich Z, Mirny LA Tags: Trends Genet Source Type: journals

The need for molecular genetic perspectives in evolutionary education (and vice versa).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Despite evolution being the central concept of biology, many biology students do not understand the core principles of evolutionary theory. Here, we propose that integrating evolution throughout the biology curriculum, and incorporating molecular biology and molecular genetic perspectives, will help students not only to achieve a better understanding of evolution, but also to appreciate how modern evolutionary biology research is practiced. However, realizing this vision will require changes in the way that biology is taught. Educators will need to teach from a broadened perspective and to utilize new strategies for ma...
Source: Trends in Genetics : TIG - October 1, 2009 Category: Genetics & Stem Cells Authors: Smith JJ, Baum DA, Moore A Tags: Trends Genet Source Type: journals

Characterizing natural variation using next-generation sequencing technologies.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Progress in evolutionary genomics is tightly coupled with the development of new technologies to collect high-throughput data. The availability of next-generation sequencing technologies has the potential to revolutionize genomic research and enable us to focus on a large number of outstanding questions that previously could not be addressed effectively. Indeed, we are now able to study genetic variation on a genome-wide scale, characterize gene regulatory processes at unprecedented resolution, and soon, we expect that individual laboratories might be able to rapidly sequence new genomes. However, at present, the analy...
Source: Trends in Genetics : TIG - October 1, 2009 Category: Genetics & Stem Cells Authors: Gilad Y, Pritchard JK, Thornton K Tags: Trends Genet Source Type: journals

Genome integrity: linking pluripotency and tumorgenicity.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Genome integrity is a fundamental issue in both cancer and stem cell biology. A series of recent studies revealed that a tumor suppressor p53, which is required for genome integrity, is critical also for stem cell pluripotency and reprogramming, further strengthening the fundamental link between cancer and pluripotency. p53 and other tumor suppressors might be barriers to reprogramming somatic cells for the generation of induced pluripotent stem cells (iPSCs), and simultaneously and systematically destroying these barriers would improve reprogramming efficiency. Therefore, it is also crucial to determine the tumorgenic...
Source: Trends in Genetics : TIG - October 1, 2009 Category: Genetics & Stem Cells Authors: Deng W, Xu Y Tags: Trends Genet Source Type: journals

Processed pseudogenes: the 'fossilized footprints' of past gene expression.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Although our knowledge of the genes and genomes of extinct organisms is improving as a result of progress in sequencing ancient DNA, the transcriptomes of extinct organisms remain inaccessible, owing to the rapid degradation of messenger RNA after death. We provide empirical evidence that gene expression levels in the reproductive tissues of mice and during early mouse development correlate highly with the rate of inherited retroposition: the source of processed pseudogenes in the genome. Thus, processed pseudogenes might serve as fossilized footprints of the expression of their parent genes, shedding light on ancient ...
Source: Trends in Genetics : TIG - September 28, 2009 Category: Genetics & Stem Cells Authors: Podlaha O, Zhang J Tags: Trends Genet Source Type: journals

The origins and impact of primate segmental duplications.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Duplicated sequences are substrates for the emergence of new genes and are an important source of genetic instability associated with rare and common diseases. Analyses of primate genomes have shown an increase in the proportion of interspersed segmental duplications (SDs) within the genomes of humans and great apes. This contrasts with other mammalian genomes that seem to have their recently duplicated sequences organized in a tandem configuration. In this review, we focus on the mechanistic origin and impact of this difference with respect to evolution, genetic diversity and primate phenotype. Although many genomes w...
Source: Trends in Genetics : TIG - September 28, 2009 Category: Genetics & Stem Cells Authors: Marques-Bonet T, Girirajan S, Eichler EE Tags: Trends Genet Source Type: journals

Functional compensation by duplicated genes in mouse.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19783063 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - September 24, 2009 Category: Genetics & Stem Cells Authors: Liang H, Li WH Tags: Trends Genet Source Type: journals

Robustness: mechanisms and consequences.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Biological systems are robust to perturbation by mutations and environmental fluctuations. New data are shedding light on the biochemical and network-level mechanisms responsible for robustness. Robustness to mutation might have evolved as an adaptation to reduce the effect of mutations, as a congruent byproduct of adaptive robustness to environmental variation, or as an intrinsic property of biological systems selected for their primary functions. Whatever its mechanism or origin, robustness to mutation results in the accumulation of phenotypically cryptic genetic variation. Partial robustness can lead to pre-adaptati...
Source: Trends in Genetics : TIG - August 27, 2009 Category: Genetics & Stem Cells Authors: Masel J, Siegal ML Tags: Trends Genet Source Type: journals

More than just orphans: are taxonomically-restricted genes important in evolution?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Comparative genome analyses indicate that every taxonomic group so far studied contains 10-20% of genes that lack recognizable homologs in other species. Do such 'orphan' or 'taxonomically-restricted' genes comprise spurious, non-functional ORFs, or does their presence reflect important evolutionary processes? Recent studies in basal metazoans such as Nematostella, Acropora and Hydra have shed light on the function of these genes, and now indicate that they are involved in important species-specific adaptive processes. Here we focus on evidence from Hydra suggesting that taxonomically-restricted genes play a role in th...
Source: Trends in Genetics : TIG - August 26, 2009 Category: Genetics & Stem Cells Authors: Khalturin K, Hemmrich G, Fraune S, Augustin R, Bosch TC Tags: Trends Genet Source Type: journals

Diversity of Polycomb group complexes in plants: same rules, different players?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Polycomb Group (PcG) proteins form an epigenetic memory system that is conserved in plants and animals and controls gene expression during development. Loss of plant PcG proteins leads to loss of organ identity and to cell overproliferation. Our understanding of plant PcG protein function has recently been advanced by the identification of additional proteins required for transcriptional repression by PcG and by the purification of an Arabidopsis PcG protein complex. These data indicate that Polycomb Repressive Complex 2 (PRC2)-like complexes in animals and plants have to associate with Plant Homeo Domain (PHD)-finger ...
Source: Trends in Genetics : TIG - August 26, 2009 Category: Genetics & Stem Cells Authors: Hennig L, Derkacheva M Tags: Trends Genet Source Type: journals

Group I-intron trans-splicing and mRNA editing in the mitochondria of placozoan animals.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Placozoa - the simplest known free-living animals - have been considered primitive, early diverging metazoans based on mitochondrial genome structure and phylogeny. Here we reanalyze placozoan mitochondrial DNAs, reported to include a highly unorthodox, fragmented and incomplete cox1 gene. We discover overlooked exons and split group I introns that mediate trans-splicing of the discontinuous placozoan cox1. Furthermore, we find that cox1 expression involves U-to-C editing, reconstituting an otherwise invariant, essential histidine involved in copper binding. These atypical features qualify placozoan mitochondrial gene ...
Source: Trends in Genetics : TIG - August 26, 2009 Category: Genetics & Stem Cells Authors: Burger G, Yan Y, Javadi P, Lang BF Tags: Trends Genet Source Type: journals

Neutral evolution on mammalian protein surfaces AQ.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Because of their low effective population sizes, natural selection is expected to have reduced effectiveness in organisms such as mammals. By comparing the amino acid substitution rates between mammalian protein surfaces and interiors, it was found that almost a third of the proteins surveyed failed to reject the null hypothesis of neutral substitutions among surface residues. Proteins with such partly neutral evolution nonetheless have no fewer protein interactions than do other proteins. I suggest that natural selection can function to preserve protein interactions without requiring strict conservation of the individ...
Source: Trends in Genetics : TIG - August 25, 2009 Category: Genetics & Stem Cells Authors: Conant GC Tags: Trends Genet Source Type: journals

Understanding cardiovascular disease through the lens of genome-wide association studies.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The past few years have seen significant advances in the identification of genetic factors that contribute to complex disease. Progress in cardiovascular diseases (CVD) has been particularly impressive, with genome-wide association studies (GWAS) leading to the identification of approximately 160 loci associated with CVD and its risk factors, many of which implicate new biological pathways. Here we focus on our growing understanding of the genetic contribution to CVD, examining the gene variants that increase the risk of particular CVD events and those underlying traditional CVD risk factors. Although GWAS face several...
Source: Trends in Genetics : TIG - August 25, 2009 Category: Genetics & Stem Cells Authors: Arking DE, Chakravarti A Tags: Trends Genet Source Type: journals

What's in a name? Y chromosomes, surnames and the genetic genealogy revolution.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Heritable surnames are highly diverse cultural markers of coancestry in human populations. A patrilineal surname is inherited in the same way as the non-recombining region of the Y chromosome and there should, therefore, be a correlation between the two. Studies of Y haplotypes within surnames, mostly of the British Isles, reveal high levels of coancestry among surname cohorts and the influence of confounding factors, including multiple founders for names, non-paternities and genetic drift. Combining molecular genetics and surname analysis illuminates population structure and history, has potential applications in fore...
Source: Trends in Genetics : TIG - August 6, 2009 Category: Genetics & Stem Cells Authors: King TE, Jobling MA Tags: Trends Genet Source Type: journals

Genetics of complex neurological disease: challenges and opportunities for modeling epilepsy in mice and rats.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Currently, approximately 20 genetic variants are known to cause Mendelian forms of human epilepsy, leaving a vast heritability undefined. Rodent models for genetically complex epilepsy have been studied for many years, but only recently have strong candidate genes emerged, including Cacna1g in the GAERS rat model of absence epilepsy and Kcnj10 in the low seizure threshold of DBA/2 mice. In parallel, a growing number of mouse mutations studied on multiple strain backgrounds reveal the impact of genetic modifiers on seizure severity, incidence or form - perhaps mimicking the complexity seen in humans. The field of experi...
Source: Trends in Genetics : TIG - August 5, 2009 Category: Genetics & Stem Cells Authors: Frankel WN Tags: Trends Genet Source Type: journals

Understanding synergy in genetic interactions.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Synergy occurs when the contribution of two mutations to the phenotype of a double mutant exceeds the expectations from the additive effects of the individual mutations. The molecular characterization of genes involved in synergistic interactions has revealed that synergy mainly results from mutations in functionally related genes. Recent research in Arabidopsis thaliana has advanced our understanding of the scenarios resulting in synergistic phenotypes. Those involving homologous loci usually result from various levels of functional redundancy. Some of these loci fail to complement each other or become dose-dependent ...
Source: Trends in Genetics : TIG - August 5, 2009 Category: Genetics & Stem Cells Authors: Pérez-Pérez JM, Candela H, Micol JL Tags: Trends Genet Source Type: journals

Developmental genome rearrangements in ciliates: a natural genomic subtraction mediated by non-coding transcripts.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Several classes of non-protein-coding RNAs have recently been identified as epigenetic regulators of developmental genome rearrangements in ciliates, providing an interesting insight into the role of genome-wide transcription. In these unicellular eukaryotes, extensive rearrangements of the germline genome occur during the development of a new somatic macronucleus from the germline micronucleus. Rearrangement patterns are not dictated by the germline sequence, but reproduce the pre-existing rearrangements of the maternal somatic genome, implying a homology-dependent global comparison of germline and somatic genomes. We...
Source: Trends in Genetics : TIG - July 8, 2009 Category: Genetics & Stem Cells Authors: Duharcourt S, Lepère G, Meyer E Tags: Trends Genet Source Type: journals

What controls nucleosome positions?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The DNA of eukaryotic genomes is wrapped in nucleosomes, which strongly distort and occlude the DNA from access to most DNA-binding proteins. An understanding of the mechanisms that control nucleosome positioning along the DNA is thus essential to understanding the binding and action of proteins that carry out essential genetic functions. New genome-wide data on in vivo and in vitro nucleosome positioning greatly advance our understanding of several factors that can influence nucleosome positioning, including DNA sequence preferences, DNA methylation, histone variants and post-translational modifications, higher order ...
Source: Trends in Genetics : TIG - July 8, 2009 Category: Genetics & Stem Cells Authors: Segal E, Widom J Tags: Trends Genet Source Type: journals

Are transposable elements simply silenced or are they under house arrest?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Despite their role as key players in evolution, it is commonly thought that transposable elements are selected against and silenced. However, their importance in chromosomal biology and, therefore, cell division suggests that their presence in many eukaryote genomes is the result of their having been selected as major components of heterochromatin. PMID: 19577319 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - July 1, 2009 Category: Genetics & Stem Cells Authors: Biémont C Tags: Trends Genet Source Type: journals

Complex human chromosomal and genomic rearrangements.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Copy number variation (CNV) is a major source of genetic variation among humans. In addition to existing as benign polymorphisms, CNVs can also convey clinical phenotypes, including genomic disorders, sporadic diseases and complex human traits. CNV results from genomic rearrangements that can represent simple deletion or duplication of a genomic segment, or be more complex. Complex chromosomal rearrangements (CCRs) have been known for some time but their mechanisms have remained elusive. Recent technology advances and high-resolution human genome analyses have revealed that complex genomic rearrangements can account fo...
Source: Trends in Genetics : TIG - June 24, 2009 Category: Genetics & Stem Cells Authors: Zhang F, Carvalho CM, Lupski JR Tags: Trends Genet Source Type: journals

The genetic landscape of intellectual disability arising from chromosome X.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
X-linked mental retardation (XLMR) or intellectual disability (ID) is a common, clinically complex and genetically heterogeneous disease arising from many mutations along the X chromosome. It affects between 1/600-1/1000 males and a substantial number of females. Research during the past decade has identified >90 different XLMR genes, affecting a wide range of cellular processes. Many more genes remain uncharacterized, especially for the non-syndromic XLMR forms. Currently, approximately 11% of X-chromosome genes are implicated in XLMR; however, apart from a few notable exceptions, most contribute individually to &l...
Source: Trends in Genetics : TIG - June 22, 2009 Category: Genetics & Stem Cells Authors: Gécz J, Shoubridge C, Corbett M Tags: Trends Genet Source Type: journals

Instability and chromatin structure of expanded trinucleotide repeats.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Trinucleotide repeat expansion underlies at least 17 neurological diseases. In affected individuals, the expanded locus is characterized by dramatic changes in chromatin structure and in repeat tract length. Interestingly, recent studies show that several chromatin modifiers, including a histone acetyltransferase, a DNA methyltransferase and the chromatin insulator CTCF can modulate repeat instability. Here, we propose that the unusual chromatin structure of expanded repeats directly impacts their instability. We discuss several potential models for how this might occur, including a role for DNA repair-dependent epigen...
Source: Trends in Genetics : TIG - June 17, 2009 Category: Genetics & Stem Cells Authors: Dion V, Wilson JH Tags: Trends Genet Source Type: journals

Non-invasive prenatal diagnosis by single molecule counting technologies.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Non-invasive prenatal diagnosis of fetal chromosomal aneuploidies and monogenic diseases by analysing fetal DNA present in maternal plasma poses a challenging goal. In particular, the presence of background maternal DNA interferes with the analysis of fetal DNA. Using single molecule counting methods, including digital PCR and massively parallel sequencing, many of the former problems have been solved. Digital mutation dosage assessment can detect the number of mutant alleles a fetus has inherited from its parents for fetal monogenic disease diagnosis, and massively parallel plasma DNA sequencing enables the direct det...
Source: Trends in Genetics : TIG - June 17, 2009 Category: Genetics & Stem Cells Authors: Chiu RW, Cantor CR, Dennis Lo YM Tags: Trends Genet Source Type: journals

Dynamics of transposable elements: towards a community ecology of the genome.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Like ecological communities, which vary in species composition, eukaryote genomes differ in the amount and diversity of transposable elements (TEs) that they harbor. Given that TEs have a considerable impact on the biology of their host species, we need to better understand whether their dynamics reflects some form of organization or is primarily driven by stochastic processes. Here, we borrow ecological concepts on species diversity to explore how interactions between TEs can contribute to structure TE communities within their genomic ecosystem. Whereas the niche theory predicts a stable diversity of TEs because of th...
Source: Trends in Genetics : TIG - June 17, 2009 Category: Genetics & Stem Cells Authors: Venner S, Feschotte C, Biémont C Tags: Trends Genet Source Type: journals

Regulome size in Prokaryotes: universality and lineage-specific variations.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19540614 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - June 17, 2009 Category: Genetics & Stem Cells Authors: Cordero OX, Hogeweg P Tags: Trends Genet Source Type: journals

Evolutionary history of the Snail/Scratch superfamily.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Snail transcription factors have crucial roles in metazoan development and disease. A phylogenetic analysis from placozoans to humans confirms that, along with the Scratch genes, Snail genes constitute a subgroup of the C(2)H(2) zinc-finger transcription factors, within which neither the SNAG domain nor the number of fingers define group identities. Independent duplications in the different metazoan groups gave rise to the current complement of Snail genes, and the origin of the Snail/Scratch family can be traced back to a protosnail gene that underwent tandem duplication in the last common ancestor of Diploblasts ...
Source: Trends in Genetics : TIG - May 31, 2009 Category: Genetics & Stem Cells Authors: Barrallo-Gimeno A, Nieto MA Tags: Trends Genet Source Type: journals

Origin and evolution of Y chromosomes: Drosophila tales.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Classically, Y chromosomes are thought to originate from X chromosomes through a process of degeneration and gene loss. Now, the availability of 12 Drosophila genomes provides an opportunity to study the origin and evolution of Y chromosomes in an informative phylogenetic context. Surprisingly, the majority of Drosophila Y-linked genes are recent acquisitions from autosomes and Y chromosome gene gains are more frequent than gene losses. Moreover, the Drosophila pseudoobscura Y chromosome lacks homology with the Y of most Drosophila species. Thus, the Drosophila Y has a different evolutionary history from canonical Y ch...
Source: Trends in Genetics : TIG - May 31, 2009 Category: Genetics & Stem Cells Authors: Bernardo Carvalho A, Koerich LB, Clark AG Tags: Trends Genet Source Type: journals

Understanding the neurogenetics of sleep: progress from Drosophila.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Most behaviors manifest themselves through interactions with environments. Sleep, however, is characterized by immobility and reduced responsiveness. Although nearly all animals sleep, the purpose of sleep remains an enduring puzzle. Drosophila melanogaster exhibits all the behavioral characteristics of mammalian sleep, enabling the use of powerful genetic approaches to dissect conserved fundamental neurogenetic aspects of sleep. Drosophila studies over the past four years have identified novel genes and pathways modulating sleep, such as Shaker and sleepless, and candidate brain regions known to function in circadian ...
Source: Trends in Genetics : TIG - May 31, 2009 Category: Genetics & Stem Cells Authors: Harbison ST, Mackay TF, Anholt RR Tags: Trends Genet Source Type: journals

Scaling laws in functional genome content across prokaryotic clades and lifestyles.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present a comprehensive analysis of the variation in these scaling laws across prokaryotic clades and lifestyles. For the large majority of functional categories, including transcription regulators, the inferred scaling laws are statistically indistinguishable across clades and lifestyles, supporting the simple hypothesis that these scaling laws are universally shared by all prokaryotes. PMID: 19457568 [PubMed - in process] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - May 31, 2009 Category: Genetics & Stem Cells Authors: Molina N, van Nimwegen E Tags: Trends Genet Source Type: journals

Do organellar genomes function as long-term redox damage sensors?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A small group of proteins that form core components of electron transfer complexes are consistently encoded by organellar genomes in multicellular organisms, suggesting functional constraint. These genomes are costly to maintain and vulnerable to mutation. We propose that they provide cell lineages with sensors of long-term redox damage, and of bioenergetic and genomic competence. This proposed adaptive function sets tonic retrograde signalling to the nucleus and anterograde responses influencing protective and cell death pathways. The nature of the proposed gain-of-function signalling mechanisms is unclear but could i...
Source: Trends in Genetics : TIG - May 31, 2009 Category: Genetics & Stem Cells Authors: Wright AF, Murphy MP, Turnbull DM Tags: Trends Genet Source Type: journals

The different levels of genetic diversity in sex chromosomes and autosomes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Sex chromosomes and autosomes differ in their effective population size, mutation and demography, all of which affect the relative level of genetic diversity within the genome. Moreover, natural selection acts differentially on the two chromosomal categories, for example, because recessive mutations are directly exposed to selection on the single X chromosome of males. Recent genome analyses reveal a heterogeneous picture of the sex-chromosome-to-autosome diversity ratio in different organisms. Reduced X chromosome diversity has been interpreted to reflect demographic features such as bottlenecks and male-biased disper...
Source: Trends in Genetics : TIG - May 31, 2009 Category: Genetics & Stem Cells Authors: Ellegren H Tags: Trends Genet Source Type: journals

The W, X, Y and Z of sex-chromosome dosage compensation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In species with highly differentiated sex chromosomes, imbalances in gene dosage between the sexes can affect overall organismal fitness. Regulatory mechanisms were discovered in several unrelated animals, which counter gene-dose differences between females and males, and these early findings suggested that dosage-compensating mechanisms were required for sex-chromosome evolution. However, recent reports in birds and moths contradict this view because these animals locally compensate only a few genes on the sex chromosomes, leaving the majority with different expression levels in males and females. These findings warra...
Source: Trends in Genetics : TIG - April 30, 2009 Category: Genetics & Stem Cells Authors: Mank JE Tags: Trends Genet Source Type: journals

How to become a parasite - lessons from the genomes of nematodes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The phylum Nematoda is biologically diverse; it includes parasites of plants and animals in addition to free-living taxa. To date, the genomes of six nematodes have been sequenced. Comparative analyses of these ecologically diverse nematodes are beginning to reveal the mechanisms by which parasites arise and how they evolve. Here, we discuss some emerging principles for the mechanisms and evolution of parasitism. First, horizontal gene transfer represents a common theme in nematode parasites. Second, the human parasite Brugia malayi lost otherwise essential genes most probably owing to the mutualistic relationship with...
Source: Trends in Genetics : TIG - April 30, 2009 Category: Genetics & Stem Cells Authors: Dieterich C, Sommer RJ Tags: Trends Genet Source Type: journals

Thirty years of Mus spretus: a promising future.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Extensive genetic polymorphisms in Mus spretus have ensured its widespread use in many areas of genetics. With the recent increase in the number of single nucleotide polymorphisms available for laboratory mouse strains, M. spretus is becoming less appealing, in particular for genetic mapping. Although M. spretus mice are aggressive and poor breeders, they have a bright future because they provide phenotypes unobserved in laboratory strains, and tools are available for modifying their genome and dissecting the genetic architecture of complex traits. Furthermore, they provide information on fundamental genetic questions,...
Source: Trends in Genetics : TIG - April 30, 2009 Category: Genetics & Stem Cells Authors: Dejager L, Libert C, Montagutelli X Tags: Trends Genet Source Type: journals