Nature Reviews Genetics » Recent news items

From the editors

Nature Reviews Genetics 11, 591 (2010). doi:10.1038/nrg2866

Studies of human evolution are more feasible than ever, but present some pressing challenges.

From the editors

Nature Reviews Genetics 11, 525 (2010). doi:10.1038/nrg2846

Why context is important for understanding gene regulation. And view our FREE audio slideshow.

From the editors

Nature Reviews Genetics 11, 451 (2010). doi:10.1038/nrg2826

'Omics' is in the eye of the beholder'Omics' technologies are transforming many subfields of genetics, but their success depends on interesting hypotheses and good scientific judgement.

Transcriptomics: Common disease pathogenesis pathways

Nature Reviews Genetics 11, 386 (2010). doi:10.1038/nrg2799

Author: Gemma K. Alderton

Several observations indicate that various human diseases could be biologically connected. In particular, some data suggest that metabolic, inflammatory and autoimmune diseases increase the risk of developing cancer, so a new study has investigated whether there is overlap in the underlying biology of these diseases.

From the editors

Nature Reviews Genetics 11, 385 (2010). doi:10.1038/nrg2806

This month we launch a series on modes of transcriptional regulation with a review on inducible gene regulation.Modes of transcriptional regulation: http://www.nature.com/nrg/series/transcriptionalregulation/index.html

From the editors

Nature Reviews Genetics 11, 309 (2010). doi:10.1038/nrg2797

New Comment articles increase our flexibility in covering the most important issues in genetics and genomics.

Human microbiome: A gut feeling for disease

Nature Reviews Genetics 11, 237 (2010). doi:10.1038/nrg2767

Author: Louisa Flintoft

Three studies showcase the growing interest in using genetics and genomics to understand how the huge numbers of bacteria that live in human guts influence our biology. The largest metagenomic survey so far of human gut microbial genes sets the scene for comparing gut microbiome

From the editors

Nature Reviews Genetics 11, 235 (2010). doi:10.1038/nrg2780

Towards models of disease pathogenesis from diverse genetic causes.

From the editors

Nature Reviews Genetics 11, 167 (2010). doi:10.1038/nrg2766

Exploring interspecies differences in biological processes leads to valuable advances.

In Brief

Nature Reviews Genetics 11, 173 (2010). doi:10.1038/nrg2762

Genome evolution

In Brief

Nature Reviews Genetics 11, 171 (2010). doi:10.1038/nrg2761

Evolution

Evolution: Illusions of conservation

Nature Reviews Genetics 11, 169 (2010). doi:10.1038/nrg2753

Author: Mary Muers

If a sequence or property appears to be conserved across evolutionary time it is often interpreted as being functionally important. But can apparently conserved patterns be produced by neutral or indirect forces? New simulations of regulatory element evolution show that they can.Enhancer elements often

Mammalian recombination hot spots: properties, control and evolution

Nature Reviews Genetics 11, 221 (2010). doi:10.1038/nrg2712

Authors: Kenneth Paigen & Petko Petkov

Recombination, together with mutation, generates the raw material of evolution, is essential for reproduction and lies at the heart of all genetic analysis. Recent advances in our ability to construct genome-scale, high-resolution recombination maps and new molecular techniques for analysing recombination products have substantially furthered

Human genomics: Into Africa

Nature Reviews Genetics 11, 170 (2010). doi:10.1038/nrg2758

Author: Magdalena Skipper

The steady increase in the number of individual human genome sequences is providing fine-scale insights into variation in the human genome. These insights inform us about human diversity and have important implications for medical applications of genomics. The first individual genome sequences and sequences of

Complex disease: Rare treasures

Nature Reviews Genetics 11, 170 (2010). doi:10.1038/nrg2754

Author: Tanita Casci

Rare variants distributed across large genomic regions make a substantial contribution to the genetic basis of complex diseases, according to a simulated genome-wide association (GWA) study that is backed by real disease-mapping data.GWA studies are based on the assumption that complex diseases are caused

From the editors

Nature Reviews Genetics 10, 507 (2009). doi:10.1038/nrg2648

Biology is gradually turning into an 'exact' science. Genetics hints at the mechanisms underlying phenotypes, and molecular genetics documents how components interact; but now, an even deeper understanding of biological phenomena is being obtained by a mathematical description of the underlying principles. Take developmental biology,

Gene regulation: Sequence, chromatin, action!

Nature Reviews Genetics 10, 512 (2009). doi:10.1038/nrg2647

Author: Louisa Flintoft

When a cell receives a signal that alters its transcriptional programme, primary response genes (PRGs) are rapidly induced. Two recent papers provide new insights into the basis of the speedy activation of mammalian PRGs.Although some mammalian PRGs depend on chromatin remodelling by SWI–SNF complexes

In Brief

Nature Reviews Genetics 10, 514 (2009). doi:10.1038/nrg2645

Phylogenetics

Complex disease: Schizophrenia: missing heritability found?

Nature Reviews Genetics 10, 509 (2009). doi:10.1038/nrg2643

Author: Chris Gunter

Although genome-wide association (GWA) studies for complex diseases or traits have now been with us for a number of years, mental disorders have proven particularly resistant to this approach. Conventional wisdom has been that problems with exact phenotyping will always make GWA studies difficult for

Exploiting and antagonizing microRNA regulation for therapeutic and experimental applications

Nature Reviews Genetics 10, 578 (2009). doi:10.1038/nrg2628

Authors: Brian D. Brown & Luigi Naldini

New technologies are emerging that utilize artificial microRNA (miRNA) target sites to exploit or inhibit endogenous miRNA regulation. This approach has been used to improve cell-specific targeting for gene and stem cell therapy studies and for animal transgenics, and also to reduce the toxicity of

Technology: The sequencing game

Nature Reviews Genetics 10, 510 (2009). doi:10.1038/nrg2646

Author: Tanita Casci

A new approach to pooling DNA samples promises to increase the number of templates that can be sequenced in a single experiment from a few dozen to over 100,000. This 'DNA Sudoku' method, named after the logic puzzle, will offer substantial cost savings to high-throughout

In Brief

Nature Reviews Genetics 10, 511 (2009). doi:10.1038/nrg2644

X inactivation

Cell signalling: Telomerase gets Wnt talking

Nature Reviews Genetics 10, 513 (2009). doi:10.1038/nrg2642

Author: Katharine H. Wrighton

What do Wnt–β-catenin signalling and telomerase have in common? Both can activate quiescent epidermal stem cells in vivo. However, how telomerase does this, and whether its role in this process is linked to Wnt–β-catenin signalling, was unknown. Steven Artandi and colleagues now reveal that

Mechanisms of change in gene copy number

Nature Reviews Genetics 10, 551 (2009). doi:10.1038/nrg2593

Authors: P. J. Hastings, James R. Lupski, Susan M. Rosenberg & Grzegorz Ira

Deletions and duplications of chromosomal segments (copy number variants, CNVs) are a major source of variation between individual humans and are an underlying factor in human evolution and in many diseases, including mental illness, developmental disorders and cancer. CNVs form at a faster rate than

Quantitative approaches in developmental biology

Nature Reviews Genetics 10, 517 (2009). doi:10.1038/nrg2548

Authors: Andrew C. Oates, Nicole Gorfinkiel, Marcos González-Gaitán & Carl-Philipp Heisenberg

The tissues of a developing embryo are simultaneously patterned, moved and differentiated according to an exchange of information between their constituent cells. We argue that these complex self-organizing phenomena can only be fully understood with quantitative mathematical frameworks that allow specific hypotheses to be formulated

The genetics of quantitative traits: challenges and prospects

Nature Reviews Genetics 10, 565 (2009). doi:10.1038/nrg2612

Authors: Trudy F. C. Mackay, Eric A. Stone & Julien F. Ayroles

A major challenge in current biology is to understand the genetic basis of variation for quantitative traits. We review the principles of quantitative trait locus mapping and summarize insights about the genetic architecture of quantitative traits that have been obtained over the past decades. We

Evolution: Protein kinases mix it up

Nature Reviews Genetics 10, 514 (2009). doi:10.1038/nrg2639

Author: Mary Muers

Phenotypic diversity is the substrate for natural selection, so identifying the components that contribute to this diversity is crucial for understanding evolution. Much attention has focused on differences in gene expression between species, but to what extent do other cellular components provide phenotypic diversity? Combining

Evolution: Turning up the heat

Nature Reviews Genetics 10, 512 (2009). doi:10.1038/nrg2638

Author: Meera Swami

How does the rate of genetic change vary in response to temperature, and what impact does this have on evolution to different environments? Two new studies have shown that the rate of mutation in thermophilic microorganisms is lower than in mesophiles but, by contrast, mammals

Regeneration: Flies get into renewal

Nature Reviews Genetics 10, 510 (2009). doi:10.1038/nrg2637

Author: Tanita Casci

How tissues might replenish themselves after injury has fascinated biologists for decades; however, research in this field has frequently been hampered by the lack of an easy-to-use experimental model.Now, a paper reports a means of studying regeneration in arguably the genetically most tractable organism of

Evolutionary analysis of the dynamics of viral infectious disease

Nature Reviews Genetics 10, 540 (2009). doi:10.1038/nrg2583

Authors: Oliver G. Pybus & Andrew Rambaut

Many organisms that cause infectious diseases, particularly RNA viruses, mutate so rapidly that their evolutionary and ecological behaviours are inextricably linked. Consequently, aspects of the transmission and epidemiology of these pathogens are imprinted on the genetic diversity of their genomes. Large-scale empirical analyses of the

MicroRNAs: HITS-CLIP hits the microRNA target

Nature Reviews Genetics 10, 510 (2009). doi:10.1038/nrg2635

Author: Elizabeth Neame

Many efforts to determine microRNA (miRNA) targets have relied on computational approaches, which are hampered by high false positive rates because the target site sequences are short and occur often in the genome. This problem has been overcome by a recent study, which combines HITS-CLIP

Fitness and its role in evolutionary genetics

Nature Reviews Genetics 10, 531 (2009). doi:10.1038/nrg2603

Author: H. Allen Orr

Although the operation of natural selection requires that genotypes differ in fitness, some geneticists may find it easier to understand natural selection than fitness. Partly this reflects the fact that the word 'fitness' has been used to mean subtly different things. In this Review I

An offer you can't refuse? Ethical implications of non-invasive prenatal diagnosis

Nature Reviews Genetics 10, 515 (2009). doi:10.1038/nrg2631

Authors: Dagmar Schmitz, Christian Netzer & Wolfram Henn

Genetic prenatal diagnosis (PND) for fetal aneuploidies has been an integral part of prenatal medicine for over 30 years. It is usually performed as a combination of initial non-invasive risk screening (NIRS) strategies, and suspicious results are followed by invasive diagnostic procedures such as amniocentesis.

Louis Kunkel

Nature Reviews Genetics 10, 430 (2009). doi:10.1038/nrg2614

The 2009 March of Dimes Prize in Developmental Biology has been awarded jointly to Kevin Campbell of the University of Iowa and to Louis Kunkel of Harvard Medical School and The Children's Hospital, Boston, for their pioneering work in identifying the genes and proteins that

Understanding what determines the frequency and pattern of human germline mutations

Nature Reviews Genetics 10, 478 (2009). doi:10.1038/nrg2529

Authors: Norman Arnheim & Peter Calabrese

Surprising findings about human germline mutation have come from applying new technologies to detect rare mutations in germline DNA, from analysing DNA sequence divergence between humans and closely related species, and from investigating human polymorphic variation. In this Review we discuss how these approaches affect

RNA world: A new class of small RNAs

Nature Reviews Genetics 10, 425 (2009). doi:10.1038/nrg2613

Author: Meera Swami

The identification of a novel class of small RNAs has provided specific insights into the function of this class, and indicates that this RNA species has a role in the DNA damage response by inhibiting protein translation.The RNAi pathway is important for dsRNA-induced and

In Brief

Nature Reviews Genetics 10, 349 (2009). doi:10.1038/nrg2609

Human genetic variationThe diversity present in 5,140 human mitochondrial genomesPereira, L.et al. Am. J. Hum. Genet.7 May 2009 (doi:10.1016/j.ajhg.2009.04.013)High-throughput sequencing is rapidly increasing the amount of data on human mitochondrial genetic variation. These authors developed

From the editors

Nature Reviews Genetics 10, 343 (2009). doi:10.1038/nrg2608

Model organisms continue to be fundamental to almost every aspect of genetic research. Three articles in this month's issue highlight the breadth of areas in which animal models provide insights, but also emphasize the need to use these organisms in the most effective way.The

Kevin Campbell

Nature Reviews Genetics 10, 351 (2009). doi:10.1038/nrg2607

The 2009 March of Dimes Prize in Developmental Biology has been awarded jointly to Kevin Campbell of the University of Iowa and to Louis Kunkel of Harvard Medical School and The Children's Hospital, Boston, for their pioneering work in identifying the genes and proteins that

Population genetics: Genetic landscapes out of Africa

Nature Reviews Genetics 10, 345 (2009). doi:10.1038/nrg2605

Author: Mary Muers

As the birthplace of modern humans, Africa holds unique significance for human population genetics. The continent is now home to approximately 900 million people in more than 2,000 different ethnolinguistic groups, and yet patterns of genetic variation in African populations have remained largely uncharacterized. A

Technology: The holy grail for plant biologists

Nature Reviews Genetics 10, 350 (2009). doi:10.1038/nrg2604

Author: Magdalena Skipper

Plant biologists and biotechnologists have long suffered from the lack of an efficient and sequence-specific method for gene targeting. Two recent reports of successful gene targeting in maize and tobacco come as a welcome improvement on the laborious conventional mutagenesis or transgenesis approaches. For the

Mapping genes for complex traits in domestic animals and their use in breeding programmes

Nature Reviews Genetics 10, 381 (2009). doi:10.1038/nrg2575

Authors: Michael E. Goddard & Ben J. Hayes

Genome-wide panels of SNPs have recently been used in domestic animal species to map and identify genes for many traits and to select genetically desirable livestock. This has led to the discovery of the causal genes and mutations for several single-gene traits but not for

Synthetic biology: Towards off-the-shelf networks

Nature Reviews Genetics 10, 348 (2009). doi:10.1038/nrg2602

Author: Tanita Casci

Synthetic biologists dream of constructing gene expression networks with predictable functions. However, they come up against a frustrating problem: because the assembly parts (ORFs and control regions) are poorly characterized and limited in number, each new circuit has to be painstakingly tweaked until it behaves

In Brief

Nature Reviews Genetics 10, 347 (2009). doi:10.1038/nrg2601

Genome instabilityChromosome instability is common in human cleavage-stage embryosVanneste, E.et al. Nature Med.26 Apr 2009 (doi:10.1038/nm.1924)This study describes the presence of a large amount of genomic instability early in human embryogenesis. The authors used new

Detecting gene–gene interactions that underlie human diseases

Nature Reviews Genetics 10, 392 (2009). doi:10.1038/nrg2579

Author: Heather J Cordell

Following the identification of several disease-associated polymorphisms by genome-wide association (GWA) analysis, interest is now focusing on the detection of effects that, owing to their interaction with other genetic or environmental factors, might not be identified by using standard single-locus tests. In addition to increasing

Towards better mouse models: enhanced genotypes, systemic phenotyping and envirotype modelling

Nature Reviews Genetics 10, 371 (2009). doi:10.1038/nrg2578

Authors: Johannes Beckers, Wolfgang Wurst & Martin Hrabé de Angelis

The mouse is the leading mammalian model organism for basic genetic research and for studying human diseases. Coordinated international projects are currently in progress to generate a comprehensive map of mouse gene functions — the first for any mammalian genome. There are still many challenges

Maintaining the brain: insight into human neurodegeneration from Drosophila melanogaster mutants

Nature Reviews Genetics 10, 359 (2009). doi:10.1038/nrg2563

Authors: Derek Lessing & Nancy M. Bonini

The fruitfly Drosophila melanogaster has enabled significant advances in neurodegenerative disease research, notably in the identification of genes that are required to maintain the structural integrity of the brain, defined by recessive mutations that cause adult onset neurodegeneration. Here, we survey these genes in

New insights into the aetiology of colorectal cancer from genome-wide association studies

Nature Reviews Genetics 10, 353 (2009). doi:10.1038/nrg2574

Authors: Albert Tenesa & Malcolm G. Dunlop

Genome-wide association studies have recently identified ten common genetic variants associated with colorectal cancer susceptibility, several suggesting the involvement of components of the transforming growth factor beta (TGFβ) superfamily signalling pathway. To date, no causal sequence variants have been identified, and risk seems to be

Human language as a culturally transmitted replicator

Nature Reviews Genetics 10, 405 (2009). doi:10.1038/nrg2560

Author: Mark Pagel

Human languages form a distinct and largely independent class of cultural replicators with behaviour and fidelity that can rival that of genes. Parallels between biological and linguistic evolution mean that statistical methods inspired by phylogenetics and comparative biology are being increasingly applied to study language.

Complex disease: Autism clues from genome-wide studies

Nature Reviews Genetics 10, 346 (2009). doi:10.1038/nrg2599

Author: Louisa Flintoft

Our understanding of the genetic contribution to autism spectrum disorders (ASDs) has expanded rapidly, but remains far from complete. Despite good evidence for roles of rare and de novo variants in some cases, the genetic basis of most cases remains unexplained and the involvement

Genomics: Milking the cow genome

Nature Reviews Genetics 10, 346 (2009). doi:10.1038/nrg2598

Author: Mary Muers

The domestic cow, Bos taurus, is not only an established part of human agriculture but with its interesting position in the phylogenetic tree — in a different clade to humans and rodents — it is also favoured in comparative genomics. Two assemblies of the

Small RNAs: A tiny stabilizer of development

Nature Reviews Genetics 10, 350 (2009). doi:10.1038/nrg2597

Author: Louisa Flintoft

A new paper provides the first experimental evidence that microRNAs (miRNAs) confer robustness, by showing that a Drosophila melanogaster miRNA buffers a developmental process against environmental fluctuation.Li and colleagues investigated the role of miR-7 in sensory organ development. Previous studies had shown that,

Gene expression: Structure versus codon bias

Nature Reviews Genetics 10, 348 (2009). doi:10.1038/nrg2596

Author: Elizabeth Neame

It is well known that codon bias and gene expression are correlated. The established explanation is that mRNAs with a high codon adaptation index (CAI) — that is, with a high number of 'preferred' codons — are translated more efficiently because there are more tRNAs

Cancer genomics: A modular approach to signalling

Nature Reviews Genetics 10, 348 (2009). doi:10.1038/nrg2595

Author: Meera Swami

Instead of considering signalling in terms of a linear sequence, the concept of modules as units of signalling activity is a useful way to represent complex biological networks, such as those involved in cancer. A recent study describes an approach to dissect oncogenic signalling pathways

The future of evo–devo: model systems and evolutionary theory

Nature Reviews Genetics 10, 416 (2009). doi:10.1038/nrg2567

Author: Ralf J. Sommer

There has been a recent trend in evolutionary developmental biology (evo–devo) towards using increasing numbers of model species. I argue that, to understand phenotypic change and novelty, researchers who investigate evo–devo in animals should choose a limited number of model organisms in which to develop

From the editors

Nature Reviews Genetics 10, 277 (2009). doi:10.1038/nrg2590

Genetic and genomic approaches are revolutionizing many aspects of infectious disease research. This was a clear message from a conference held in March, jointly organized by the American Society of Human Genetics, The Human Genome Organization and Nature Publishing Group. The meeting — Genetics and

In Brief

Nature Reviews Genetics 10, 284 (2009). doi:10.1038/nrg2589

TranscriptomicsmRNA-Seq whole-transcriptome analysis of a single cellTang, F.et al. Nature Methods6 Apr 2009 (doi: 10.1038/nmeth.1315)Next-generation sequencing enables accurate and in-depth transcriptome analysis (RNA-Seq), but usually requires microgram amounts of RNA, precluding single cell studies. These authors

In Brief

Nature Reviews Genetics 10, 281 (2009). doi:10.1038/nrg2588

TechnologyConditional mutagenesis in DrosophilaChoi, C. M. & Vilain, S.et al. Science324, 54 (2009)Although it is relatively straightforward to conditionally knock out genes in several species, notably in mice, analogous techniques in flies

Genetics of gene expression: Putting radiation response on the map

Nature Reviews Genetics 10, 278 (2009). doi:10.1038/nrg2587

Author: Louisa Flintoft

Mapping the genetic variation that underlies differences in gene expression between individuals provides new insights into mechanisms of gene regulation and the genetic basis of phenotypic variation. A new study on human cells explores the genetic basis of response to a medically important exposure: ionizing

Human disease: Psychiatric disorders: a role for defective proliferation

Nature Reviews Genetics 10, 282 (2009). doi:10.1038/nrg2586

Author: Leonie Welberg

Mutations in the gene disrupted in schizophrenia 1 (DISC1) have been associated with increased risk for schizophrenia as well as other psychiatric disorders, including bipolar disorder and major depression. DISC1 is known to regulate diverse processes in postmitotic neurons during development, such as

Validating, augmenting and refining genome-wide association signals

Nature Reviews Genetics 10, 318 (2009). doi:10.1038/nrg2544

Authors: John P. A. Ioannidis, Gilles Thomas & Mark J. Daly

Studies using genome-wide platforms have yielded an unprecedented number of promising signals of association between genomic variants and human traits. This Review addresses the steps required to validate, augment and refine such signals to identify underlying causal variants for well-defined phenotypes. These steps include: large-scale

Survival of the flexible: hormonal growth control and adaptation in plant development

Nature Reviews Genetics 10, 305 (2009). doi:10.1038/nrg2558

Authors: Hanno Wolters & Gerd Jürgens

Plant development is subject to hormonal growth control and adapts to environmental cues such as light or stress. Recently, significant progress has been made in elucidating hormone synthesis, signalling and degradation pathways, and in resolving spatial and temporal aspects of hormone responses. Here we review

Epigenetics: A silent inheritance

Nature Reviews Genetics 10, 283 (2009). doi:10.1038/nrg2585

Author: Francesca Cesari

Polycomb repressor complex 1 (PRC1) proteins remain bound to chromatin during DNA replication, reports a new study in Cell. This finding suggests that the retention of chromatin regulatory proteins throughout DNA replication might be an important mechanism of epigenetic inheritance.Chromatin templates that are

Gene regulation: A new toolbox for mapping regulatory sites

Nature Reviews Genetics 10, 282 (2009). doi:10.1038/nrg2584

Author: Meera Swami

Large-scale experimental approaches for identifying sites of protein–DNA interaction are mainly based on chromatin immunoprecipitation (ChIP), which relies on prior knowledge of regulatory factors and can only interrogate sites for one protein at a time. Two new studies overcome these limitations by exploiting the simple

Genetic susceptibility to SLE: new insights from fine mapping and genome-wide association studies

Nature Reviews Genetics 10, 285 (2009). doi:10.1038/nrg2571

Authors: Isaac T. W. Harley, Kenneth M. Kaufman, Carl D. Langefeld, John B. Harley & Jennifer A. Kelly

Genome-wide association studies and fine mapping of candidate regions have rapidly advanced our understanding of the genetic basis of systemic lupus erythematosus (SLE). More than 20 robust associations have now been identified and confirmed, providing insights at the molecular level that refine our understanding of

Non-genetic heterogeneity — a mutation-independent driving force for the somatic evolution of tumours

Nature Reviews Genetics 10, 336 (2009). doi:10.1038/nrg2556

Authors: Amy Brock, Hannah Chang & Sui Huang

Clonal populations of mammalian cells are inherently heterogeneous. They contain cells that display non-genetic variability resulting from gene expression noise and the fact that gene networks have multiple stable states. These stable, heritable variants within one cell type can exhibit different levels of responsiveness to

Plant development: Paternal control regulates division

Nature Reviews Genetics 10, 280 (2009). doi:10.1038/nrg2582

Author: Elizabeth Neame

The phenomenon of parent-of-origin effects is well documented in animal embryogenesis. In flowering plants, however, only a few cases of maternal control of embryogenesis have been identified and, until recently, there were no documented cases of paternal control. Bayer and colleagues describe the first paternal

Population genetics: Separating demography from selection

Nature Reviews Genetics 10, 280 (2009). doi:10.1038/nrg2581

Author: Mary Muers

It is hoped that identifying genes that have undergone selection in the human lineage will help to reveal which genes underlie human-specific traits or human phenotypic variation. A recent paper has tackled an important challenge in picking out such genes: how to distinguish between genetic

Development: Drosophila embryos are doing it for themselves

Nature Reviews Genetics 10, 279 (2009). doi:10.1038/nrg2580

Author: Tanita Casci

Canalization — the ability of developing organisms to produce consistent phenotypic outcomes despite biochemical fluctuations — was first described 60 years ago, but a direct mechanistic description of this complex phenomenon has been lacking. A quantitative and experimental approach to analysing embryonic development in Drosophila

Linking DNA methylation and histone modification: patterns and paradigms

Nature Reviews Genetics 10, 295 (2009). doi:10.1038/nrg2540

Authors: Howard Cedar & Yehudit Bergman

Both DNA methylation and histone modification are involved in establishing patterns of gene repression during development. Certain forms of histone methylation cause local formation of heterochromatin, which is readily reversible, whereas DNA methylation leads to stable long-term repression. It has recently become apparent that DNA

Data sharing in genomics — re-shaping scientific practice

Nature Reviews Genetics 10, 331 (2009). doi:10.1038/nrg2573

Authors: Jane Kaye, Catherine Heeney, Naomi Hawkins, Jantina de Vries & Paula Boddington

Funding bodies have recently introduced a requirement that data sharing must be a consideration of all funding applications in genomics. As with all new developments this condition has had an impact on scientific practice, particularly in the area of publishing and in the conduct of

Functional genomics: Structure provides clues

Nature Reviews Genetics 10, 284 (2009). doi:10.1038/nrg2576

Author: Meera Swami

Most genomic functions are encoded in the ∼98% of the genome that does not encode proteins, but the identification of non-coding functional elements has proved tricky. A new study describes a structure-based comparative method for identifying functional elements and shows that DNA structure is a

Viral manipulation of the host epigenome for oncogenic transformation

Nature Reviews Genetics 10, 290 (2009). doi:10.1038/nrg2539

Authors: Roberto Ferrari, Arnold J. Berk & Siavash K. Kurdistani

The cancerous cellular state is associated with multiple epigenetic alterations, but elucidating the precise order of such alterations during tumorigenic progression and their contributions to the transformed phenotype remains a significant challenge in cancer biology. Here we discuss recent findings on how viral oncoproteins exploit

From the editors

Nature Reviews Genetics 10, 217 (2009). doi:10.1038/nrg2572

Since the first human genome sequences were published in 2001, an overriding focus for human geneticists has been to catalogue genetic differences between individuals and relate them to differences in phenotype, particularly with respect to disease susceptibility. In this issue, a Review by Kelly Frazer

In Brief

Nature Reviews Genetics 10, 223 (2009). doi:10.1038/nrg2570

Gene regulationTranscriptional infidelity promotes heritable phenotypic change in a bistable gene networkGordonA. J. E.et al. PLoS Biol.7, e1000044 (2009)This study shows that transient errors occuring during transcription can have heritable phenotypic consequences for cells.

In Brief

Nature Reviews Genetics 10, 221 (2009). doi:10.1038/nrg2569

Genome evolutionA burst of segmental duplications in the genome of the African great ape ancestorMarques-Bonet, T.et al. Nature457, 877–881 (2009)These authors generated maps of segmental duplications in the human genome and the

Epigenetics: Taking a position on regulatory diversity

Nature Reviews Genetics 10, 220 (2009). doi:10.1038/nrg2568

Author: Louisa Flintoft

Epigenetic differences between individual cells, populations or species are established contributors to differences in gene expression. Whereas previous work has focused mainly on the contribution of proteins that act in trans to epigenetic differences, studies using yeast now reveal that differences in nucleosome positioning

Human genetic variation and its contribution to complex traits

Nature Reviews Genetics 10, 241 (2009). doi:10.1038/nrg2554

Authors: Kelly A. Frazer, Sarah S. Murray, Nicholas J. Schork & Eric J. Topol

The last few years have seen extensive efforts to catalogue human genetic variation and correlate it with phenotypic differences. Most common SNPs have now been assessed in genome-wide studies for statistical associations with many complex traits, including many important common diseases. Although these studies have

Reply: A unified classification system for eukaryotic transposable elements should reflect their phylogeny

Nature Reviews Genetics 10, 276 (2009). doi:10.1038/nrg2165-c4

Author: Thomas Wicker, François Sabot, Aurélie Hua-Van, Jeffrey L. Bennetzen, Pierre Capy, Boulos Chalhoub, Andrew Flavell, Philippe Leroy, Michele Morgante, Olivier Panaud, Etienne Paux, Phillip SanMiguel & Alan H. Schulman

The goal of our Guidelines article (A unified classification system for eukaryotic transposable elements Nature Rev. Genet.8, 973–982 (2007)), as Seberg and Petersen correctly surmise (A unified classification system for eukaryotic transposable elements should reflect their

A unified classification system for eukaryotic transposable elements should reflect their phylogeny

Nature Reviews Genetics 10, 276 (2009). doi:10.1038/nrg2165-c3

Authors: Ole Seberg & Gitte Petersen

To assist genome annotators in naming transposable elements (TEs), Wicker et al. propose in their Guidelines article (A unified classification system for eukaryotic transposable elements. Nature Rev. Genet.8, 973–982 (2007)) a classification and nomenclatural system

Replication timing and epigenetic reprogramming of gene expression: a two-way relationship?

Nature Reviews Genetics 10, 269 (2009). doi:10.1038/nrg2555

Authors: Anita Göndör & Rolf Ohlsson

An overall link between the potential for gene transcription and the timing of replication in S phase is now well established in metazoans. Here we discuss emerging evidence that highlights the possibility that replication timing is causally linked with epigenetic reprogramming. In particular, we bring

Ethical implications of epigenetics research

Nature Reviews Genetics 10, 224 (2009). doi:10.1038/nrg2562

Authors: Mark A. Rothstein, Yu Cai & Gary E. Marchant

New advances in epigenetics research are being reported at an accelerating rate. Intriguing research findings, primarily from animal studies, show that epigenetic changes tend to occur at a much higher frequency than mutations in DNA sequence, that the susceptibility to epigenetic changes is greater at

Systems genetics: Networking complex traits

Nature Reviews Genetics 10, 219 (2009). doi:10.1038/nrg2566

Author: Meera Swami

Determining the genetic architecture of complex traits poses a challenge because most phenotypic variation is caused by numerous interactions between a multitude of environmentally sensitive genes. A recent study that uses systems genetics to analyse complex traits in Drosophila melanogaster is an important step

Epigenetics: RNAi protects across the generations

Nature Reviews Genetics 10, 220 (2009). doi:10.1038/nrg2565

Author: Louisa Flintoft

RNAi is increasingly being recognized as a means of protecting the genome from harmful epigenetic changes. Two new studies in plants describe how RNAi can prevent or reverse the reactivation of transposable elements (TEs), which might otherwise wreak havoc in the genomes of successive generations.

Population genetics: A portrait of yeast

Nature Reviews Genetics 10, 222 (2009). doi:10.1038/nrg2561

Author: Tanita Casci

The importance of yeast for fermentation has shaped our shared history with this organism for thousands of years. By analysing the genomes of dozens of isolates of domestic and wild yeast two studies now document the effect of evolutionary processes on the yeast genome —

A census of human transcription factors: function, expression and evolution

Nature Reviews Genetics 10, 252 (2009). doi:10.1038/nrg2538

Authors: Juan M. Vaquerizas, Sarah K. Kummerfeld, Sarah A. Teichmann & Nicholas M. Luscombe

Transcription factors are key cellular components that control gene expression: their activities determine how cells function and respond to the environment. Currently, there is great interest in research into human transcriptional regulation. However, surprisingly little is known about these regulators themselves. For example, how many

Development: Linking the loops for digit identity

Nature Reviews Genetics 10, 222 (2009). doi:10.1038/nrg2559

Author: Mary Muers

Developmental pathways need to be robust against environmental and genetic variation to enable reliable morphogenesis, yet the mechanisms that buffer signalling in vertebrate development are largely unknown. Dissection of the genetic interactions and kinetics of feedback loops has now given insight into how robustness is

New insights into the genetics of addiction

Nature Reviews Genetics 10, 225 (2009). doi:10.1038/nrg2536

Authors: Ming D. Li & Margit Burmeister

Drug addiction is a common brain disorder that is extremely costly to the individual and to society. Genetics contributes significantly to vulnerability to this disorder, but identification of susceptibility genes has been slow. Recent genome-wide linkage and association studies have implicated several regions and genes

Beyond odds ratios — communicating disease risk based on genetic profiles

Nature Reviews Genetics 10, 264 (2009). doi:10.1038/nrg2516

Authors: Peter Kraft, Sholom Wacholder, Marilyn C. Cornelis, Frank B. Hu, Richard B. Hayes, Gilles Thomas, Robert Hoover, David J. Hunter & Stephen Chanock

The brisk discovery of novel inherited disease markers by genome-wide association (GWA) studies has raised expectations for predicting disease risk by analysing multiple common alleles. However, the statistics used during the discovery phase of research (such as odds ratios or p values for association)

The evolution of Fox genes and their role in development and disease

Nature Reviews Genetics 10, 233 (2009). doi:10.1038/nrg2523

Authors: Sridhar Hannenhalli & Klaus H. Kaestner

The forkhead box (Fox) family of transcription factors, which originated in unicellular eukaryotes, has expanded over time through multiple duplication events, and sometimes through gene loss, to over 40 members in mammals. Fox genes have evolved to acquire a specialized function in many key biological

Translation: Ribosomal footprints

Nature Reviews Genetics 10, 222 (2009). doi:10.1038/nrg2557

Author: Elizabeth Neame

Translation can now be measured accurately on a genome-wide scale thanks to a novel ribosome profiling technique that uses deep sequencing to track translation with subcodon resolution. This new technique could overcome the uncertainty that is inherent in inferring protein levels from mRNA levels, owing

Genetically sociable

Nature Reviews Genetics 10, 220 (2009). doi:10.1038/nrg2553

Author: Elizabeth Neame

Can you count your friends on one hand? Or are you constantly double-booked? The answer is likely to lie in your genes, according to a new study, “Model of genetic variation in human social networks”, published in the Proceedings of the National Academy

Transcriptomics: Processing adds to the complexity

Nature Reviews Genetics 10, 154 (2009). doi:10.1038/nrg2552

Author: Louisa Flintoft

A recent study reveals how some of the increasingly apparent complexity of mammalian transcriptomes arises. It identifies an unanticipated abundance of stable, capped small RNAs in mammalian cells, which seem to be processed from both protein-coding and non-coding RNAs.Deep sequencing identified 102,159 new small

Cancer genetics: Networking on the fly

Nature Reviews Genetics 10, 150 (2009). doi:10.1038/nrg2551

Author: Nicola McCarthy

There are now many ways in which genes that are mutated in particular cancer types can be identified, including starting from less genetically complex organisms such as Drosophila melanogaster. Kevin White and colleagues have taken this approach and have identified SPOP as a

In Brief

Nature Reviews Genetics 10, 153 (2009). doi:10.1038/nrg2550

RNA interferenceDrosophila

In Brief

Nature Reviews Genetics 10, 151 (2009). doi:10.1038/nrg2549

ChromatinRole of Jhdm2a in regulating metabolic gene expression and obesity resistanceTateishi, K.et al. Nature4 Feb 2009 (doi:10.1038/nature07777)This paper reveals a physiological role for a chromatin-modifying protein — the histone H3 lysine 9 (H3K9) demethylase JHDM2A.

From the editors

Nature Reviews Genetics 10, 149 (2009). doi:10.1038/nrg2547

How much of the genome is transcribed and what is the function of the RNA output? It used to be possible to give straightforward answers to these questions. With a few exceptions, transcription was thought to start from defined regions — promoters of protein-coding genes

Mapping complex disease traits with global gene expression

Nature Reviews Genetics 10, 184 (2009). doi:10.1038/nrg2537

Authors: William Cookson, Liming Liang, Gonçalo Abecasis, Miriam Moffatt & Mark Lathrop

Variation in gene expression is an important mechanism underlying susceptibility to complex disease. The simultaneous genome-wide assay of gene expression and genetic variation allows the mapping of the genetic factors that underpin individual differences in quantitative levels of expression (expression QTLs; eQTLs). The availability of

Development: Deciphering the Wingless gradient

Nature Reviews Genetics 10, 154 (2009). doi:10.1038/nrg2546

Author: Elizabeth Neame

A key principle of developmental biology is that during pattern formation a cell detects the local concentration of a morphogen within a gradient, which guides the cell down the appropriate differentiation pathway. But how can such simple information reliably activate the range of intricate signalling

Evo–devo: Failsafe flowers

Nature Reviews Genetics 10, 152 (2009). doi:10.1038/nrg2545

Author: Tanita Casci

The design of regulatory circuits determines their function — for example, whether they behave like developmental switches — but the specific details of the wiring can also be influenced by evolutionary pressures. A study of flower organ development shows that the interaction between two key