Genome sequencing for healthy individuals.
Abstract Genome sequencing of healthy individuals has the potential to lead to improved well-being and disease prevention, but numerous challenges remain that must be addressed to realize these benefits and, importantly, these benefits must be equitable across society. PMID: 24035073 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - September 11, 2013 Category: Genetics & Stem Cells Authors: Sanderson SC Tags: Trends Genet Source Type: research

Genetic underpinnings of division of labor in the honeybee (Apis mellifera).
Abstract Honeybees have been studied for centuries, starting with Aristotle, who wrote the first book about bee breeding. More than 2000 years later, the honeybee entered the genomic era as the first social insect whose genome was sequenced, leading to significant insight into the molecular mechanisms underlying social behavior. In addition, gene expression studies and knockdown using RNAi have extended the understanding of social interactions. Much of the work has focused on caste determination - the mechanism that results in reproductive division of labor, division of labor within the worker caste, and worker re...
Source: Trends in Genetics : TIG - September 5, 2013 Category: Genetics & Stem Cells Authors: Lattorff HM, Moritz RF Tags: Trends Genet Source Type: research

The role of AUTS2 in neurodevelopment and human evolution.
Abstract The autism susceptibility candidate 2 (AUTS2) gene is associated with multiple neurological diseases, including autism, and has been implicated as an important gene in human-specific evolution. Recent functional analysis of this gene has revealed a potential role in neuronal development. Here, we review the literature regarding AUTS2, including its discovery, expression, association with autism and other neurological and non-neurological traits, implication in human evolution, function, regulation, and genetic pathways. Through progress in clinical genomic analysis, the medical importance of this gene is ...
Source: Trends in Genetics : TIG - September 2, 2013 Category: Genetics & Stem Cells Authors: Oksenberg N, Ahituv N Tags: Trends Genet Source Type: research

LongevityMap: a database of human genetic variants associated with longevity.
We describe here its content and interface, and discuss how it can help to unravel the genetics of human longevity. PMID: 23998809 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - August 30, 2013 Category: Genetics & Stem Cells Authors: Budovsky A, Craig T, Wang J, Tacutu R, Csordas A, Lourenço J, Fraifeld VE, de Magalhães JP Tags: Trends Genet Source Type: research

Finding the lost treasures in exome sequencing data.
Abstract Exome sequencing is one of the most cost-efficient sequencing approaches for conducting genome research on coding regions. However, significant portions of the reads obtained in exome sequencing come from outside of the designed target regions. These additional reads are generally ignored, potentially wasting an important source of genomic data. There are three major types of unintentionally sequenced read that can be found in exome sequencing data: reads in introns and intergenic regions, reads in the mitochondrial genome, and reads originating in viral genomes. All of these can be used for reliable data...
Source: Trends in Genetics : TIG - August 21, 2013 Category: Genetics & Stem Cells Authors: Samuels DC, Han L, Li J, Quanghu S, Clark TA, Shyr Y, Guo Y Tags: Trends Genet Source Type: research

The role of epigenetics in hybrid vigour.
Abstract Hybrid vigour, or heterosis, refers to the increased yield and biomass of hybrid offspring relative to the parents. Although this has been exploited in plants for agriculture and horticulture, the molecular and cellular mechanisms underlying hybrid vigour are largely unknown. Genetic analyses show that there are a large number of quantitative trait loci (QTLs) that contribute to the heterotic phenotype, indicating that it is a complex phenomenon. Gene expression in hybrids is regulated by the interactions of the two parental epigenetic systems and the underlying genomes. Increasing understanding of the in...
Source: Trends in Genetics : TIG - August 14, 2013 Category: Genetics & Stem Cells Authors: Groszmann M, Greaves IK, Fujimoto R, James Peacock W, Dennis ES Tags: Trends Genet Source Type: research

Sex chromosome dosage compensation: definitely not for everyone.
Abstract Sex chromosomes often entail gene dose differences between the sexes, which if not compensated for, lead to differences between males and females in the expression of sex-linked genes. Recent work has shown that different organisms respond to sex chromosome dose in a variety of ways, ranging from complete sex chromosome dosage compensation in some species to active compensation of only a minority genes in other organisms. Although we still do not understand the implications of the diversity in sex chromosome dosage compensation, its realization has created exciting new opportunities to study the evolution...
Source: Trends in Genetics : TIG - August 14, 2013 Category: Genetics & Stem Cells Authors: Mank JE Tags: Trends Genet Source Type: research

The role of gene conversion in preserving rearrangement hotspots in the human genome.
Abstract Hotspots of non-allelic homologous recombination (NAHR) have a crucial role in creating genetic diversity and are also associated with dozens of genomic disorders. Recent studies suggest that many human NAHR hotspots have been preserved throughout the evolution of primates. NAHR hotspots are likely to remain active as long as the segmental duplications (SDs) promoting NAHR retain sufficient similarity. Here, we propose an evolutionary model of SDs that incorporates the effect of gene conversion and compare it with a null model that assumes SDs evolve independently without gene conversion. The gene convers...
Source: Trends in Genetics : TIG - August 13, 2013 Category: Genetics & Stem Cells Authors: Fawcett JA, Innan H Tags: Trends Genet Source Type: research

The zebrafish as a model for complex tissue regeneration.
Abstract For centuries, philosophers and scientists have been fascinated by the principles and implications of regeneration in lower vertebrate species. Two features have made zebrafish an informative model system for determining mechanisms of regenerative events. First, they are highly regenerative, able to regrow amputated fins, as well as a lesioned brain, retina, spinal cord, heart, and other tissues. Second, they are amenable to both forward and reverse genetic approaches, with a research toolset regularly updated by an expanding community of zebrafish researchers. Zebrafish studies have helped identify new m...
Source: Trends in Genetics : TIG - August 5, 2013 Category: Genetics & Stem Cells Authors: Gemberling M, Bailey TJ, Hyde DR, Poss KD Tags: Trends Genet Source Type: research

CENP-A and the CENP nomenclature: response to Talbert and Henikoff.
PMID: 23910159 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - August 1, 2013 Category: Genetics & Stem Cells Authors: Earnshaw WC, Cleveland DW Tags: Trends Genet Source Type: research

How old is my gene?
Abstract Gene functions, interactions, disease associations, and ecological distributions are all correlated with gene age. However, it is challenging to estimate the intricate series of evolutionary events leading to a modern-day gene and then to reduce this history to a single age estimate. Focusing on eukaryotic gene families, we introduce a framework that can be used to compare current strategies for quantifying gene age, discuss key differences between these methods, and highlight several common problems. We argue that genes with complex evolutionary histories do not have a single well-defined age. As a resul...
Source: Trends in Genetics : TIG - July 31, 2013 Category: Genetics & Stem Cells Authors: Capra JA, Stolzer M, Durand D, Pollard KS Tags: Trends Genet Source Type: research

A new frontier in synthetic biology: automated design of small RNA devices in bacteria.
Abstract RNA devices provide synthetic biologists with tools for manipulating post-transcriptional regulation and conditional detection of cellular biomolecules. The use of computational methods to design RNA devices has improved to the stage where it is now possible to automate the entire design process. These methods utilize structure prediction tools that optimize nucleotide sequences, together with fragments of known independent functionalities. Recently, this approach has been used to create an automated method for the de novo design of riboregulators. Here, we describe how it is possible to obtain riboregula...
Source: Trends in Genetics : TIG - July 23, 2013 Category: Genetics & Stem Cells Authors: Rodrigo G, Landrain TE, Shen S, Jaramillo A Tags: Trends Genet Source Type: research

Phylogeny as the basis for naming histones.
PMID: 23876620 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - July 19, 2013 Category: Genetics & Stem Cells Authors: Talbert PB, Henikoff S Tags: Trends Genet Source Type: research

Telomerase at the intersection of cancer and aging.
Abstract Although cancer and aging have been studied as independent diseases, mounting evidence suggests that cancer is an aging-associated disease and that cancer and aging share many molecular pathways. In particular, recent studies validated telomerase activation as a potential therapeutic target for age-related diseases; in addition, abnormal telomerase expression and telomerase mutations have been associated with many different types of human tumor. Here, we revisit the connection between telomerase and cancer and aging in light of recent findings supporting a role for telomerase not only in telomere elongati...
Source: Trends in Genetics : TIG - July 19, 2013 Category: Genetics & Stem Cells Authors: Bernardes de Jesus B, Blasco MA Tags: Trends Genet Source Type: research

Balancing chromatin remodeling and histone modifications in transcription.
Abstract Chromatin remodelers use the energy of ATP hydrolysis to reposition or evict nucleosomes or to replace canonical histones with histone variants. By regulating nucleosome dynamics, remodelers gate access to the underlying DNA for replication, repair, and transcription. Nucleosomes are subject to extensive post-translational modifications that can recruit regulatory proteins or alter the local chromatin structure. Just as extensive crosstalk has been observed between different histone post-translational modifications, there is growing evidence for both coordinated and antagonistic functional relations betwe...
Source: Trends in Genetics : TIG - July 16, 2013 Category: Genetics & Stem Cells Authors: Petty E, Pillus L Tags: Trends Genet Source Type: research

Multiple functions of the noncanonical Wnt pathway.
, Cabello J Abstract Thirty years after the identification of WNTs, understanding of their signal transduction pathways continues to expand. Here, we review recent advances in characterizing the Wnt-dependent signaling pathways in Caenorhabditis elegans linking polar signals to rearrangements of the cytoskeleton in different developmental processes, such as proper mitotic spindle orientation, cell migration, and engulfment of apoptotic corpses. In addition to the well-described transcriptional outputs of the canonical and noncanonical Wnt pathways, new branches regulating nontranscriptional outputs that control RA...
Source: Trends in Genetics : TIG - July 8, 2013 Category: Genetics & Stem Cells Authors: Gómez-Orte E, Sáenz-Narciso B, Moreno S, Cabello J Tags: Trends Genet Source Type: research

Developmental roles of histone H3 variants and their chaperones.
Abstract Animal development and lifetime potential exploit a balance between the stability and plasticity of cellular identity. Within the nucleus, this is controlled by an interplay involving lineage-specific transcription factors and chromatin dynamics. Histone H3 variants contribute to chromatin dynamics through the timing and sites of their incorporation, promoted by dedicated histone chaperones. Moreover, their individual modifications and binding partners provide distinct features at defined genomic loci. We highlight here the importance of the H3.3 replacement variant for the nuclear reprogramming that occu...
Source: Trends in Genetics : TIG - July 2, 2013 Category: Genetics & Stem Cells Authors: Filipescu D, Szenker E, Almouzni G Tags: Trends Genet Source Type: research

Deciphering the evolution of herbicide resistance in weeds.
rre V Abstract Resistance to herbicides in arable weeds is increasing rapidly worldwide and threatening global food security. Resistance has now been reported to all major herbicide modes of action despite the development of resistance management strategies in the 1990s. We review here recent advances in understanding the genetic bases and evolutionary drivers of herbicide resistance that highlight the complex nature of selection for this adaptive trait. Whereas early studied cases of resistance were highly herbicide-specific and largely under monogenic control, cases of greatest concern today generally involve re...
Source: Trends in Genetics : TIG - July 2, 2013 Category: Genetics & Stem Cells Authors: Délye C, Jasieniuk M, Le Corre V Tags: Trends Genet Source Type: research

Human housekeeping genes, revisited.
Abstract Housekeeping genes are involved in basic cell maintenance and, therefore, are expected to maintain constant expression levels in all cells and conditions. Identification of these genes facilitates exposure of the underlying cellular infrastructure and increases understanding of various structural genomic features. In addition, housekeeping genes are instrumental for calibration in many biotechnological applications and genomic studies. Advances in our ability to measure RNA expression have resulted in a gradual increase in the number of identified housekeeping genes. Here, we describe housekeeping gene de...
Source: Trends in Genetics : TIG - June 27, 2013 Category: Genetics & Stem Cells Authors: Eisenberg E, Levanon EY Tags: Trends Genet Source Type: research

Replication timing regulation of eukaryotic replicons: Rif1 as a global regulator of replication timing.
Abstract Origins of DNA replication on eukaryotic genomes have been observed to fire during S phase in a coordinated manner. Studies in yeast indicate that origin firing is affected by several factors, including checkpoint regulators and chromatin modifiers. However, it is unclear what the mechanisms orchestrating this coordinated process are. Recent studies have identified factors that regulate the timing of origin activation, including Rif1 which plays crucial roles in the regulation of the replication timing program in yeast as well as in higher eukaryotes. In mammalian cells, Rif1 appears to regulate the struc...
Source: Trends in Genetics : TIG - June 25, 2013 Category: Genetics & Stem Cells Authors: Yamazaki S, Hayano M, Masai H Tags: Trends Genet Source Type: research

The impact of climate change on plant epigenomes.
PMID: 23806639 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - June 24, 2013 Category: Genetics & Stem Cells Authors: Liu QA Tags: Trends Genet Source Type: research

The faster-X effect: integrating theory and data.
Abstract Population genetics theory predicts that X (or Z) chromosomes could play disproportionate roles in speciation and evolutionary divergence, and recent genome-wide analyses have identified situations in which X or Z-linked divergence exceeds that on the autosomes (the so-called 'faster-X effect'). Here, we summarize the current state of both the theory and data surrounding the study of faster-X evolution. Our survey indicates that the faster-X effect is pervasive across a taxonomically diverse array of evolutionary lineages. These patterns could be informative of the dominance or recessivity of beneficial m...
Source: Trends in Genetics : TIG - June 19, 2013 Category: Genetics & Stem Cells Authors: Meisel RP, Connallon T Tags: Trends Genet Source Type: research

Ancient cis-regulatory constraints and the evolution of genome architecture.
Abstract The order of genes along metazoan chromosomes has generally been thought to be largely random, with few implications for organismal function. However, two recent studies, reporting hundreds of pairs of genes that have remained linked in diverse metazoan species over hundreds of millions of years of evolution, suggest widespread functional implications for gene order. These associations appear to largely reflect cis-regulatory constraints, with either (i) multiple genes sharing transcriptional regulatory elements, or (ii) regulatory elements for a developmental gene being found within a neighboring 'bystan...
Source: Trends in Genetics : TIG - June 18, 2013 Category: Genetics & Stem Cells Authors: Irimia M, Maeso I, Roy SW, Fraser HB Tags: Trends Genet Source Type: research

The origin of aging: imperfectness-driven non-random damage defines the aging process and control of lifespan.
Abstract Physicochemical properties preclude ideal biomolecules and perfect biological functions. This inherent imperfectness leads to the generation of damage by every biological process, at all levels, from small molecules to cells. The damage is too numerous to be repaired, is partially invisible to natural selection, and manifests as aging. I propose that the inherent imperfectness of biological systems is the true root of the aging process. Because each biomolecule generates specific forms of damage, the cumulative damage is largely non-random and is indirectly encoded in the genome. I consider this concept i...
Source: Trends in Genetics : TIG - June 12, 2013 Category: Genetics & Stem Cells Authors: Gladyshev VN Tags: Trends Genet Source Type: research

The genomic determinants of genotype x environment interactions in gene expression.
Abstract Predicting phenotype from genotype is greatly complicated by the polygenic nature of most traits and by the complex interactions between phenotype and the environment. Here, we review recent whole-genome approaches to understand the underlying principles, mechanisms, and evolutionary impacts of genotype x environment (GxE) interactions, defined as genotype-specific phenotypic responses to different environments. There is accumulating evidence that GxE interactions are ubiquitous, accounting perhaps for the greater part of the phenotypic variation seen across genotypes. Such interactions appear to be the c...
Source: Trends in Genetics : TIG - June 12, 2013 Category: Genetics & Stem Cells Authors: Grishkevich V, Yanai I Tags: Trends Genet Source Type: research

Pleiotropy: what do you mean? Reply to Zhang and Wagner.
PMID: 23746964 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - June 6, 2013 Category: Genetics & Stem Cells Authors: Paaby AB, Rockman MV Tags: Trends Genet Source Type: research

Mitochondrial disorders: aetiologies, models systems, and candidate therapies.
Abstract It has become evident that many human disorders are characterised by mitochondrial dysfunction either at a primary level, due to mutations in genes whose encoded products are involved in oxidative phosphorylation, or at a secondary level, due to the accumulation of mitochondrial DNA (mtDNA) mutations. This has prompted keen interest in the development of cell and animal models and in exploring innovative therapeutic strategies to modulate the mitochondrial deficiencies observed in these diseases. Key advances in these areas are outlined in this review, with a focus on Leber hereditary optic neuropathy (LH...
Source: Trends in Genetics : TIG - June 4, 2013 Category: Genetics & Stem Cells Authors: Farrar GJ, Chadderton N, Kenna PF, Millington-Ward S Tags: Trends Genet Source Type: research

Brave New World of human-rights DNA collection.
Abstract Noncriminal DNA databases may serve a societal role in identifying victims of crime and human trafficking. However, how do we safeguard personal privacy of innocent victims and family members? PMID: 23706944 [PubMed - in process] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - May 31, 2013 Category: Genetics & Stem Cells Authors: Kim J, Katsanis SH Tags: Trends Genet Source Type: research

Gene dosage effects: nonlinearities, genetic interactions, and dosage compensation.
Abstract High-throughput genomic analyses have shown that many mutations, including loss-of-function (LOF) mutations, are present in diseased as well as in healthy individuals. Gene dosage effects due to deletions, duplications, and LOF mutations provide avenues to explore oligo- and multigenic inheritance. Here, we focus on several mechanisms that mediate gene dosage effects and analyze biochemical interactions among multiple gene products that are sources of nonlinear relations connecting genotypes and phenotypes. We also explore potential mechanisms that compensate for gene dosage effects. Understanding these i...
Source: Trends in Genetics : TIG - May 17, 2013 Category: Genetics & Stem Cells Authors: Veitia RA, Bottani S, Birchler JA Tags: Trends Genet Source Type: research

Properties and rates of germline mutations in humans.
Abstract All genetic variation arises via new mutations; therefore, determining the rate and biases for different classes of mutation is essential for understanding the genetics of human disease and evolution. Decades of mutation rate analyses have focused on a relatively small number of loci because of technical limitations. However, advances in sequencing technology have allowed for empirical assessments of genome-wide rates of mutation. Recent studies have shown that 76% of new mutations originate in the paternal lineage and provide unequivocal evidence for an increase in mutation with paternal age. Although mo...
Source: Trends in Genetics : TIG - May 16, 2013 Category: Genetics & Stem Cells Authors: Campbell CD, Eichler EE Tags: Trends Genet Source Type: research

Are gene loops the cause of transcriptional noise?
Abstract Expression levels of the same mRNA or protein vary significantly among the cells of an otherwise identical population. Such biological noise has great functional implications and is largely due to transcriptional bursting, the episodic production of mRNAs in short, intense bursts, interspersed by periods of transcriptional inactivity. Bursting has been demonstrated in a wide range of pro- and eukaryotic species, attesting to its universal importance. However, the mechanistic origins of bursting remain elusive. A different type of phenomenon, which has also been suggested to be widespread, is the physical ...
Source: Trends in Genetics : TIG - May 8, 2013 Category: Genetics & Stem Cells Authors: Hebenstreit D Tags: Trends Genet Source Type: research

Alternative pre-mRNA splicing in neurons: growing up and extending its reach.
Abstract Alternative pre-mRNA splicing determines the protein output of most neuronally expressed genes. Many examples have been described of protein function being modulated by coding changes in different mRNA isoforms. Several recent studies demonstrate that, through the coupling of splicing to other processes of mRNA metabolism, alternative splicing can also act as an on/off switch for gene expression. Other regulated splicing events may determine how an mRNA is utilized in its later cytoplasmic life by changing its localization or translation. These studies make clear that the multiple steps of post-transcript...
Source: Trends in Genetics : TIG - May 3, 2013 Category: Genetics & Stem Cells Authors: Zheng S, Black DL Tags: Trends Genet Source Type: research

Optogenetics in primates: a shining future?
Abstract To understand the functional role of specific neurons in micro- and macro-brain circuitry, health, and disease, it is critical to control their activity precisely. This ambitious goal was first achieved by optogenetics, allowing researchers to increase or decrease neural activity artificially with high temporal and spatial precision. In contrast to the revolution optogenetics engendered in invertebrate and rodent research, only a few studies have reported optogenetic-induced neuronal and behavioral effects in primates. Such studies are nonetheless critical before optogenetics can be applied in a clinical ...
Source: Trends in Genetics : TIG - April 25, 2013 Category: Genetics & Stem Cells Authors: Gerits A, Vanduffel W Tags: Trends Genet Source Type: research

Widespread decay of vitamin-related pathways: coincidence or consequence?
Abstract The advent of modern genomics has provided an unparalleled opportunity to consider the gene complement of an organism, and scrutinize metabolic pathways that are no longer active. This approach has led to an increasing number of reports of vitamin-associated pathway deterioration, with many indicating that independent gene-loss events of one or a few key genes have led to vitamin auxotrophy. Nonfunctional unitary pseudogenes belonging to these pathways are found in several species, demonstrating that these are recent evolutionary processes. Here, we examine the commonalities in the cellular roles and meta...
Source: Trends in Genetics : TIG - April 24, 2013 Category: Genetics & Stem Cells Authors: Helliwell KE, Wheeler GL, Smith AG Tags: Trends Genet Source Type: research

Many ways to die, one way to arrive: how selection acts through pregnancy.
Abstract When considering selective forces shaping human evolution, the importance of pregnancy to fitness should not be underestimated. Although specific mortality factors may only impact upon a fraction of the population, birth is a funnel through which all individuals must pass. Human pregnancy places exceptional energetic, physical, and immunological demands on the mother to accommodate the needs of the fetus, making the woman more vulnerable during this time-period. Here, we examine how metabolic imbalances, infectious diseases, oxygen deficiency, and nutrient levels in pregnancy can exert selective pressures...
Source: Trends in Genetics : TIG - April 5, 2013 Category: Genetics & Stem Cells Authors: Brown EA, Ruvolo M, Sabeti PC Tags: Trends Genet Source Type: research

Long noncoding RNAs in development and disease of the central nervous system.
Abstract The central nervous system (CNS) is a complex biological system composed of numerous cell types working in concert. The intricate development and functioning of this highly ordered structure depends upon exquisite spatial and temporal control of gene expression in the cells comprising the CNS. Thus, gene regulatory networks that control cell fates and functions play critical roles in the CNS. Failure to develop and maintain intricate regulatory networks properly leads to impaired development or neural dysfunction, which might manifest as neurological disorders. Long noncoding RNAs (lncRNAs) are emerging a...
Source: Trends in Genetics : TIG - April 4, 2013 Category: Genetics & Stem Cells Authors: Ng SY, Lin L, Soh BS, Stanton LW Tags: Trends Genet Source Type: research

Genetic pastures.
PMID: 23482329 [PubMed - in process] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - April 1, 2013 Category: Genetics & Stem Cells Authors: Macrae R Tags: Trends Genet Source Type: research

Molecular advances in QTL discovery and application in pig breeding.
Abstract Thousands of quantitative trait loci (QTL) have been identified for a wide range of economically important phenotypes in pigs. Recently, QTL analyses have begun to use high-density single nucleotide polymorphism (SNP) panels and applications have extended beyond experimental intercrosses to outbred populations by exploiting long-range linkage disequilibrium that results in higher resolution QTL mapping. Relevant phenotypes generally fall under categories of growth and body composition, carcass and meat quality, reproduction, and disease resistance. A few expression QTL (eQTL) studies have been performed t...
Source: Trends in Genetics : TIG - April 1, 2013 Category: Genetics & Stem Cells Authors: Ernst CW, Steibel JP Tags: Trends Genet Source Type: research

WEE1 tyrosine kinase, a novel epigenetic modifier.
Abstract The cell cycle requires cells to duplicate their chromatin, DNA, and histones, while retaining a subset of epigenetic marks, in a highly coordinated manner. The WEE1 kinase was identified as an important regulator during S phase, preventing entry into mitosis until DNA replication has been completed. Interestingly, WEE1 has also emerged as a key player in regulating histone synthesis. It phosphorylates histone H2B at tyrosine 37 in the nucleosomes found upstream of the histone gene cluster, and this suppresses histone transcription in late S phase. These observations highlight a dual role for WEE1 as both...
Source: Trends in Genetics : TIG - March 25, 2013 Category: Genetics & Stem Cells Authors: Mahajan K, Mahajan NP Tags: Trends Genet Source Type: research

Does your gene need a background check? How genetic background impacts the analysis of mutations, genes, and evolution.
Abstract The premise of genetic analysis is that a causal link exists between phenotypic and allelic variation. However, it has long been documented that mutant phenotypes are not a simple result of a single DNA lesion, but are instead due to interactions of the focal allele with other genes and the environment. Although an experimentally rigorous approach focused on individual mutations and isogenic control strains has facilitated amazing progress within genetics and related fields, a glimpse back suggests that a vast complexity has been omitted from our current understanding of allelic effects. Armed with tradit...
Source: Trends in Genetics : TIG - February 28, 2013 Category: Genetics & Stem Cells Authors: Chandler CH, Chari S, Dworkin I Tags: Trends Genet Source Type: research

Evolving approaches to the ethical management of genomic data.
Abstract The ethical landscape in the field of genomics is rapidly shifting. Plummeting sequencing costs, along with ongoing advances in bioinformatics, now make it possible to generate an enormous volume of genomic data about vast numbers of people. The informational richness, complexity, and frequently uncertain meaning of these data, coupled with evolving norms surrounding the sharing of data and samples and persistent privacy concerns, have generated a range of approaches to the ethical management of genomic information. As calls increase for the expanded use of broad or even open consent, and as controversy g...
Source: Trends in Genetics : TIG - February 27, 2013 Category: Genetics & Stem Cells Authors: McEwen JE, Boyer JT, Sun KY Tags: Trends Genet Source Type: research

Genetic basis of cell-cell fusion mechanisms.
Abstract Cell-cell fusion in sexually reproducing organisms is a mechanism to merge gamete genomes and, in multicellular organisms, it is a strategy to sculpt organs, such as muscle, bone, and placenta. Moreover, this mechanism has been implicated in pathological conditions, such as infection and cancer. Studies of genetic model organisms have uncovered a unifying principle: cell fusion is a genetically programmed process. This process can be divided in three stages: competence (cell induction and differentiation); commitment (cell determination, migration, and adhesion); and cell fusion (membrane merging and cyto...
Source: Trends in Genetics : TIG - February 27, 2013 Category: Genetics & Stem Cells Authors: Aguilar PS, Baylies MK, Fleissner A, Helming L, Inoue N, Podbilewicz B, Wang H, Wong M Tags: Trends Genet Source Type: research

The origin of the tetrapod limb: from expeditions to enhancers.
Abstract More than three centuries ago natural philosophers, and later anatomists, recognized a fundamental organization to the skeleton of tetrapod limbs. Composed of three segments, stylopod, zeugopod, and autopod, this pattern has served as the basis for a remarkably broad adaptive radiation from wings and flippers to hands and digging organs. A central area of inquiry has been tracing the origins of the elements of this Bauplan in the fins of diverse fish. Can equivalents of the three segments, and the developmental processes that pattern them, be seen in fish fins? In addition, if so, how do these data inform...
Source: Trends in Genetics : TIG - February 20, 2013 Category: Genetics & Stem Cells Authors: Schneider I, Shubin NH Tags: Trends Genet Source Type: research

Worms under stress: C. elegans stress response and its relevance to complex human disease and aging.
Abstract Many organisms have stress response pathways, components of which share homology with players in complex human disease pathways. Research on stress response in the nematode worm Caenorhabditis elegans has provided detailed insights into the genetic and molecular mechanisms underlying complex human diseases. In this review we focus on four different types of environmental stress responses - heat shock, oxidative stress, hypoxia, and osmotic stress - and on how these can be used to study the genetics of complex human diseases. All four types of responses involve the genetic machineries that underlie a numbe...
Source: Trends in Genetics : TIG - February 18, 2013 Category: Genetics & Stem Cells Authors: Rodriguez M, Snoek LB, De Bono M, Kammenga JE Tags: Trends Genet Source Type: research

Improving fruit and wine: what does genomics have to offer?
Abstract Will we still be drinking wines made from Pinot Noir and eating McIntosh apples in the 23rd century? Elite grape and apple cultivars, vegetatively propagated for centuries, are highly susceptible to evolving pathogens. In response, growers continually expand their agrochemical weaponry at enormous environmental costs. By contrast, breeders are seeking disease-resistant, tastier alternatives to the handful of dominant cultivars by exploring genetic diversity in these fruits. However, this is a formidable task because consumers cling to ancient cultivars, and breeding long-lived woody perennials is laboriou...
Source: Trends in Genetics : TIG - February 18, 2013 Category: Genetics & Stem Cells Authors: Myles S Tags: Trends Genet Source Type: research

Amish revisited: next-generation sequencing studies of psychiatric disorders among the Plain people.
Abstract The rapid development of next-generation sequencing (NGS) technology has led to renewed interest in the potential contribution of rarer forms of genetic variation to complex non-mendelian phenotypes such as psychiatric illnesses. Although challenging, family-based studies offer some advantages, especially in communities with large families and a limited number of founders. Here we revisit family-based studies of mental illnesses in traditional Amish and Mennonite communities - known collectively as the Plain people. We discuss the new opportunities for NGS in these populations, with particular emphasis on...
Source: Trends in Genetics : TIG - February 16, 2013 Category: Genetics & Stem Cells Authors: Hou L, Faraci G, Chen DT, Kassem L, Schulze TG, Shugart YY, McMahon FJ Tags: Trends Genet Source Type: research

Rethinking our intellectual origins: response to Kalinka et al.
PMID: 23422050 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - February 16, 2013 Category: Genetics & Stem Cells Authors: Crabtree GR Tags: Trends Genet Source Type: research

Our robust intellect.
PMID: 23419455 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - February 15, 2013 Category: Genetics & Stem Cells Authors: Kalinka AT, Kelava I, Lewitus E Tags: Trends Genet Source Type: research

A population genetics view of animal domestication.
Abstract The fundamental shift associated with the domestication of plants and animals allowed for a dramatic increase in human population sizes and the emergence of modern society. Despite its importance and the decades of research devoted to studying it, questions regarding the origins and processes of domestication remain. Here, we review recent theoretical advances and present a perspective that underscores the crucial role that population admixture has played in influencing the genomes of domestic animals over the past 10000 years. We then discuss novel approaches to generating and analysing genetic data, emp...
Source: Trends in Genetics : TIG - February 14, 2013 Category: Genetics & Stem Cells Authors: Larson G, Burger J Tags: Trends Genet Source Type: research

RNA-binding proteins in Mendelian disease.
Abstract RNA-binding proteins (RBPs) control all aspects of RNA fate, and defects in their function underlie a broad spectrum of human pathologies. We focus here on two recent studies that uncovered the in vivo mRNA interactomes of human cells, jointly implicating over 1100 proteins in RNA binding. Surprisingly, over 350 of these RBPs had no prior RNA binding-related annotation or domain homology. The datasets also contain many proteins that, when mutated, cause Mendelian diseases, prominently neurological, sensory, and muscular disorders and cancers. Disease mutations in these proteins occur throughout their doma...
Source: Trends in Genetics : TIG - February 14, 2013 Category: Genetics & Stem Cells Authors: Castello A, Fischer B, Hentze MW, Preiss T Tags: Trends Genet Source Type: research