Genetics

We show that commercially available mice are a resource for detecting single genes by genome-wide association. We surveyed 66 populations and identified those with properties conducive to high-resolution mapping. Importantly, we show that the same alleles contribute to variation in different colonies, so that when mapping progress stalls in one colony, another can be used in its stead. As a proof of principle, we detect the same QTL in different colonies influencing CD4⁺/CD8⁺ ratios and refine this mapping to the gene level. We show that a deletion in the promoter of H2-Ea is the molecular change that strongly contributes to setting the ratio of CD4+ and CD8+ lymphocytes. Our results make it possible for geneticists to make informed choices on the use of colonies for genome-wide association studies of complex traits in mice.

Cancer is a disease of two distinct, but related, genomes: the inherited genome and the tumor genome. Despite the fact that the tumor genome arises from the germline, the genomes are typically studied as separate entities. For example, germline genetic studies focus on how inherited variation is related to a particular trait such as disease risk, whereas tumor genetic studies focus on areas of recurrent aberrations such as amplifications to identify genes involved in tumor biology. In this study, we integrated both germline and tumor genetic information to pinpoint areas of the human genome that are likely undergoing selection during the evolution of the tumor. Our results support the notion that combining germline and tumor genetic data can identify regions relevant to cancer biology.

Alzheimer's disease (AD) is the leading cause of dementia in the ageing population. Symptoms include memory loss and decline in understanding and reasoning. Alois Alzheimer, who reported the first case of AD, observed plaques and tangles in the brains of patients. The plaques are made up of amyloid protein, while the tangles are of tau protein. One of the main scientific ideas about AD is that it starts with build-up of amyloid, which then alters tau protein, causing the disease. Another protein, called GSK-3, also seems to play a part. Simple invertebrates such as flies are useful for understanding human diseases. We have created an AD model in the fruit fly Drosophila where amyloid protein is present in the nerve cells of the adult fly; this caused the flies to be impaired in their survival, nerve function, and behavior. We found that amyloid increased the activity of GSK-3, and so we experimentally turned down its activity and found that this improved the survival and behavior of the flies. Importantly, turning down the activity of GSK-3 in flies that did not have amyloid did not seem to harm them. GSK-3 could therefore be a good target for drugs against AD.

Cells sense mechanical forces and design an appropriate response crucial for cell and organ shape and differentiation during development, as well as for physiological adaptation. In particular, cardiac muscle continuously adapts to the mechanical constraints generated by its own rhythmic contractile activity. Consequently, defects in mechanosensation lead to severe pathologies, including cardiomyopathies and atherosclerosis. However, despite their well recognized functional importance, the molecular mechanisms of mechanotransduction are poorly understood. Here we study the Drosophila heart to investigate the genetic basis of mechanotransduction. We show that the heart responds to mechanical constraints by diastolic heart arrests, and we demonstrate that this phenotype can be used to identify genes controlling this particular mechanotransduction pathway. We show that the cation channel, Painless, first identified in the pain response pathway, also plays an essential function in the mechanotransduction pathway. The model system we have developed allows, for the first time, analysis of gene function in a mechanotransduction process in vivo, in the presence of endogenous mechanical constraints. These results establish the basis for an in-depth characterization of mechanotransduction pathways.

miRNAs are small RNAs found in many multi-cellular species that inhibit gene expression. Many of them play important roles in cancer and cell fate determination, but the function of most miRNAs is uncertain. Using live cell imaging and automated expression analysis, we found a miRNA gene, mir-57, is expressed in a position rather than tissue dependent way. Hox genes also regulate cell fate patterning along anterior-posterior (a-p) axis across different tissues. By investigating interactions between genes of these classes expressed in mir-57 expressing cells, we demonstrated by both genetic analysis and gene expression assays that a negative feedback loop between a posterior Hox gene, nob-1, and mir-57 regulates posterior cell fate determination in C. elegans. On the one hand, the Hox gene is required for normal activation of mir-57 expression, and on the other, the Hox gene functions as a direct target of and is repressed by the miRNA. Given the conservation of the two genes, a negative feedback loop between Hox and miRNA genes might be broadly used across species to regulate cell fate along the a-p axis. Detailed expression analysis may provide a general way to dissect the regulatory role of miRNAs.

In the course of cancer development, cells lose regulation of the cell cycle and quality control of DNA replication. As a result, many genomic alterations accumulate, among them amplifications and deletions of chromosomal regions of varying sizes. Oncogenes that drive transformation often reside in amplified regions, while tumor suppressors are deleted, yet for thousands of genes the effect of altering gene copy number is unknown. Since only genomic alterations that ultimately affect protein levels can have functional importance, a global proteomic approach that directly measures such changes is desirable. Here, we examined output of chromosomal alterations on the proteins in a system-wide manner. We analyzed the global protein expression of cancer cells compared to normal cells using mass-spectrometry–based quantitative proteomics and quantified a large part of the expressed proteome. We compared the protein data to genomic data and matched changes in gene copy number to protein expression level changes for each gene. Overall, gene copy number changes explain only a few percent of observed protein expression changes. Knowledge of when genomic and proteomic changes correlate may help in a better understanding of regulatory mechanisms in tumor development.

Germ cells transmit the genome from one generation to the next. The identity and immortality of germ cells are crucial for the perpetuation of species, yet the mechanisms that regulate these properties remain elusive. In C.elegans, a histone methyltransferase MES-4 is required for survival of the primordial germ cells. MES-4 methylates histone H3 at lysine 36 (H3K36), a modification previously linked to transcription elongation and involved in preventing aberrant transcription initiation within the body of genes. Surprisingly, our genome-wide analysis of MES-4 binding sites in C. elegans embryos revealed that MES-4 is capable of associating with genes that were expressed in the germ line of the parent worms but are no longer being actively transcribed in embryos. To our knowledge, this is the first example of transcription-uncoupled H3K36 methylation. We suggest that MES-4-generated H3K36 methylation serves an “epigenetic role,” by marking germline-expressed genes and by carrying the memory of gene expression from one generation of germ cells to the next.

Eukaryotic DNA replication begins at specific sites in the genome called replication origins, which are bound by the proteins that comprise the origin recognition complex (ORC). In budding yeast, there are more replication origins available than are used in any particular cell division cycle. Each origin has a characteristic time during the cell division cycle when the DNA replication machinery is assembled at a particular origin and begins to replicate DNA. Previous studies have indicated that differences in replication timing and origin use/availability may be a consequence of the chromatin structure surrounding an origin. Here we present a genome-wide analysis of nucleosome architecture of replication origins aligned by their ORC-binding site. We find that origins can be built with a variety of nucleosome occupancy patterns, and that these patterns are influenced by adjacent genomic features. Finally, we determined the genome-wide consequences of ORC depletion on nucleosome architecture at origins. ORC depletion allowed encroachment of flanking nucleosomes towards the origin and changed the nucleosome phasing, indicating that ORC acts as a barrier to position and phase nucleosomes. Our analysis provides a comprehensive, genome-wide view of replication origins that reveals a previously unappreciated diversity in origin structure.

Solid tumors usually have many differences in their chemical environments, such as low oxygen, depletion of glucose, high acidity (low pH), and accumulation of lactate, from normal tissues. These changes are usually called tumor microenvironmental stresses. In this study, we have used microarrays to compare the transcriptional response and metabolic adaptation in response to these different stresses seen in the tumor microenvironments. Through these comparisons, we have found that lactic acidosis triggers a starvation response, highly similar to glucose deprivation, even in the presence of abundant nutrients and oxygen. Even the cells seem to be starved; cells under lactic acidosis have decreased glucose uptake. We found this unexpected biological behavior was due to the paradoxical induction of a glucose-sensing Mondo-TXNIP pathway. The activation of this novel anti-tumor pathway under lactic acidosis contributes to the anti-Warburg effect and the restriction of cell growth in tumorigenesis by limiting nutrient availability and its inactivation may be required for tumor progression under these microenvironmental stresses.

This paper discusses and provides unique insight into an important problem raised by the current state of genetic studies into disease susceptibility, namely whether we can reuse genetic data from participants genotyped as controls in one study when cases (people with a disease of interest) are obtained from other studies, or whether each new study needs its own controls. We are interested in whether studies where cases and controls are sampled differently will give correct answers and are as powerful statistically as when new control data is also genotyped. Because of the huge investments made recently in large scale genotyping of cases and controls for various diseases, this is a timely question. This question is especially important in understanding the genetic causes of disease in as-yet relatively understudied population groups, such as African-Americans, in order to speed up progress when this is possible. We give theoretical results about the power of studies that reuse existing control genotypes based on statistical considerations. We also provide analysis of real data from a major study of the genetic causes of breast cancer in African-American women in order to shed practical light upon this issue.

An apple a day keeps the doctor away, but can knowing its genetic secrets help feed the nine billion people expected on this planet by 2050? Scientists hope so, especially considering they have added wheat this week to the list of crops that have had their genetic instruction set read. [More]



Wheat - DNA - Apple - Agriculture - Field Crops

Realistic stem cell therapies to replace diseased or damaged tissue may still be years away, but researchers have uncovered a promising new use for these undifferentiated cells: they can be programmed to become patient-specific laboratory models of inherited liver disease. These new tools could be useful for teasing out disease mechanisms and testing new drug therapies.

Scientists from the University of Cambridge's Institute for Medical Research obtained skin cells from 10 patients--seven who had various forms of inherited liver disease, and three healthy controls. They reprogrammed the skin cells, rejuvenating them into an embryolike state (using the four-gene approach described in 2007). The researchers then cultured these so-called induced pluripotent stem cells (iPS cells) in a mixture of chemical factors that triggered their conversion into liver cells, which had the appearance and functional properties of native liver cells.

The Age of Digital Entanglement By Danny Hillis

Mutations in either TSC1 or TSC2 result in tuberous sclerosis, a rare genetic disease that causes benign tumors. In this issue of PLoS Genetics, Hsieh et al. report that TSC1 and TSC2 in Drosophila regulate dE2F1 protein expression and cooperate with RBF1 to control cellular survival and proliferation. This image is an eye-antennal imaginal disc that contains tsc2 mutant clones. In the tsc2 mutant clones (GFP negative), dE2F1 proteins (red) are expressed at a higher level compared to the neighboring wild type clones (GFP positive cells). The difference can be clearly seen in photoreceptors that are marked by ELAV (blue).

Image Credit: Ting-Chiu Hsieh and Nam-Sung Moon

Patients affected by autosomal dominant retinitis pigmentosa (ADRP) experience gradual loss of vision, and mutations in the visual pigment Rhodopsin—a G protein-coupled receptor that mediates phototransduction—are associated with ADRP. The most common ADRP mutation is the substitution of proline 23 by histidine (Rh^P23H), which causes Rh misfolding and aggregation. It is currently unclear how mutant Rh^P23H leads to photoreceptor neuron (PN) degeneration in ADRP. We used the fruitfly Drosophila melanogaster in which Rh1^P37H (the equivalent of mammalian Rh^P23H) was overexpressed in PNs. We found that the presence of both mutant Rh1^P37H and endogenous Rh1 is required for neurodegeneration in Rh1^P37H flies. To understand the impact of Rh1 misfolding and clearance on PN degeneration, we inactivated the chaperone VCP/ter94, which escorts misfolded proteins out of the ER (a process termed retrotranslocation) and delivers them for proteasomal degradation. Rh1^P37H flies with decreased VCP function displayed more misfolded Rh1^P37H but, remarkably, showed a potent suppression of PN degeneration and blindness. Treatment of Rh1^P37H flies with VCP or proteasome inhibitors also mitigated PN degeneration. Our results suggest that excessive retrotranslocation and/or degradation of visual pigment is deleterious for PN expressing misfolded Rh^P23H.

Almost all living organisms deteriorate with time through the process of aging or senescence. Because most studies on senescence examined organisms possessing a juvenile state, it was thought that bacteria, which reproduce by producing two apparently identical daughter cells, were immortal and not senescent. Recent studies have demonstrated that bacteria senesce because one daughter is allocated a larger share of the mother's load of non-genetic damage. Nonetheless, it is still equivocal whether bacterial senescence renders them mortal. I have developed a model that demonstrates that bacteria can be immortal if they experience damage below a threshold rate. A fit of the model to data shows that bacteria grown under standard laboratory conditions are immortal because they encounter a rate below the threshold. Because bacteria often experience higher damage rates in nature, it is likely that bacteria are generally mortal. The allocation of more damage to one daughter and the resulting mortality is the price bacteria pay to survive higher damage rates. These results suggest that senescence originated with the evolution of the first single-celled organisms and that it is ancestral in all multicellular organisms.

Calcium ions are essential for many physiological processes, including neurosecretion and neuronal and muscle excitation. Paradoxically, abnormal accumulation of calcium ions is associated with cell death and has been documented as an early event in muscle and neural degenerative diseases. One mechanism to avoid detrimental calcium accumulation is to link the calcium increase with activation of calcium-dependent potassium ion channels, thereby reducing cell excitability and preventing further calcium influx. This negative feedback requires these potassium channels to be localized in close proximity to sites of calcium entry. In a Caenorhabditis elegans genetic screen, we identified α-catulin, known as a cytoskeletal regulatory protein in mammals, important for the localization of calcium-dependent potassium channels in both muscles and neurons. In muscle, α-catulin controls the localization of the dystrophin complex, a multimeric protein complex implicated in muscular dystrophy. The dystrophin complex in turn tethers the calcium-dependent potassium channels near calcium channels. In neurons, the α-catulin-mediated localization of the potassium channels is independent of the dystrophin complex. Lack of α-catulin results in mislocalization of the potassium channels, and in turn causes defects in neuromuscular function. Our results support the idea that cytoskeletal proteins function as anchor molecules that localize ion channels to specific cellular domains.

Single rare causal alleles and/or collections of multiple rare alleles have been suggested to create “synthetic associations” with common variants in genome-wide association studies (GWAS). This model predicts that associations with common variants will not be consistent across populations. In this study, we examined 19 T2D variants for association with T2D risk in 6,142 cases and 7,403 controls from five racial/ethnic populations in the Multiethnic Cohort (European Americans, African Americans, Latinos, Japanese Americans, and Native Hawaiians). In racial/ethnic pooled analysis, all 19 variants were associated with T2D risk in the same direction as previous reports in Europeans, and the sum total of risk variants was significantly associated with T2D risk in each racial/ethnic group. The consistent associations across populations do not support the Goldstein hypothesis that rare causal alleles underlie GWAS signals. We also did not find evidence that these markers underlie racial/ethnic disparities in T2D prevalence. Large-scale GWAS and sequencing studies in these populations are necessary in order to both improve the current set of markers at these risk loci and identify new risk variants for T2D that may be difficult, or impossible, to detect in European populations.

Arachnomelia is a defect in skeletal development of cattle. Affected calves are born dead with elongated limbs and facial deformities. The causative mutation for this recessive condition had previously been mapped to a ~7 Mb interval. We exploited the special structure of cattle families to identify the causative mutation by a purely genetic approach. The rich pedigree records in cattle breeding allowed us to identify the founder animal of arachnomelia, a Brown Swiss bull born in 1957. A few generations later several cattle received two copies of the same chromosome segment from the father of this bull due to inbreeding. One copy was passed through the founder animal and acquired the causative mutation, while the other copy was transmitted through a different line of animals and stayed in its ancestral state. Using next-generation sequencing, we sequenced the entire critical interval in one of these inbred animals. As expected, we found only one single heterozygous position, which consequently represents the causative mutation for arachnomelia. The mutation affects the gene for sulfite oxidase, thus indicating a previously unrecognized important role for this enzyme in bone development. Our findings can immediately be applied to remove this deleterious mutation from the cattle breeding population.