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Nature Genetics publishes the very highest quality research in genetics. It encompasses genetic and functional genomic studies on human traits and on other model organisms, including mouse, fly, nematode and yeast. Current emphasis is on the genetic basis



 



Finally accepting plant domestication

2016-12-28

Agriculture has depended since its Neolithic origins upon spontaneous or induced genetic variation. Human selection on naturally occurring variation in flowering is the most frequent source of domesticated crop plants. In the current era of rapid technological advance in reading and writing genomes, we advocate universal access to some safe modular variation in flower, leaf and color traits that can be operated without labs or restrictions by ordinary farmers and gardeners.






Copy number alterations unmasked as enhancer hijackers

2016-12-28

Our understanding of how DNA copy number changes contribute to disease, including cancer, has to a large degree been focused on the changes in gene dosage that they generate and has neglected the effects of the DNA rearrangements that lead to their formation. A new study reports an innovative analytical framework for copy number alterations that are oncogenic primarily owing to the genomic rearrangements that underlie them.



A multitrait GWAS sheds light on insulin resistance

2016-12-28

A genome-wide study of fasting insulin, HDL cholesterol and triglycerides, designed to depict insulin resistance, identified 53 independent loci associated with a limited capacity to store fat in a healthy way. The increased power of this multitrait approach provides insights into an otherwise difficult-to-grasp phenotype.



How hormones regulate floral architecture in barley

2016-12-28

A defining characteristic of grasses, including major cereal crops, is the way in which flowers are arranged on an inflorescence. A new study finds that regulation of hormone levels during development is crucial for determining the arrangement of flowers on a barley inflorescence, opening new doors for increasing grain yield.



Tumor-suppressor genes that escape from X-inactivation contribute to cancer sex bias

2016-11-21

Andrew Lane and colleagues analyze somatic alterations across 21 tumor types for evidence of sex bias. They find that an excess of genes on the non-pseudoautosomal region of the X chromosome harbor loss-of-function mutations more frequently in males, suggesting that biallelic expression of these genes in females contributes to reduced cancer incidence in females across a variety of tumor types.



Integrative genomic analysis implicates limited peripheral adipose storage capacity in the pathogenesis of human insulin resistance

2016-11-14

Luca Lotta, Robert Scott, Stephen O’Rahilly, Claudia Langenberg, David Savage, Nicholas Wareham, Inês Barroso and colleagues identify 53 genomic regions associated with insulin resistance phenotypes. Their findings suggest that limited storage capacity of peripheral adipose tissue is an important etiological component in insulin-resistant cardiometabolic disease and highlight genes and mechanisms underpinning this link.



Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects

2016-11-21

The CNV analysis group of the Psychiatric Genomic Consortium analyzes a large schizophrenia cohort to examine genomic copy number variants (CNVs) and disease risk. They find an enrichment of CNV burden in cases versus controls and identify 8 genome-wide significant loci as well as novel suggestive loci conferring either risk or protection to schizophrenia.



The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

2016-11-14

Michael Talkowski and colleagues analyze balanced chromosomal abnormalities in 273 individuals by whole-genome sequencing. Their findings suggest that sequence-level resolution improves prediction of clinical outcomes for balanced rearrangements and provides insight into pathogenic mechanisms such as altered gene regulation due to changes in chromosome topology.



Titin-truncating variants affect heart function in disease cohorts and the general population

2016-11-21

Stuart Cook and colleagues study the role of TTN (titin)-truncating variants using a combination of heart physiology experiments in rats and genomic analysis in humans. Their data show that TTN variants are associated with a range of cardiac phenotypes in healthy individuals and in patients with dilated cardiomyopathy.



Genome-wide association analyses using electronic health records identify new loci influencing blood pressure variation

2016-11-14

Thomas Hoffmann, Neil Risch and colleagues use longitudinal electronic health records from almost 100,000 individuals to conduct genome-wide association studies for blood pressure measurements. They find new significant loci that replicate in independent cohorts and can double the variance explained by using multiple blood pressure data points.



Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking

2016-11-21

Hanno Glimm, Jan Korbel and colleagues present a computational framework called cis expression structural alteration mapping (CESAM), which they use to identify somatic copy-number alterations affecting cis-regulatory elements in cancer. They find that enhancer hijacking leads to overexpression of IRS4 and IGF2 in cancer.



Qki deficiency maintains stemness of glioma stem cells in suboptimal environment by downregulating endolysosomal degradation

2016-11-14

Jian Hu and colleagues use mouse models to show that Qki deficiency promotes gliomagenesis by allowing neural stem cells to maintain their stemness outside the subventricular zone. Mechanistically, they show that Qki deficiency decreases endolysosome-mediated degradation of receptors that are essential for maintaining self-renewal, allowing cells to cope with low ligand levels outside of their niche.



Inactivation of Capicua drives cancer metastasis

2016-11-21

Trever Bivona and colleagues use an in vivo lung cancer metastasis model to show that the transcriptional repressor Capicua (CIC) suppresses invasion and metastasis. CIC inactivation leads to upregulation of ETV4 and MMP24, which is necessary and sufficient for metastasis.



An iPSC-derived vascular model of Marfan syndrome identifies key mediators of smooth muscle cell death

2016-11-28

Sanjay Sinha and colleagues use a vascular model derived from human induced pluripotent stem cells from patients with Marfan syndrome with fibrillin-1 alterations to study aortic aneurysms. They find defects that mimic Marfan pathology as well as novel targets for treatment and can rescue the phenotype by correcting the mutation through genome editing.



Transient transcription in the early embryo sets an epigenetic state that programs postnatal growth

2016-11-14

Déborah Bourc’his and colleagues report that mouse embryos deficient for Liz (long isoform of Zdbf2) develop normally but fail to activate Zdbf2 in the postnatal brain and show growth reduction. These data suggest that transcription during an early embryonic stage may program a stable epigenetic state with later physiological consequences.



The genome and transcriptome of Japanese flounder provide insights into flatfish asymmetry

2016-12-05

Songlin Chen, Manfred Schartl, Qingyin Wang, Deborah M. Power and colleagues analyze the genome of the Japanese flounder and its transcriptome dynamics during metamorphosis. They report a role for thyroid hormone and retinoic acid signaling, as well as phototransduction pathways, in the regulation of craniofacial asymmetry.



Multiethnic genome-wide meta-analysis of ectopic fat depots identifies loci associated with adipocyte development and differentiation

2016-12-05

Audrey Chu, Matthew Steinhauser, Caroline Fox and colleagues report results of genome-wide association meta-analyses of ectopic-fat traits in individuals of European, African, Hispanic and Chinese ancestry. They identify seven new loci associated with ectopic-fat traits and present functional studies suggesting physiological roles for ATXN1 and UBE2E2 in adipogenesis.



Disease variants alter transcription factor levels and methylation of their binding sites

2016-12-05

Peter 't Hoen, Lude Franke, Bastiaan Heijmans and colleagues present a combined analysis of methylome and transcriptome data from a large collection of whole-blood samples to infer the downstream effects of disease-associated variants. They identify a large number of trait-associated SNPs influencing methylation of CpG sites in trans, providing insights into the downstream functional effects of many disease-associated variants.



Identification of context-dependent expression quantitative trait loci in whole blood

2016-12-05

Bastiaan Heijmans, Peter ’t Hoen, Lude Franke and colleagues describe a strategy to identify context-dependent expression quantitative trait loci (eQTLs). They apply their method to peripheral blood RNA–seq data from 2,116 unrelated individuals and discover 23,060 significant cis-regulated genes, of which 12% showed context-dependent eQTL effects.



ADARB1 catalyzes circadian A-to-I editing and regulates RNA rhythm

2016-11-28

Yoshitaka Fukada, Hikari Yoshitane and colleagues report that rhythmic expression of ADARB1, an RNA-editing enzyme that catalyzes adenosine-to-inosine conversion, controls mRNA oscillations in the mouse liver. Mice with Adarb1 mutations exhibit short-period rhythms in locomotor activity and gene expression.



Genome-wide analyses for personality traits identify six genomic loci and show correlations with psychiatric disorders

2016-12-05

Chi-Hua Chen and colleagues report a GWAS for five personality traits and identify four loci associated with extraversion and two associated with neuroticism at genome-wide significance. They find that the five personality traits are genetically correlated and identify genetic correlations between personality traits and psychiatric disorders.



VRS2 regulates hormone-mediated inflorescence patterning in barley

2016-11-14

Thorsten Schnurbusch, Helmy Youssef and colleagues show that VRS2, a transcription factor of the SHI family, regulates floral organ patterning and phase duration during spike development in barley. Their data establish a link between the SHI protein family and sucrose metabolism during organ growth and development.



Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato

2016-12-05

Zachary Lippman, José Jiménez-Gómez and colleagues show that cultivated tomatoes have lost day-length-sensitive flowering, compared to their wild relatives, as a result of cis-regulatory variation affecting expression of SP5G, a paralog of the florigen gene SFT. They engineered SP5G loss-of-function mutant plants, resulting in rapid flowering and early yield.