Nature Genetics

05/17/2017

Online Nature Rev Genetics Genetics of coronary artery disease by Khera & Kathiresan Sek Kathiresan MD http://go.nature.com/2qwtDvV

05/08/2017

#Genome sequencing of the Silver birch (Salojärvi et al.) http://go.nature.com/2pro2pk #OA

05/05/2017

Transcriptional profiling of human oocytes and preimplantation embryos highlights DUX4-family proteins as activators of cleavage-stage genes and repetitive elements. The study shows that Dux expression converts mouse embryonic stem cells into two-cell (2C) embryo-like cells, suggesting that mouse DUX and human DUX4 act as drivers of the mammalian cleavage/2C state. Article by Peter Hendrickson et al: http://go.nature.com/2qptNV4 $

05/04/2017

Conservation and innovation in the DUX4-family gene network : Nature Genetics : Nature Research

A new study reports that human DUX4, which is linked to facioscapulohumeral dystrophy, and mouse DUX activate genes associated with cleavage-stage embryos, including retrotransposons, in muscle cells.

Article by Jennifer Whiddon: http://go.nature.com/2qpBEC5 $

Stephen Tapscott and colleagues report that human DUX4, which is linked to facioscapulohumeral dystrophy, and mouse DUX activate genes associated with cleavage-stage embryos, including retrotransposons, in muscle cells. They suggest that the ancestral DUX4-regulated genes characteristic of cleavage-...

05/03/2017

DUX-family transcription factors regulate zygotic genome activation in placental mammals : Nature Genetics

A new study finds that both human DUX4 and mouse Dux are expressed before zygotic genome activation (ZGA) and lead to activation of ZGA-associated genes. Dux knockout in mouse embryonic stem cells prevents cycling through a 2-cell-like state, and zygotic depletion of Dux impairs embryonic development.

Article by Alberto De Iaco et al.: http://go.nature.com/2pABpGE #SharedIt

05/02/2017

DNA sequence homology induces cytosine-to-thymine mutation by a heterochromatin-related pathway in Neurospora : Nature Genetics : Nature Research

Eugene Gladyshev and Nancy Kleckner report that the DNMT1-like cytosine methylase DIM-2 can mediate repeat-induced point mutation through C-to-T mutation of repetitive DNA in Neurospora crassa. They show that this process requires heterochromatin factors and propose a model whereby direct interactions between homologous double-stranded DNA can initiate the formation of heterochromatin. http://go.nature.com/2qw4LTR $

Eugene Gladyshev and Nancy Kleckner report that the DNMT1-like cytosine methylase DIM-2 can mediate RIP (repeat-induced point mutation) through cytosine-to-thymine mutation of repetitive DNA in Neurospora crassa. They show that this process requires heterochromatin factors and propose a model whereb...

05/01/2017

The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression : Nature Genetics : Nature Research

The genome sequence of the golden orb-weaver spider provides new insights into how spiders create silk for building their webs

Article by Paul Babb et al.: go.nature.com/2pPcFeK (Open)
Image Credit: Charles J Sharp via Wikipedia: https://tinyurl.com/l3v3ys8

Benjamin Voight and colleagues report the annotated genome of the golden orb-weaver spider. They describe 28 spider silk genes (spidroins), characterize their expression in distinct silk gland types and identify non-spidroin genes with expression patterns suggesting potential roles in silk productio...

04/28/2017

Innate and adaptive immunity shape circulating HCV strains : Nature Genetics : Nature Research

News and Views article by Silvana Gaudieri & Michaela Lucas highlights a study reporting genome-to-genome analysis of host-HCV genetic interactions http://go.nature.com/2oLUC4B

An unbiased genome-to-genome analysis in chronic hepatitis C virus (HCV) infection confirms the innate and adaptive arms of the immune system as drivers of viral evolution. Viral adaptation has a critical role in the interaction between host and pathogen and has important clinical implications for i...

04/28/2017

Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes : Nature Genetics : Nature Research

Genomic analysis of 133 ovarian cancers identifies seven subgroups using point mutation and structural variation signatures

Article by Yi Kan Wang & Ali Bashashati et al.: http://go.nature.com/2q7U2OS ($)

Sohrab Shah, David Huntsman and colleagues report the genomic analysis of 133 ovarian cancers spanning different subtypes. They identify seven subgroups using point mutation and structural variation signatures and use these genomic features to stratify ovarian cancers both between and within histoty...

04/27/2017

A SMARCD2-containing mSWI/SNF complex is required for granulopoiesis : Nature Genetics : Nature Research

News and Views by Brittany Michel & Cigall Kadoch highlights two recent studies reporting a key role for SWI/SNF complex protiens in granulopoiesis http://go.nature.com/2qeYnQL

Mammalian SWI/SNF complexes have critical roles in development and differentiation, and are implicated in the pathogenesis of several diseases; however, the mechanisms underpinning disease manifestation and the specificity of the subunits mutated are incompletely understood. Newly identified loss-of...

04/27/2017

The future of human genome editing : Nature Genetics : Nature Research

We recommend constant oversight and evaluation of human germline genome editing to balance prudence with discovery, and risk with progress. http://go.nature.com/2q7Rvbd

With the advent of precision genome editing, the ability to modify living organisms has proceeded with remarkable speed and breadth. Any application of this technology to the human germ line must be tightly coupled to deliberate consideration of the consequences, both scientific and social, of intro...

04/27/2017

From the archives (2004): Large-scale structural variation in the human genome : Free Association

New blog post about one of our landmark papers, featuring comments from Steve Scherer and Charles Lee http://go.nature.com/2pDcP8H

has been lucky to publish many exciting papers, more than a few of which can be described as “landmark” papers—publications that have had a dramatic and long-lasting impact on a field. In 2004, the Journal published such

04/27/2017

Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk : Nature Genetics : Nature Research

Analysis of genotype data from ∼370,000 women identifies 389 independent signals that associate with age at menarche, implicating ∼250 genes. These analyses suggest causal inverse associations, independent of BMI, between puberty timing and risks for breast and endometrial cancers in women and prostate cancer in men.

http://go.nature.com/2pt8Yeq ($)

John Perry, Ken Ong and colleagues analyze genotype data on [sim]370,000 women and identify 389 independent signals that associate with age at menarche, implicating [sim]250 genes. Their analyses suggest causal inverse associations, independent of BMI, between puberty timing and risks for breast and...

04/26/2017

Becoming weeds : Nature Genetics : Nature Research

News and Views by C Neal Stewart Jr highlights a new study on weedy rice evolution http://go.nature.com/2pirymy

A new resequencing analysis of weedy rice (Oryza sativa L.) biotypes illuminates distinct evolutionary paths and outcomes of de-domestication and ferality. This largest effort to date in weedy plant genomics gives a better understanding of weediness while also providing a promising source of alleles...

04/26/2017

Nature Ecology & Evolution

Nature Ecology & Evolution

Two new papers in Nature Ecology & Evolution explore how new genes are born. One takes an experimental approach, the other a bioinformatic approach. Your can read the stories behind both papers on our community site.

https://natureecoevocommunity.nature.com/users/30793-joanna-masel/posts/16390-de-novo-gene-birth
https://natureecoevocommunity.nature.com/users/34835-rafik-neme/posts/16396-exploring-random-sequence-space-in-the-name-of-de-novo-genes

04/26/2017

The May issue of Nature Genetics is online Now! Epigenome energy landscapes, weedy rice evolution, citrus genomes and more! http://go.nature.com/2plGhz1

04/26/2017

Functional screen of MSI2 interactors identifies an essential role for SYNCRIP in myeloid leukemia stem cells : Nature Genetics : Nature Research

A new study identifies 24 genes that interact with MSI2 protein and are required for leukemia in vivo.

Article by Ly Vu et al.: http://go.nature.com/2q7CTVN ($)

Michael Kharas and colleagues characterize the MSI2 protein interactome in leukemia cells and subsequently perform a functional screen identifying 24 genes required for leukemia in vivo. They focus on the RNA-binding protein SYNCRIP, showing that it regulates Hoxa9 and other transcripts involved in…

04/25/2017

Celebrating DNA Day

Happy #DNADay17! Access Nature Research articles on genetics to mark DNA Day 2017 #SN_DNADay http://go.nature.com/2otaZms

Author guidance and resources for International Pediatric Research Foundation

04/25/2017

Adiposity amplifies the genetic risk of fatty liver disease conferred by multiple loci : Nature Genetics : Nature Research

Adiposity significantly amplifies the effects of some genetic variants on nonalcoholic fatty liver disease.

Article by Stefan Stender et al.: http://go.nature.com/2paI7kf ($)

Jonathan Cohen, Helen Hobbs and colleagues show that adiposity significantly amplifies the effects of PNPLA3, TM6SF2, and GCKR sequence variants on nonalcoholic fatty liver disease. They find that synergy between adiposity and genotype influences the full spectrum of the disease, from steatosis to h...

04/24/2017

Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila : Nature Genetics

Environmental changes affect how epialleles in genetically identical Drosophila strains are expressed. These "epilines" can be reset to a naïve state, indicating that the inheritance of this phenotypic variability is epigenetic.

Article by Filippo Ciabrelli et al.: go.nature.com/2ooF0s0 #SharedIt

04/20/2017

From the archives (1995): Guidelines for interpreting and reporting linkage results : Free Association

New blog post from the Nature Genetics editors highlights a classic paper from our archives by Eric Lander & Leonid Kruglyak from 1995. http://go.nature.com/2oTMSyy #NatGen25

, recommending clear statistical guidelines for reporting linkage results for complex traits. The paper had an immediate impact, setting the bar for what could or could not be called “significant” in the literature. Although originally focused on human genetic linkage studies, the guidelines set for...

04/20/2017

Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation : Nature Genetics

Patrick Ellinor and colleagues report meta-analyses of common and rare variant association studies for atrial fibrillation across multiple populations. They identify 12 new loci, some of which implicate genes in atrial electrical and mechanical function.

Article by Ingrid Christophersen et al.: http://go.nature.com/2oEOV9G #SharedIt

04/20/2017

Identification of six new genetic loci associated with atrial fibrillation in the Japanese population : Nature Genetics

Kaoru Ito, Yoichiro Kamatani, Toshihiro Tanaka and colleagues report a genome-wide association study for atrial fibrillation in the Japanese population. They identify six new loci, five of which are not associated with atrial fibrillation in individuals of European ancestry, suggesting that they may be specific to the Japanese population.

Article by Siew-Kee Low et al.: http://go.nature.com/2oie3SG #SharedIt

04/19/2017

Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

A cassava haplotype map (HapMapII) constructed from deep-sequencing data of 241 accessions finds >28 million segregating variants. The study reports that clonal propagation has led to fixation of deleterious mutations, which have been ineffectively purged, owing to limited recombination.

Article by Punna Ramu et al: http://go.nature.com/2on8SQC

04/18/2017

Nature Genetics 25th Anniversary

Check out our editors' selection of highlighted papers from the archives to celebrate 25 years of Nature Genetics #NatGen25

http://go.nature.com/2n4dOOo

Celebrating 25 years of Nature Genetics!

04/18/2017

Contrasting evolutionary genome dynamics between domesticated and wild yeasts : Nature Genetics : Nature Research

A new study reports complete genome assemblies based on long-read sequencing of 7 Saccharomyces cerevisiae and 5 Saccharomyces paradoxus strains to compare the evolutionary dynamics between these domesticated and wild yeast species.

Article by Jia-Xing Yue et al.: http://go.nature.com/2oESf4E

Jia-Xing Yue, Gianni Liti and colleagues use long-read sequencing to generate complete genome assemblies of 7 Saccharomyces cerevisiae and 5 Saccharomyces paradoxus strains. They use these data to define boundaries between chromosomal core and subtelomeric regions and to compare the evolutionary dyn...

04/17/2017

Pathogenic variants that alter protein code often disrupt splicing : Nature Genetics

A new study using a massively parallel splicing assay (MaPSy) to analyze 4,964 exonic, disease-causing mutations finds that 10% of these exonic mutations affect splicing.

Article by Rachel Soemedi & Kamil Cygan et al.: go.nature.com/2oi65ZG #SharedIt

04/14/2017

Home : NYU Nature Conference on Neurogenetics

Don't miss your chance to present at the NYU Nature Conference on Neurogenetics! Abstracts due Apr 19 http://buff.ly/2phZPlr #neurogen17

August 9-11, 2017
Kimmel Center for University Life, New York University, New York, NY, USA

04/14/2017

NYU Nature Conference on Neurogenetics

Don't miss your chance to present at the NYU Nature Conference on Neurogenetics! Abstract submissions due April 19: go.nature.com/2picYLA #neurogen17

August 9-11, 2017
Kimmel Center for University Life, New York University, New York, NY

04/12/2017

Spatial heterogeneity in medulloblastoma : Nature Genetics

An analysis of spatial heterogeneity in medulloblastoma finds that somatic mutations affecting genes suitable for targeted therapeutics are spatially heterogeneous, while gene expression landscapes are more homogeneous

Article by A Sorana Morrissy, Florence Cavalli, Marc Remke et al.: http://go.nature.com/2o13Auq #SharedIt

04/11/2017

IFN-λ3, not IFN-λ4, likely mediates IFNL3–IFNL4 haplotype–dependent hepatic inflammation and fibrosis : Nature Genetics

A previous association of the IFNL3–IFNL4 region with hepatic inflammation and fibrosis implicated either IFN-λ3 or IFN-λ4. A new study finds greater evidence for a functional role of IFN-λ3.

Article by Mohammed Eslam et al.: http://go.nature.com/2oRNUOo #SharedIt

04/11/2017

events.columbia.edu

Very exciting program lineup for Columbia University's Precision Medicine conference on April 28th. Register here: http://events.columbia.edu/go/conference

04/11/2017

Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus : Nature Genetics

A systematic genome-to-genome study of 542 individuals chronically infected with hepatitis C virus finds effects of both the innate and adaptive immune systems on the HCV genome

Article by M. Azim Ansari, Vincent Pedergnana et al.: http://go.nature.com/2ojMXLz #SharedIt

04/10/2017

Population- and individual-specific regulatory variation in Sardinia : Nature Genetics

Analysis of gene expression data from 624 Sardinians finds a high frequency of splicing and expression QTLs near genes involved in malarial resistance and multiple sclerois
Article by Mauro Pala, Zachary Zappala et al.: http://go.nature.com/2ny0odA #SharedIt

04/10/2017

Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction : Nature Genetics : Nature Research

Genomic studies of citrus suggest that regions containing energy- and reproduction-associated genes may be under selection in cultivated citrus

Article by Xia Wang, Yuantao Xu, Siqi Zhang, Li Cao et al.:
http://go.nature.com/2oYlpy2 #openacces
Image credit: Scott Bauer, USDA (via Wikipedia)

Qiang Xu and colleagues sequence four citrus species de novo, along with 100 accessions, including primitive, wild and cultivated citrus. Their genomic analyses associate the CitRWP gene with polyembryony and suggest that regions harboring energy- and reproduction-associated genes are probably under...

04/07/2017

Mutation rates of Mycobacterium tuberculosis: From the archives (2013) : Free Association

New blog post highlighting a paper from our archives (2013): Mutation rates of Mycobacterium tuberculosis
http://go.nature.com/2oJhi9i #NatGen25 #NatGenblog

is a global problem, and understanding the origins and dynamics of the emergence of resistance is an important scientific and public health endeavor.

04/03/2017

Resequencing at scale in neurodevelopmental disorders : Nature Genetics

News & Views by David Fitzpatrick on identifying genes involved in neurodevelopmental disorders from large-scale sequencing studies
http://go.nature.com/2nPluTF #SharedIt