July 2011 Volume 43 Number 7, pp 613 - 720
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EDITORIAL
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Milestone in Anhui p613
doi:10.1038/ng.881
Our first Nature Conference in China emphasized the value of extending
genome-wide association studies (GWAS) to populations worldwide as a way
to promote cooperation and high standards in research while gaining a
wealth of biological insights into common and complex diseases and traits.
http://links.ealert.nature.com/ctt?kn=74&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
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NEWS AND VIEWS
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Mapping higher order structure of chromatin domains pp615 - 616
Celso A Espinoza and Bing Ren
doi:10.1038/ng.869
Large-scale mapping of chromatin state and transcription factor binding
have uncovered many broad chromatin domains along linear genomic DNA,
but it is unclear how these functional domains are organized in
three-dimensional nuclear space. A new study now shows that many domains
exist as loops connected by CCTC-binding factor (CTCF), providing new
insights into the higher-order structure of chromatin organization in the nucleus.
http://links.ealert.nature.com/ctt?kn=71&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
The long reach of noncoding RNAs pp616 - 617
Elena Sotillo and Andrei Thomas-Tikhonenko
doi:10.1038/ng.870
Transcription of genomic loci containing protein-coding genes often yields
not only cognate mRNAs but also assorted noncoding RNAs (ncRNAs), which
typically map in the vicinity of transcription start sites. A new study
shows that far from being random byproducts of gene expression, many long ncRNAs
(lncRNAs) are synthesized in a coordinate fashion and control important
cellular processes, such as survival in the face of DNA damage.
http://links.ealert.nature.com/ctt?kn=77&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Regulating mRNA complexity in the mammalian brain pp618 - 619
Thomas A Cooper
doi:10.1038/ng.815
Although there are only 22,000 human genes, most express multiple mRNA
isoforms through alternative splicing and selection of alternative 5'
and 3' ends. A new study identifies the role of alternative splicing
in maintaining neuronal excitability in the adult mouse brain.
http://links.ealert.nature.com/ctt?kn=86&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
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RESEARCH HIGHLIGHTS
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Research highlights p620
doi:10.1038/ng.878
http://links.ealert.nature.com/ctt?kn=93&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
----------------------
ARTICLES
----------------------
Extensive and coordinated transcription of noncoding RNAs within cell-cycle
promoters pp621 - 629
Tiffany Hung et al.
doi:10.1038/ng.848
David Wong, Howard Chang and colleagues report the identification of long
noncoding RNAs transcribed from the promoters of cell cycle genes. Many of
these RNAs have periodic expression during the cell cycle and are regulated
by oncogenic stimuli, stem cell differentiation or DNA damage.
Abstract: http://links.ealert.nature.com/ctt?kn=7&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=88&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
CTCF-mediated functional chromatin interactome in pluripotent cells pp630 - 638
Lusy Handoko et al.
doi:10.1038/ng.857
Chia-Lin Wei, Yijun Ruan and colleagues used chromatin interaction analysis
by paired-end tag sequencing (ChIA-PET) to determine the CTCF-chromatin
interactome in mouse embryonic stem cells.
Abstract: http://links.ealert.nature.com/ctt?kn=3&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=79&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
A genetic interaction network of five genes for human polycystic kidney and
liver diseases defines polycystin-1 as the central determinant of cyst formation pp639 - 647
Sorin V Fedeles et al.
doi:10.1038/ng.860
Stefan Somlo and colleagues show that the polycystic liver disease genes Prkcsh and
Sec63 are required for the proper biogenesis of polycystin complexes. They further
show that a Pkd1 transgene can rescue the cystic phenotype of Prkcsh and Sec63
mutant mice, identifying polycystin-1 as the central determinant of cyst formation.
Abstract: http://links.ealert.nature.com/ctt?kn=5&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=80&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Subspecific origin and haplotype diversity in the laboratory mouse pp648 - 655
Hyuna Yang et al.
doi:10.1038/ng.847
Fernando Pardo-Manuel de Villena, Gary Churchill and colleagues provide a
high-resolution phylogenetic map of mouse inbred strains based on comparisons
to wild-caught mice. They show that the genomes of classical strains are
overwhelmingly derived from Mus musculus domesticus whereas wild-derived
laboratory strains include a broad sampling of diversity from multiple
subspecies with pervasive introgression. The subspecific origin, haplotype
diversity and identity-by-descent map of laboratory strains can be visualized at
http://links.ealert.nature.com/ctt?kn=31&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0 .
Abstract: http://links.ealert.nature.com/ctt?kn=1&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=106&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
An integrated approach to characterize genetic interaction networks in yeast
metabolism pp656 - 662
Balazs Szappanos et al.
doi:10.1038/ng.846
Balazs Papp and colleagues construct a genetic interaction map of yeast
metabolism and use a genome-scale systems biology model to examine the structure
of the metabolic network. They use an automated machine-learning method to
reconcile differences between the experimental and computational genetic
interaction maps. In contrast to previous studies, they do not find evidence
for prevalent positive interactions in essential metabolic genes.
Abstract: http://links.ealert.nature.com/ctt?kn=2&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=112&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
----------------------
LETTERS
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Exome sequencing identifies MAX mutations as a cause of hereditary
pheochromocytoma pp663 - 667
Inaki Comino-Mendez et al.
doi:10.1038/ng.861
Alberto Cascon, Mercedes Robledo and colleagues show that MAX germline mutations
confer susceptibility to hereditary pheochromocytoma. This finding supports
a key role for MAX and its interaction partners in tumors of neural crest cell origin.
Abstract: http://links.ealert.nature.com/ctt?kn=27&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=103&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations
and 3p21.1 losses in malignant pleural mesothelioma pp668 - 672
Matthew Bott et al.
doi:10.1038/ng.855
Marc Ladanyi and colleagues show that the nuclear deubiquitinase BAP1 is commonly
inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma
(MPM). They further show that knockdown of BAP1 in MPM cell lines affects E2F and
Polycomb target genes, implicating transcriptional deregulation in disease pathogenesis.
Abstract: http://links.ealert.nature.com/ctt?kn=26&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=97&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
A cooperative microRNA-tumor suppressor gene network in acute T-cell lymphoblastic
leukemia (T-ALL) pp673 - 678
Konstantinos J Mavrakis et al.
doi:10.1038/ng.858
Hans-Guido Wendel and colleagues identify five miRNAs that are capable of
promoting T-ALL in a mouse model and that account for the majority of miRNA
expression in human T-ALL. They show that these miRNAs produce overlapping
and cooperative effects on tumor suppressor genes implicated in the pathogenesis of T-ALL.
Abstract: http://links.ealert.nature.com/ctt?kn=30&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=41&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Genome-wide association study identifies three new susceptibility loci for
esophageal squamous-cell carcinoma in Chinese populations pp679 - 684
Chen Wu et al.
doi:10.1038/ng.849
Dongxin Lin and colleagues report a genome-wide association study for esophageal
squamous-cell carcinoma in Chinese populations. They identify three new
susceptibility loci at 5q11, 6p21 and 21q22.
Abstract: http://links.ealert.nature.com/ctt?kn=29&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=45&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Genome-wide association identifies three new susceptibility loci for Paget's
disease of bone pp685 - 689
doi:10.1038/ng.845
Omar Albagha, Stuart Ralston and colleagues report the identification of
three new loci associated with risk for Paget's disease of bone.
Abstract: http://links.ealert.nature.com/ctt?kn=22&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=36&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Genome-wide association study identifies two new susceptibility loci for
atopic dermatitis in the Chinese Han population pp690 - 694
Liang-Dan Sun et al.
doi:10.1038/ng.851
Xue-Jun Zhang, Zhi-Rong Yao and colleagues report a genome-wide association study
for atopic dermatitis in the Chinese Han population. They identified two new
susceptibility loci at 5q22 and 20q13.
Abstract: http://links.ealert.nature.com/ctt?kn=23&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=35&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Genome-wide association study reveals three susceptibility loci for common
migraine in the general population pp695 - 698
Daniel I Chasman et al.
doi:10.1038/ng.856
Markus Schurks and colleagues report a genome-wide association study for
common migraine. They identify three new susceptibility loci at PRDM16, TRPM8 and LRP1.
Abstract: http://links.ealert.nature.com/ctt?kn=24&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=60&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Identification of common variants influencing risk of the tauopathy progressive
supranuclear palsy pp699 - 705
Gunter U Hoglinger et al.
doi:10.1038/ng.859
Gerard Schellenberg and colleagues report a genome-wide association study for
progressive supranuclear palsy, a movement disorder with prominent tau neuropathology.
They identified three new risk loci and confirmed the known risk locus at MAPT.
Abstract: http://links.ealert.nature.com/ctt?kn=18&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=61&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian
brain pp706 - 711
Lauren T Gehman et al.
doi:10.1038/ng.841
The Rbfox family of RNA binding proteins mediate alternative splicing. Douglas
Black and colleagues show that targeted deletion of the mouse Rbfox1 gene in the
CNS alters splice isoforms of a subset of genes and is associated with neural
hyperexcitability with spontaneous and drug-induced seizures.
Abstract: http://links.ealert.nature.com/ctt?kn=19&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=92&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Variation in genome-wide mutation rates within and between human families pp712 - 714
doi:10.1038/ng.862
Matthew Hurles and colleagues report the first direct comparative analysis of male
and female germline mutation rates from whole-genome sequences of two parent-offspring
trios sequenced as part of the 1000 Genomes Project. They identify variation in paternal
and maternal mutation rates between these two families.
Abstract: http://links.ealert.nature.com/ctt?kn=20&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=54&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Arabidopsis REF6 is a histone H3 lysine 27 demethylase pp715 - 719
Falong Lu et al.
doi:10.1038/ng.854
Xiaofeng Cao and colleagues report that REF6 is a histone H3 lysine 27 demethylase
in Arabidopsis. REF6 demethylates H3K27me3 and H3K27me2 and ref6 mutant plants
resemble mutations in H3K27me3-mediated gene silencing.
Abstract: http://links.ealert.nature.com/ctt?kn=21&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=11&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
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CORRIGENDUM
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Corrigendum: Mutations in FRMD7, a newly identified member of the FERM family,
cause X-linked idiopathic congenital nystagmus p720
Patrick Tarpey et al.
doi:10.1038/ng0711-720
http://links.ealert.nature.com/ctt?kn=9&ms=MzY3NjYzODQS1&r=MTc2NTYxNjY4OQS2&b=2&j=MTA1MDgzNzM5S0&mt=1&rt=0
=========================== ADVERTISEMENT ===========================
Nature Reviews Genetics
Poster on Synthetic Biology: Applications Come of Age
Authors: Ahmad S. Khalil and James J. Collins
July 2011
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