December 2010 Volume 42 Number 12, pp 1031 - 1143
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----------------------
EDITORIAL
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In praise of maize p1031
doi:10.1038/ng1210-1031
The field of genetics owes its existence and most of its methods to
agriculture. This year, genomic strategies and tools have notably
begun to pay back the favor. Crop plants may be not only the
discipline's most readily translated applications but also its
most fruitful model organisms.
http://links.ealert.nature.com/ctt?kn=78&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
----------------------
BOOK REVIEW
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Evolutionary genetics quantified p1033
Trudy F C Mackay reviews Elements of Evolutionary Genetics by Brian
Charlesworth and Deborah Charlesworth
doi:10.1038/ng1210-1033
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NEWS AND VIEWS
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LincRNAs join the pluripotency alliance pp1035 - 1036
Jia-Hui Ng and Huck-Hui Ng
doi:10.1038/ng1210-1035
A new study shows that somatic cell reprogramming is accompanied by
changes in the expression of large intergenic non-coding RNAs
(lincRNAs). Some of these reprogramming-induced lincRNAs are directly
targeted by key pluripotency factors and regulate reprogramming,
implicating lincRNAs in the reinstatement and maintenance of
pluripotency.
http://links.ealert.nature.com/ctt?kn=83&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
New mutations and intellectual function pp1036 - 1038
James R Lupski
doi:10.1038/ng1210-1036
Exome-based sequencing is a powerful approach for studying rare
genetic diseases. A new study now applies this technology to
demonstrate an important role for de novo mutations in sporadic
mental retardation.
http://links.ealert.nature.com/ctt?kn=91&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
FTO gains function pp1038 - 1039
George Stratigopoulos and Rudolph L Leibel
doi:10.1038/ng1210-1038
Previous genome-wide association studies have identified a strong
association between FTO and human obesity, although the mechanism
by which FTO affects obesity remains unknown. A new study suggests
that the obesity risk alleles are gain-of-function.
http://links.ealert.nature.com/ctt?kn=97&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
----------------------
RESEARCH HIGHLIGHTS
----------------------
Research highlights p1041
doi:10.1038/ng1210-1041
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ANALYSIS
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RNA sequencing shows no dosage compensation of the active X-chromosome
pp1043 - 1047
Yuanyan Xiong et al.
doi:10.1038/ng.711
Jianzhi Zhang and Xionglei He report analyses of published RNA
sequencing data examining relative expression levels between genes
located on the X chromosome and genes located on autosomes. Unlike
previous reports of dosage compensation between the X chromosome
and autosomes, their analyses detect an X:autosome expression ratio
of ~0.5.
Abstract: http://links.ealert.nature.com/ctt?kn=7&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
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----------------------
BRIEF COMMUNICATION
----------------------
Fine-mapping at three loci known to affect fetal hemoglobin levels
explains additional genetic variation pp1049 - 1051
Genevieve Galarneau et al.
doi:10.1038/ng.707
Guillaume Lettre and colleagues report fine-mapping at three loci
associated with variation in fetal hemoglobin levels. Their findings
implicate multiple common and rare variants at these loci that
collectively explain a substantial fraction of the heritable
variation in this trait.
Abstract: http://links.ealert.nature.com/ctt?kn=3&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
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----------------------
ARTICLES
----------------------
Resequencing of 31 wild and cultivated soybean genomes identifies
patterns of genetic diversity and selection pp1053 - 1059
Hon-Ming Lam et al.
doi:10.1038/ng.715
Jun Wang and colleagues report whole-genome resequencing of 17 wild
and 14 cultivated soybean accessions. They characterize population
structure, patterns of linkage disequilibrium and selection in
soybeans.
Abstract: http://links.ealert.nature.com/ctt?kn=5&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=112&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
The developmental dynamics of the maize leaf transcriptome
pp1060 - 1067
Pinghua Li et al.
doi:10.1038/ng.703
Thomas Brutnell and colleagues report RNA-Seq analysis of the maize
leaf transcriptome during stages of leaf development. They identify
dynamic changes in gene expression during the progression of leaf
development.
Abstract: http://links.ealert.nature.com/ctt?kn=1&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=117&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Common variants in 22 loci are associated with QRS duration and
cardiac ventricular conduction pp1068 - 1076
Nona Sotoodehnia et al.
doi:10.1038/ng.716
Nona Sotoodehnia and colleagues report a meta-analysis of 14
genome-wide association studies for QRS interval, an electrocardiogram
measurement of cardiac ventricular conduction. They identify 22 loci
associated with QRS duration.
Abstract: http://links.ealert.nature.com/ctt?kn=2&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=109&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Thirty new loci for age at menarche identified by a meta-analysis of
genome-wide association studies pp1077 - 1085
Cathy E Elks et al.
doi:10.1038/ng.714
Ken Ong and colleagues report meta-analysis of 32 genome-wide
association studies for age at menarche. They identify 30 loci newly
associated with age at menarche, including four that were previously
associated with BMI.
Abstract: http://links.ealert.nature.com/ctt?kn=30&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=102&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Overexpression of Fto leads to increased food intake and results in
obesity pp1086 - 1092
Chris Church et al.
doi:10.1038/ng.713
Genetic variants at the FTO gene are associated with obesity in
humans. Now, Roger Cox and colleagues analyze mice globally
overexpressing Fto and show that increased Fto expression leads to
obesity in mice.
Abstract: http://links.ealert.nature.com/ctt?kn=29&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=44&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Targets and dynamics of promoter DNA methylation during early mouse
development pp1093 - 1100
Julie Borgel et al.
doi:10.1038/ng.708
Michael Weber and colleagues present profiles of DNA methylation
during early development of the mouse embryonic lineage in vivo.
They profile 10% of the mouse genome covering all known gene promoters.
They show that DNA methylation is targeted to specific gene promoters
and is required to maintain gene repression.
Abstract: http://links.ealert.nature.com/ctt?kn=32&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=48&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
miR-212 and miR-132 are required for epithelial stromal interactions
necessary for mouse mammary gland development pp1101 - 1108
Ahmet Ucar et al.
doi:10.1038/ng.709
Kamal Chowdhury and colleagues show that the microRNA-212/132 family
is necessary for mouse mammary gland development. microRNA-212 and
microRNA-132 are required in the mammary stroma, not the epithelium.
Abstract: http://links.ealert.nature.com/ctt?kn=31&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=39&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
----------------------
LETTERS
----------------------
A de novo paradigm for mental retardation pp1109 - 1112
Lisenka E L M Vissers et al.
doi:10.1038/ng.712
Joris Veltman, Han Brunner and colleagues report results of a family
based exome sequencing study of ten individuals with unexplained
mental retardation. They identified and validated de novo mutations
in nine genes, six of which are likely to be pathogenic based on
functional criteria, suggesting an important role for de novo point
mutations in the etiology of unexplained mental retardation.
Abstract: http://links.ealert.nature.com/ctt?kn=25&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=127&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Large intergenic non-coding RNA-RoR modulates reprogramming of human
induced pluripotent stem cells pp1113 - 1117
Sabine Loewer et al.
doi:10.1038/ng.710
George Daley and John Rinn and colleagues identify large intergenic
non-coding RNAs that are upregulated during reprogramming of induced
pluripotent stem cells, and they show a functional role for large
intergenic non-coding RNA-RoR in induced pluripotent stem cell
derivation.
Abstract: http://links.ealert.nature.com/ctt?kn=26&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=79&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Genome-wide meta-analysis increases to 71 the number of confirmed
Crohn's disease susceptibility loci pp1118 - 1125
Andre Franke et al.
doi:10.1038/ng.717
Miles Parkes and colleagues report results of a large genome-wide
association meta-analysis and replication study for Crohn's disease.
They identify 30 new susceptibility loci for this inflammatory bowel
disease and implicate several interesting candidate genes in disease
pathogenesis.
Abstract: http://links.ealert.nature.com/ctt?kn=27&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=65&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
A genome-wide association study of Hodgkin's lymphoma identifies new
susceptibility loci at 2p16.1 (REL), 8q24.21 and 10p14 (GATA3)
pp1126 - 1130
Victor Enciso-Mora et al.
doi:10.1038/ng.696
Richard Houlston and colleagues report results of a genome-wide
association study of Hodgkin's lymphoma. They identify three new
susceptibility loci at 2p16 (REL), 8q24 and 10p14 (GATA3) and confirm
a strong role for the HLA region in disease etiology.
Abstract: http://links.ealert.nature.com/ctt?kn=20&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=55&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Exome sequencing identifies ACAD9 mutations as a cause of complex I
deficiency pp1131 - 1134
Tobias B Haack et al.
doi:10.1038/ng.706
Holger Prokisch and colleagues report whole-exome sequencing of an
individual with severe complex I deficiency, followed by screening
in an additional 120 cases. They identify mutations in ACAD9 as
causal for complex I deficiency.
Abstract: http://links.ealert.nature.com/ctt?kn=21&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=58&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Natural variation at Strubbelig Receptor Kinase 3 drives immune-
triggered incompatibilities between Arabidopsis thaliana accessions
pp1135 - 1139
Ruben Alcazar et al.
doi:10.1038/ng.704
Matthieu Reymond and colleagues show that natural genetic variants at
the SRF3 locus underlie genetic incompatibilities between European
and central Asian accessions of Arabidopsis.
Abstract: http://links.ealert.nature.com/ctt?kn=22&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=15&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Yersinia pestis genome sequencing identifies patterns of global
phylogenetic diversity pp1140 - 1143
Giovanna Morelli et al.
doi:10.1038/ng.705
Mark Achtman and colleagues report the whole-genome sequencing of 11
Yersinia pestis isolates, the causative agent of the plague. Their
phylogeographic analysis on a larger dataset of Y. pestis global
isolates suggests historical routes of transmission.
Abstract: http://links.ealert.nature.com/ctt?kn=23&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=12&m=36023576&r=MTc2NTYxNjY4OQS2&b=2&j=ODc5NzgzNTAS1&mt=1&rt=0
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