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Plos Genetics : Alu Recombination-mediated Structural Deletions in...

By: Barbara J. Trask

Description : With more than 1.2 million copies, Alu elements are one of the most important sources of structural variation in primate genomes. Here, we compare the chimpanzee and human genomes to determine the extent of Alu recombination-mediated deletion (ARMD) in the chimpanzee genome since the divergence of the chimpanzee and human lineages (:6 million y ago). Combining computational data analysis and experimental verification, we have identified 663 chimpanzee linea...

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Plos Genetics : Bms1 is Mutated in Aplasia Cutis Congenita, Volume 9

By: Paul A. Trainor

Description : Aplasia cutis congenita (ACC) manifests with localized skin defects at birth of unknown cause, mostly affecting the scalp vertex. Here, genome-wide linkage analysis and exome sequencing was used to identify the causative mutation in autosomal dominant ACC. A heterozygous Arg-to-His missense mutation (p.R930H) in the ribosomal GTPase BMS1 is identified in ACC that is associated with a delay in 18S rRNA maturation, consistent with a role of BMS1 in processing...

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Plos Genetics : Common Genetic Variants and Modification of Penetr...

By: James M. Ford

Description : The considerable uncertainty regarding cancer risks associated with inherited mutations of BRCA2 is due to unknown factors. To investigate whether common genetic variants modify penetrance for BRCA2 mutation carriers, we undertook a two-staged genome-wide association study in BRCA2 mutation carriers. In stage 1 using the Affymetrix 6.0 platform, 592,163 filtered SNPs genotyped were available on 899 young (,40 years) affected and 804 unaffected carriers of E...

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Plos Genetics : the Aspergillus Nidulansmapk Module Anste11-ste50-...

By: Hiten D. Madhani

Description : The sexual Fus3 MAP kinase module of yeast is highly conserved in eukaryotes and transmits external signals from the plasma membrane to the nucleus. We show here that the module of the filamentous fungus Aspergillus nidulans (An) consists of the AnFus3 MAP kinase, the upstream kinases AnSte7 and AnSte11, and the AnSte50 adaptor. The fungal MAPK module controls the coordination of fungal development and secondary metabolite production. It lacks the membrane ...

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Plos Genetics : Psip1, Volume 8

By: Wolf Reik

Description : Increasing evidence suggests that chromatin modifications have important roles in modulating constitutive or alternative splicing. Here we demonstrate that the PWWP domain of the chromatin-associated protein Psip1/Ledgf can specifically recognize tri-methylated H3K36 and that, like this histone modification, the Psip1 short (p52) isoform is enriched at active genes. We show that the p52, but not the long (p75), isoform of Psip1 co-localizes and interacts wi...

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Plos Genetics : a Method for Similarity Search of Genomic Position...

By: Judith Blake

Description : With the advancement of genome research, it is becoming clear that genes are not distributed on the genome in random order. Clusters of genes distributed at localized genome positions have been reported in several eukaryotes. Various correlations have been observed between the expressions of genes in adjacent or nearby positions along the chromosomes depending on tissue type and developmental stage. Moreover, in several cases, their transcripts, which contr...

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Plos Genetics : the Demoiselle of X-inactivation ; 50 Years Old an...

By: Wendy A. Bickmore

Description : In humans, sexual dimorphism is associated with the presence of two X chromosomes in the female, whereas males possess only one X and a small and largely degenerate Y chromosome. How do men cope with having only a single X chromosome given that virtually all other chromosomal monosomies are lethal? Ironically, or even typically many might say, women and more generally female mammals contribute most to the job by shutting down one of their two X chromosomes ...

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Plos Genetics : Genome-wide Analysis Reveals Selection for Importa...

By: Joshua M. Akey

Description : Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an FST-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, cont...

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Plos Genetics : a Survey of Genomic Traces Reveals a Common Sequen...

By: Dirk Schu¨beler

Description : While it is widely held that an organism’s genomic information should remain constant, several protein families are known to modify it. Members of the AID/APOBEC protein family can deaminate DNA. Similarly, members of the ADAR family can deaminate RNA. Characterizing the scope of these events is challenging. Here we use large genomic data sets, such as the two billion sequences in the NCBI Trace Archive, to look for clusters of mismatches of the same type, ...

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Plos Genetics : Neurospora Cop9 Signalosome Integrity Plays Major ...

By: Ning Wei

Description : The COP9 signalosome (CSN) is a highly conserved multifunctional complex that has two major biochemical roles : cleaving NEDD8 from cullin proteins and maintaining the stability of CRL components. We used mutation analysis to confirm that the JAMM domain of the CSN-5 subunit is responsible for NEDD8 cleavage from cullin proteins in Neurospora crassa. Point mutations of key residues in the metal-binding motif (EXnHXHX10D) of the CSN-5 JAMM domain disrupted C...

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Plos Genetics : Introducing Plos Genetics, Volume 1

By: Wayne N. Frankel

Description : Editorial of Introducing PLoS Genetics

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Plos Genetics : Rna–mediated Epigenetic Heredity Requires the Cyto...

By: Wendy A. Bickmore

Description : RNA–mediated transmission of phenotypes is an important way to explain non-Mendelian heredity. We have previously shown that small non-coding RNAs can induce hereditary epigenetic variations in mice and act as the transgenerational signalling molecules. Two prominent examples for these paramutations include the epigenetic modulation of the Kit gene, resulting in altered fur coloration, and the modulation of the Sox9 gene, resulting in an overgrowth phenotyp...

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Plos Genetics : Adaptive Copy Number Evolution in Malaria Parasite...

By: Molly Przeworski

Description : Copy number polymorphism (CNP) is ubiquitous in eukaryotic genomes, but the degree to which this reflects the action of positive selection is poorly understood. The first gene in the Plasmodium folate biosynthesis pathway, GTP-cyclohydrolase I (gch1), shows extensive CNP. We provide compelling evidence that gch1 CNP is an adaptive consequence of selection by antifolate drugs, which target enzymes downstream in this pathway. (1) We compared gch1 CNP in paras...

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Plos Genetics : a Role for the Adult Fat Body in Drosophila Male C...

By: David L. Stern

Description : Mating behavior in Drosophila depends critically on the sexual identity of specific regions in the brain, but several studies have identified courtship genes that express products only outside the nervous system. Although these genes are each active in a variety of non-neuronal cell types, they are all prominently expressed in the adult fat body, suggesting an important role for this tissue in behavior. To test its role in male courtship, fat body was femin...

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Plos Genetics : Nrxn3is a Novel Locus for Waist Circumference ; a ...

By: Emmanouil T. Dermitzakis

Description : Central abdominal fat is a strong risk factor for diabetes and cardiovascular disease. To identify common variants influencing central abdominal fat, we conducted a two-stage genome-wide association analysis for waist circumference (WC). In total, three loci reached genome-wide significance. In stage 1, 31,373 individuals of Caucasian descent from eight cohort studies confirmed the role of FTO and MC4R and identified one novel locus associated with WC in th...

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Plos Genetics : Analysis of Ribosomal Protein Gene Structures ; Im...

By: Takashi Gojobori

Description : Many spliceosomal introns exist in the eukaryotic nuclear genome. Despite much research, the evolution of spliceosomal introns remains poorly understood. In this paper, we tried to gain insights into intron evolution from a novel perspective by comparing the gene structures of cytoplasmic ribosomal proteins (CRPs) and mitochondrial ribosomal proteins (MRPs), which are held to be of archaeal and bacterial origin, respectively. We analyzed 25 homologous pairs...

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Plos Genetics : Regulatory Cross-talk Links Vibrio Cholerae Chromo...

By: William F. Burkholder

Description : There is little knowledge of factors and mechanisms for coordinating bacterial chromosome replication and segregation. Previous studies have revealed that genes (and their products) that surround the origin of replication (oriCII) of Vibrio cholerae chromosome II (chrII) are critical for controlling the replication and segregation of this chromosome. rctB, which flanks one side of oriCII, encodes a protein that initiates chrII replication: rctA, which flank...

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Plos Genetics : Quaking Regulates Hnrnpa1 Expression Through Its 3...

By: Harry T. Orr

Description : In mice, Quaking (Qk) is required for myelin formation: in humans, it has been associated with psychiatric disease. QK regulates the stability, subcellular localization, and alternative splicing of several myelin-related transcripts, yet little is known about how QK governs these activities. Here, we show that QK enhances Hnrnpa1 mRNA stability by binding a conserved 39 UTR sequence with high affinity and specificity. A single nucleotide mutation in the bin...

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Plos Genetics : Identification of the First Atrip–deficient Patien...

By: Andrew O. M. Wilkie

Description : A homozygous mutational change in the Ataxia-Telangiectasia and RAD3 related (ATR) gene was previously reported in two related families displaying Seckel Syndrome (SS). Here, we provide the first identification of a Seckel Syndrome patient with mutations in ATRIP, the gene encoding ATR–Interacting Protein (ATRIP), the partner protein of ATR required for ATR stability and recruitment to the site of DNA damage. The patient has compound heterozygous mutations ...

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Plos Genetics : the E1A-associated P400 Protein Modulates Cell Fat...

By: Asifa Akhtar

Description : The p400 E1A-associated protein, which mediates H2A.Z incorporation at specific promoters, plays a major role in cell fate decisions : it promotes cell cycle progression and inhibits induction of apoptosis or senescence. Here, we show that p400 expression is required for the correct control of ROS metabolism. Depletion of p400 indeed increases intracellular ROS levels and causes the appearance of DNA damage, indicating that p400 maintains oxidative stress b...

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