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Contents
OCTOBER 2012
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VOLUME 2
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ISSUE 10
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www.g3journal.org
INVESTIGATIONS AND AUTHOR SUMMARIES
1137–1144
Competition Between Conjugation and M13 Phage Infection in Escherichia coli in the Absence of
Selection Pressure: A Kinetic Study
Zhenmao Wan and Noel L. Goddard
Interest in the use of bacteriophage as biosanitation agents motivated this study to understand the
underlying competition dynamics in a model system. The experiments and modeling allowed the
authors to define a number of physical parameters governing the process. Additionally, they show that
a regime exists where conjugation persists despite phage inhibition or selective pressure.
1145–1159
Fractionation, Stability, and Isolate-Specificity of QTL for Resistance to Phytophthora infestans in
Cultivated Tomato (Solanum lycopersicum)
Emily B. Johnson, J. Erron Haggard, and Dina A. St.Clair
The cultivated tomato (Solanum lycopersicum) is susceptible to late blight disease (Phytophthora
infestans). Two quantitative resistance loci (QTL) were identified previously on chromosomes 5 and 11
of wild S. habrochaites and introgressed into S. lycopersicum. High-resolution mapping with sub-nearisogenic lines suggested a complex genetic architecture, pleiotropy, and/or tightly linked genes. Each
original single QTL on chromosomes 5 and 11 fractionated into multiple QTL for both foliar and stem
resistances. Foliar and stem resistance QTL frequently co-localized, and a majority of QTL were stably
detected across multiple environments. Map-based comparisons revealed co-localization of QTL with
other Solanaceae resistance genes/QTL, indicating functional conservation.
1161–1168
A Genetic Screen to Discover Pathways Affecting Cohesin Function in Schizosaccharomyces pombe
Identifies Chromatin Effectors
Zhiming Chen, Scott McCroskey, Weichao Guo, Hua Li, and Jennifer L. Gerton
Cohesion, the force that holds sister chromatids together from the time of DNA replication until separation
at the metaphase to anaphase transition, is mediated by the cohesin complex. Cohesin is also involved in
DNA damage repair, chromosome condensation, and gene regulation. The authors conducted a genetic
interaction screen in S. pombe with two cohesin mutants. These mutants shared negative interactions with
deletions of genes involved in DNA replication and heterochromatin. Deletions of chromatin effectors
rescued the growth and lagging chromosomes in a cohesin mutant at the nonpermissive temperature.
Overall their screen reveals an intimate association between cohesin and chromatin.
1169–1178
Identification of Genes Underlying Hypoxia Tolerance in Drosophila by a P-element Screen
Priti Azad, Dan Zhou, Rachel Zarndt, and Gabriel G. Haddad
Whether in pathological conditions or at high altitude, hypoxia can severely affect survival, early
development, and the fitness of organisms, including humans. Hypoxia-tolerant organisms such as fruit
flies provide a unique opportunity to study the effect of genes influencing hypoxia tolerance or injury
in vivo. To identify genes involved in hypoxia tolerance, the authors screened the P-SUP P-element
insertion lines available for all the chromosomes of Drosophila. By screening 2,187 lines they identified
44 genes that have a strong hypoxia tolerance phenotype. Interestingly, the authors found that
regulation by single genes can play an important role in survival and development during hypoxia.
Volume 2 |
October 2012
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ii
1179–1184
A Fast and Efficient Approach for Genomic Selection with High-Density Markers
Vitara Pungpapong, William M. Muir, Xianran Li, Dabao Zhang, and Min Zhang
With the recent advances in high-throughput genotyping, a large number of genetic markers are
increasingly available and more efficient approaches for genomic selection are desirable. Compared to
BayesB using simulation studies, the proposed penalized orthogonal-components regression (POCRE)
method can reduce the computing time by 93% while reaching similar accuracy in predicting breeding
values. In real data analysis, POCRE and BayesB are comparable.
1185–1195
Multiple Pathways Regulate Minisatellite Stability During Stationary Phase in Yeast
Maire K. Kelly, Laura Brosnan, Peter A. Jauert, Maitreya J. Dunham, and David T. Kirkpatrick
Factors controlling the stability of repetitive minisatellite DNA sequences are not well-understood.
The authors previously identified a novel yeast colony morphology phenotype, blebbing, in which
microcolonies arise on the surface of the main colony. The microcolonies derive from cells in which
a reporter minisatellite tract has undergone tract length alterations specifically during stationary phase.
In this study, the authors identify multiple new pathways that give rise to stationary phase-specific tract
alterations; a common feature of the pathways is a connection to ssDNA formation. Given that most
cells in multicellular organisms are in stationary phase, their findings have broad applicability for
genome stability.
1197–1205
PUF-8, a Pumilio Homolog, Inhibits the Proliferative Fate in the Caenorhabditis elegans Germline
Hilary Racher and Dave Hansen
A population of stem cells is maintained in the distal end of the C. elegans gonad, with the GLP-1/Notch
signaling pathway promoting the proliferative fate. Here the authors demonstrate that a Pumilio
homologue, PUF-8, helps to maintain the balance between the proliferative fate and meiotic entry of
this stem cell population by inhibiting the proliferative fate. Loss of puf-8 activity enhances the overproliferation phenotype of gain-of-function mutations in the GLP-1/Notch signaling pathway. PUF-8 is
expressed throughout the entire region containing proliferative cells, suggesting that it may function by
dampening the proliferative promoting activity of GLP-1/Notch signaling.
1207–1212
Light-Inducible System for Tunable Protein Expression in Neurospora crassa
Jennifer M. Hurley, Chen-Hui Chen, Jennifer J. Loros, and Jay C. Dunlap
In the model organism Neurospora crassa, several regulatable promoters have been used for
heterologous gene expression, but all suffer from leaky expression, absent stimuli, or an inability to
induce protein expression at levels above those seen in vivo. To increase and better control in vivo
protein expression, the authors harnessed the light-induced vvd promoter. The vvd promoter is
dependent upon light for induction, shows a graded response, and is rapidly inhibited to the inactive
state when returned to the dark.
1213–1221
Global Gene Expression in Coprinopsis cinerea Meiotic Mutants Reflects Checkpoint Arrest
Erika Anderson, Claire Burns, and Miriam E. Zolan
Thousands of genes exhibit changing expression over the course of meiosis, but meiotically induced
genes are not necessarily essential for meiosis itself. By examining the transcriptional profiles of two
mutants in which meiosis arrests, the authors identify genes differentially expressed in arrested cells
compared to wild type. This approach efficiently identifies genes likely to be involved in meiosis and
sporulation. A group of early meiotic genes that continue to be expressed in arrested cells might have
roles in meiotic progression. Late meiotic genes that fail to be induced in the mutants are likely to be
involved in sporulation.
1223–1232
Suppression Analysis of esa1 Mutants in Saccharomyces cerevisiae Links NAB3 to Transcriptional
Silencing and Nucleolar Functions
Christie S. Chang, Astrid Clarke, and Lorraine Pillus
A genetic screen was performed in Saccharomyces cerevisiae to identify dosage suppressors of
a conditional allele of ESA1, the gene encoding an essential lysine-acetyltransferase. When
overexpressed, four genes (LYS20, LEU2, VAP1, and NAB3) suppressed the lethality of a temperaturesensitive esa1 mutant. The NAB3 suppressor, which encodes an RNA processing factor, also rescued an
rDNA silencing defect of the esa1 mutant. Nab3 mutants were found to be defective in rDNA silencing.
The localization and posttranslational acetylation of Nab3 were both altered in an esa1 mutant. Thus,
the authors propose that Nab3 function is influenced by its posttranslational acetylation by Esa1.
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1233–1241
Second-Generation Genetic Linkage Map of Catfish and Its Integration with the BAC-Based
Physical Map
Parichart Ninwichian, Eric Peatman, Hong Liu, Huseyin Kucuktas, Benjaporn Somridhivej, Shikai Liu,
Ping Li, Yanliang Jiang, Zhenxia Sha, Ludmilla Kaltenboeck, Jason W. Abernathy, Wenqi Wang,
Fei Chen, Yoona Lee, Lilian Wong, Shaolin Wang, Jianguo Lu, and Zhanjiang Liu
Through genetic mapping of the BAC end-associated microsatellites, the authors integrated 52.8% of
the catfish physical map with the linkage map. This map includes 2,557 markers with a genetic distance
of 2,546 cM and a physical distance of 393 Kb/cM. The increased marker density highlights variations
in recombination rates within and among catfish chromosomes, possibly reflecting variations of
chromosome-level similarities between channel catfish and blue catfish. Markers belonging to a single
physical contig for a number of physical contigs are mapped to different linkage groups, suggesting
inter-chromosome duplications. This integrated map should enable comparative studies and provide
a framework for assembly of whole genome scaffolds.
1243–1256
Overlapping ETS and CRE Motifs (G/CCGGAAGTGACGTCA) Preferentially Bound by GABPa
and CREB Proteins
Raghunath Chatterjee, Jianfei Zhao, Ximiao He, Andrey Shlyakhtenko, Ishminder Mann,
Joshua J. Waterfall, Paul Meltzer, B. K. Sathyanarayana, Peter C. FitzGerald, and Charles Vinson
Using a method to detect pairs of co-occurring TFBSs, the authors identified an overlapping ETS and
CRE motif in human promoters. EMSA shows that ETS protein GABPα and B-ZIP protein CREB
preferentially bind this motif only when they overlap at a specific length. In contrast, another ETS
protein, ETV5, competes with CREB to bind this motif, and binding of one protein precludes the
binding of the other. De novo motif detection using in vivo GABPα and CREB ChIP-seq data identified
an ETS-CRE motif. The majority of the occurrences of this motif are in unmethylated regulatory regions
and regulate a specific class of genes.
1257–1268
Exploration of the Genetic Organization of Morphological Modularity on the Mouse Mandible Using a Set
of Interspecific Recombinant Congenic Strains Between C57BL/6 and Mice of the Mus spretus Species
Gaëtan Burgio, Michel Baylac, Evelyne Heyer, and Xavier Montagutelli
This study aimed to investigate the genetic variation of the mandible shape in the mouse and to answer
a highly disputed question in the field of the evolutionary biology and genetics: Is the evolution of shape
driven by morphological units (modules) acting in coordinate manner? To answer this question, the
authors conducted a sophisticated genetic study using a combination of an interspecific introgression
and a powerful morphometric approach. The study demonstrated that the genetic makeup in the mouse
mandible is subjected to a complex genetic coordination acting in a modular manner.
1269–1278
SlWUS1; An X-linked Gene Having No Homologous Y-Linked Copy in Silene latifolia
Yusuke Kazama, Kiyoshi Nishihara, Roberta Bergero, Makoto T. Fujiwara, Tomoko Abe,
Deborah Charlesworth, and Shigeyuki Kawano
The dioecious plant Silene latifolia has young heteromorphic sex chromosomes. Characterization of
sex-linked genes makes it possible to study the evolutionary history of the young sex chromosomes.
The authors identified a new X-linked gene, SlWUS1. Mapping analysis and phylogenetic analysis of
SlWUS1 orthologues in closely related Silene species revealed that this gene has no Y-linked homologue
(an X-only gene), and was lost from the Y during the evolution of the sex chromosomes. The identified
X-only gene will improve existing knowledge about the effect of dosage compensation and sexual
selection of genes on the evolving sex chromosomes.
1279–1289
Functional Analysis With a Barcoder Yeast Gene Overexpression System
Alison C. Douglas, Andrew M. Smith, Sara Sharifpoor, Zhun Yan, Tanja Durbic, Lawrence E. Heisler,
Anna Y. Lee, Owen Ryan, Hendrikje Göttert, Anu Surendra, Dewald van Dyk, Guri Giaever,
Charles Boone, Corey Nislow, and Brenda J. Andrews
Systematic analysis of gain-of-function phenotypes associated with gene overexpression has been
somewhat constrained by the lack of appropriate reagents. In particular, synthetic dosage lethality
(SDL), in which gene overexpression compromises cellular fitness in a specific mutant background, has
yet to be explored under conditions that enable highly parallel analyses of complex pools of strains in
liquid assays. The authors describe a novel functional genomics platform that enables a highly parallel
and systematic assessment of overexpression phenotypes in pooled cultures. The platform consists of
three novel yeast arrays that enable assessment of genome-wide SDL interactions in pooled cultures
using microarrays or sequencing.
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