Publications of Philip N Benfey :chronological combined listing:
%% Papers Published
@article{fds152733,
Author = {KL Gallagher and PN Benfey},
Title = {Both the conserved GRAS domain and nuclear localization are
required for SHORT-ROOT movement.},
Journal = {The Plant journal : for cell and molecular
biology},
Year = {2008},
Month = {December},
Abstract = {Transcription factor movement is well established in plants.
Since the initial report of KNOTTED movement, more than a
dozen transcription factors have been shown to move in
plants. However, the developmental significance of movement
is not known. Using the SHORT-ROOT (SHR) transcription
factor as a tool for studying cell-to-cell trafficking, we
show that movement of SHR from its site of synthesis is
necessary for normal development of the Arabidopsis root. We
identify multiple regions of SHR that are required for
intra- and intercellular movement of SHR, including a region
that is necessary for movement but not activity. We made the
surprising discovery that the capacity for intercellular
movement may be conserved among other GRAS family proteins.
Finally, we provide evidence that movement requires both
cytoplasmic and nuclear localization, strongly suggesting a
mechanistic link between nuclear transport and cell-to-cell
movement.},
Key = {fds152733}
}
@article{fds152746,
Author = {TA Long and SM Brady and PN Benfey},
Title = {Systems approaches to identifying gene regulatory networks
in plants.},
Journal = {Annual review of cell and developmental biology, United
States},
Volume = {24},
Pages = {81-103},
Year = {2008},
Month = {November},
ISSN = {1081-0706},
Abstract = {Complex gene regulatory networks are composed of genes,
noncoding RNAs, proteins, metabolites, and signaling
components. The availability of genome-wide mutagenesis
libraries; large-scale transcriptome, proteome, and
metabalome data sets; and new high-throughput methods that
uncover protein interactions underscores the need for
mathematical modeling techniques that better enable
scientists to synthesize these large amounts of information
and to understand the properties of these biological
systems. Systems biology approaches can allow researchers to
move beyond a reductionist approach and to both integrate
and comprehend the interactions of multiple components
within these systems. Descriptive and mathematical models
for gene regulatory networks can reveal emergent properties
of these plant systems. This review highlights methods that
researchers are using to obtain large-scale data sets, and
examples of gene regulatory networks modeled with these
data. Emergent properties revealed by the use of these
network models and perspectives on the future of systems
biology are discussed.},
Key = {fds152746}
}
@article{fds152766,
Author = {J Colinas and SC Schmidler and G Bohrer and B Iordanov and PN
Benfey},
Title = {Intergenic and genic sequence lengths have opposite
relationships with respect to gene expression.},
Journal = {PLoS ONE, United States},
Volume = {3},
Number = {11},
Pages = {e3670},
Year = {2008},
Month = {November},
ISSN = {1932-6203},
Abstract = {Eukaryotic genomes are mostly composed of noncoding DNA
whose role is still poorly understood. Studies in several
organisms have shown correlations between the length of the
intergenic and genic sequences of a gene and the expression
of its corresponding mRNA transcript. Some studies have
found a positive relationship between intergenic sequence
length and expression diversity between tissues, and
concluded that genes under greater regulatory control
require more regulatory information in their intergenic
sequences. Other reports found a negative relationship
between expression level and gene length and the
interpretation was that there is selection pressure for
highly expressed genes to remain small. However, a
correlation between gene sequence length and expression
diversity, opposite to that observed for intergenic
sequences, has also been reported, and to date there is no
testable explanation for this observation. To shed light on
these varied and sometimes conflicting results, we performed
a thorough study of the relationships between sequence
length and gene expression using cell-type (tissue) specific
microarray data in Arabidopsis thaliana. We measured median
gene expression across tissues (expression level),
expression variability between tissues (expression pattern
uniformity), and expression variability between replicates
(expression noise). We found that intergenic (upstream and
downstream) and genic (coding and noncoding) sequences have
generally opposite relationships with respect to expression,
whether it is tissue variability, median, or expression
noise. To explain these results we propose a model, in which
the lengths of the intergenic and genic sequences have
opposite effects on the ability of the transcribed region of
the gene to be epigenetically regulated for differential
expression. These findings could shed light on the role and
influence of noncoding sequences on gene
expression.},
Key = {fds152766}
}
@article{fds152734,
Author = {AS Iyer-Pascuzzi and PN Benfey},
Title = {Transcriptional networks in root cell fate
specification.},
Journal = {Biochimica et biophysica acta},
Year = {2008},
Month = {October},
Abstract = {Cell fate in the Arabidopsis root is determined by
positional information mediated by plant hormones and
interpreted by transcriptional networks. In this review, we
summarize recent advances in our understanding of the
regulatory networks that control cell fate within the root
meristem, and in the interplay of these networks with
phytohormones. Recent work describing the importance of
chromatin organization in tissue patterning is also
highlighted. A new, high resolution root expression map
detailing the transciptome of nearly all cell types in the
Arabidopsis root across developmental timepoints will
provide a framework for understanding these
networks.},
Key = {fds152734}
}
@article{fds152735,
Author = {I De Smet and V Vassileva and B De Rybel and MP Levesque and W
Grunewald, D Van Damme and G Van Noorden and M Naudts and G Van
Isterdael and R De Clercq and JY Wang and N Meuli and S Vanneste and J
Friml, P Hilson and G Jürgens and GC Ingram and D Inzé and PN Benfey and T Beeckman},
Title = {Receptor-like kinase ACR4 restricts formative cell divisions
in the Arabidopsis root.},
Journal = {Science (New York, N.Y.), United States},
Volume = {322},
Number = {5901},
Pages = {594-7},
Year = {2008},
Month = {October},
Keywords = {Arabidopsis • Arabidopsis Proteins • Cell
Division* • Cell Lineage • Gene Expression
Profiling • Gene Expression Regulation, Plant •
Genes, Plant • Meristem • Mutation • Plant
Roots • Receptors, Cell Surface • cytology* •
enzymology • enzymology* • genetics •
genetics* • growth & development •
metabolism*},
Abstract = {During the development of multicellular organisms,
organogenesis and pattern formation depend on formative
divisions to specify and maintain pools of stem cells. In
higher plants, these activities are essential to shape the
final root architecture because the functioning of root
apical meristems and the de novo formation of lateral roots
entirely rely on it. We used transcript profiling on sorted
pericycle cells undergoing lateral root initiation to
identify the receptor-like kinase ACR4 of Arabidopsis as a
key factor both in promoting formative cell divisions in the
pericycle and in constraining the number of these divisions
once organogenesis has been started. In the root tip
meristem, ACR4 shows a similar action by controlling cell
proliferation activity in the columella cell lineage. Thus,
ACR4 function reveals a common mechanism of formative cell
division control in the main root tip meristem and during
lateral root initiation.},
Key = {fds152735}
}
@article{fds152736,
Author = {B Chaudhuri and F Hörmann and S Lalonde and SM Brady and DA Orlando and P
Benfey, WB Frommer},
Title = {Protonophore- and pH-insensitive glucose and sucrose
accumulation detected by FRET nanosensors in Arabidopsis
root tips.},
Journal = {The Plant journal : for cell and molecular
biology},
Year = {2008},
Month = {September},
Abstract = {Although soil contains only traces of soluble carbohydrates,
plant roots take up glucose and sucrose efficiently when
supplied in artificial media. Soluble carbohydrates and
other small metabolites found in soil are in part products
from exudation from plant roots. The molecular nature of the
transporters for uptake and exudation is unknown. Here,
fluorescence resonance energy transfer (FRET) glucose and
sucrose sensors were used to characterize accumulation and
elimination of glucose and sucrose in Arabidopsis roots
tips. Using an improved image acquisition set-up, FRET
responses to perfusion with carbohydrates were detectable in
roots within less than 10 sec and over a wide concentration
range. Accumulation was fully reversible within 10-180 sec
after glucose or sucrose had been withdrawn; elimination may
be caused by metabolism and/or efflux. The rate of
elimination was unaffected by pre-incubation with high
concentrations of glucose, suggesting that elimination is
not due to accumulation in a short-term buffer such as the
vacuole. Glucose and sucrose accumulation was insensitive to
protonophores, was comparable in media differing in
potassium levels, and was similar at pH 5.8, 6.8 and 7.8,
suggesting that both influx and efflux may be mediated by
proton-independent transport systems. High-resolution
expression mapping in root tips showed that only a few
proton-dependent transport of the STP (Sugar Transport
Protein) and SUT/SUC (Sucrose Transporter/Carrier) families
are expressed in the external cell layers of root tips. The
root expression maps may help to pinpoint candidate genes
for uptake and release of carbohydrates from
roots.},
Key = {fds152736}
}
@article{fds152737,
Author = {K Swarup and E Benková and R Swarup and I Casimiro and B Péret and Y
Yang, G Parry and E Nielsen and I De Smet and S Vanneste and MP
Levesque, D Carrier and N James and V Calvo and K Ljung and E Kramer and R
Roberts, N Graham and S Marillonnet and K Patel and JD Jones and CG
Taylor, DP Schachtman and S May and G Sandberg and P Benfey and J Friml and I Kerr and T Beeckman and L Laplaze and MJ Bennett},
Title = {The auxin influx carrier LAX3 promotes lateral root
emergence.},
Journal = {Nature cell biology, England},
Volume = {10},
Number = {8},
Pages = {946-54},
Year = {2008},
Month = {August},
Keywords = {Arabidopsis • Arabidopsis Proteins • Carrier
Proteins • Gene Expression Regulation, Plant •
Indoleacetic Acids • Membrane Transport Proteins •
Plant Growth Regulators • Plant Roots • cytology
• genetics • growth & development* •
pharmacology • pharmacology* •
physiology*},
Abstract = {Lateral roots originate deep within the parental root from a
small number of founder cells at the periphery of vascular
tissues and must emerge through intervening layers of
tissues. We describe how the hormone auxin, which originates
from the developing lateral root, acts as a local inductive
signal which re-programmes adjacent cells. Auxin induces the
expression of a previously uncharacterized auxin influx
carrier LAX3 in cortical and epidermal cells directly
overlaying new primordia. Increased LAX3 activity reinforces
the auxin-dependent induction of a selection of
cell-wall-remodelling enzymes, which are likely to promote
cell separation in advance of developing lateral root
primordia.},
Key = {fds152737}
}
@article{fds152738,
Author = {JJ Petricka and PN Benfey},
Title = {Root layers: complex regulation of developmental
patterning.},
Journal = {Current opinion in genetics & development,
England},
Volume = {18},
Number = {4},
Pages = {354-61},
Year = {2008},
Month = {August},
Abstract = {Developmental patterning events involve cell fate
specification and maintenance processes in diverse,
multicellular organisms. The simple arrangement of tissue
layers in the Arabidopsis thaliana root provides a highly
tractable system for the study of these processes. This
review highlights recent work addressing the patterning of
root tissues focusing on the factors involved and their
complex regulation. In the past two years studies of root
patterning have indicated that chromatin remodeling, protein
movement, transcriptional networks, and an auxin gradient,
all contribute to the complexity inherent in developmental
patterning events within the root. As a result, future
research advances in this field will require tissue-specific
information at both the single gene and global
level.},
Key = {fds152738}
}
@article{fds152739,
Author = {JR Dinneny and TA Long and JY Wang and JW Jung and D Mace and S Pointer and C
Barron, SM Brady and J Schiefelbein and PN Benfey},
Title = {Cell identity mediates the response of Arabidopsis roots to
abiotic stress.},
Journal = {Science (New York, N.Y.), United States},
Volume = {320},
Number = {5878},
Pages = {942-5},
Year = {2008},
Month = {May},
Keywords = {Abscisic Acid • Algorithms • Arabidopsis •
Arabidopsis Proteins • Culture Media • Gene
Expression Profiling • Gene Expression Regulation,
Plant* • Genes, Plant • Iron • Mutation
• Plant Epidermis • Plant Roots • Promoter
Regions (Genetics) • Response Elements • Salinity*
• Transcription Factors • Transcription, Genetic
• cytology • cytology* • genetics •
growth & development • metabolism • physiology
• physiology*},
Abstract = {Little is known about the way developmental cues affect how
cells interpret their environment. We characterized the
transcriptional response to high salinity of different cell
layers and developmental stages of the Arabidopsis root and
found that transcriptional responses are highly constrained
by developmental parameters. These transcriptional changes
lead to the differential regulation of specific biological
functions in subsets of cell layers, several of which
correspond to observable physiological changes. We showed
that known stress pathways primarily control semiubiquitous
responses and used mutants that disrupt epidermal patterning
to reveal cell-layer-specific and inter-cell-layer effects.
By performing a similar analysis using iron deprivation, we
identified common cell-type-specific stress responses and
revealed the crucial role the environment plays in defining
the transcriptional outcome of cell-fate
decisions.},
Key = {fds152739}
}
@article{fds152740,
Author = {PN Benfey and T Mitchell-Olds},
Title = {From genotype to phenotype: systems biology meets natural
variation.},
Journal = {Science (New York, N.Y.), United States},
Volume = {320},
Number = {5875},
Pages = {495-7},
Year = {2008},
Month = {April},
Keywords = {Animals • Epistasis, Genetic • Gene Regulatory
Networks • Genetic Techniques • Genomics •
Genotype* • Humans • Metabolic Networks and
Pathways • Models, Genetic • Phenotype* •
Plants • Polymorphism, Genetic • Quantitative
Trait Loci • Systems Biology* • Variation
(Genetics)* • genetics*},
Abstract = {The promise that came with genome sequencing was that we
would soon know what genes do, particularly genes involved
in human diseases and those of importance to agriculture. We
now have the full genomic sequence of human, chimpanzee,
mouse, chicken, dog, worm, fly, rice, and cress, as well as
those for a wide variety of other species, and yet we still
have a lot of trouble figuring out what genes do. Mapping
genes to their function is called the "genotype-to-phenotype
problem," where phenotype is whatever is changed in the
organism when a gene's function is altered.},
Key = {fds152740}
}
@article{fds152741,
Author = {JR Dinneny and PN Benfey},
Title = {Plant stem cell niches: standing the test of
time.},
Journal = {Cell, United States},
Volume = {132},
Number = {4},
Pages = {553-7},
Year = {2008},
Month = {February},
Keywords = {Indoleacetic Acids • Meristem • Plant Roots •
Plant Shoots • Plants • cytology • cytology*
• metabolism},
Abstract = {Similar to animal stem cells, plant stem cells require
special niche microenvironments to continuously generate the
tissues that constitute the plant body. Recent work using
computer modeling and live imaging is helping to elucidate
some of the mechanisms responsible for the specification and
maintenance of stem cells in the root and
shoot.},
Key = {fds152741}
}
@article{fds140631,
Author = {SM Brady and DA Orlando and JY Lee and JY Wang and J Koch, JR Dinneny and D
Mace, U Ohler and PN Benfey},
Title = {A high-resolution root spatiotemporal map reveals dominant
expression patterns.},
Journal = {Science (New York, N.Y.), United States},
Volume = {318},
Number = {5851},
Pages = {801-6},
Year = {2007},
Month = {November},
ISSN = {1095-9203},
Keywords = {Arabidopsis • Gene Expression Profiling • Gene
Expression Regulation, Developmental* • Gene Expression
Regulation, Plant* • Green Fluorescent Proteins •
Oligonucleotide Array Sequence Analysis • Plant Roots
• cytology • genetics* • growth &
development},
Abstract = {Transcriptional programs that regulate development are
exquisitely controlled in space and time. Elucidating these
programs that underlie development is essential to
understanding the acquisition of cell and tissue identity.
We present microarray expression profiles of a
high-resolution set of developmental time points within a
single Arabidopsis root and a comprehensive map of nearly
all root cell types. These cell type-specific
transcriptional signatures often predict previously unknown
cellular functions. A computational pipeline identified
dominant expression patterns that demonstrate
transcriptional similarity between disparate cell types.
Dominant expression patterns along the root's longitudinal
axis do not strictly correlate with previously defined
developmental zones, and in many cases, we observed
expression fluctuation along this axis. Both robust
co-regulation of gene expression and potential phasing of
gene expression were identified between individual roots.
Methods that combine these profiles demonstrate
transcriptionally rich and complex programs that define
Arabidopsis root development in both space and
time.},
Key = {fds140631}
}
@article{fds140632,
Author = {H Cui and MP Levesque and T Vernoux and JW Jung and AJ Paquette and KL
Gallagher, JY Wang and I Blilou and B Scheres and PN
Benfey},
Title = {An evolutionarily conserved mechanism delimiting SHR
movement defines a single layer of endodermis in
plants.},
Journal = {Science (New York, N.Y.), United States},
Volume = {316},
Number = {5823},
Pages = {421-5},
Year = {2007},
Month = {April},
ISSN = {1095-9203},
Keywords = {Arabidopsis • Arabidopsis Proteins • Cell Nucleus
• Evolution • Feedback, Biochemical • Gene
Expression • Genes, Plant • Models, Biological
• Oligonucleotide Array Sequence Analysis • Oryza
sativa • Plant Proteins • Plant Roots •
Plants, Genetically Modified • Promoter Regions
(Genetics) • Protein Binding • Protein Transport
• Recombinant Fusion Proteins • Transcription
Factors • Transcription, Genetic • cytology •
cytology* • genetics • growth & development •
metabolism • metabolism*},
Abstract = {Intercellular protein movement plays a critical role in
animal and plant development. SHORTROOT (SHR) is a moving
transcription factor essential for endodermis specification
in the Arabidopsis root. Unlike diffusible animal
morphogens, which form a gradient across multiple cell
layers, SHR movement is limited to essentially one cell
layer. However, the molecular mechanism is unknown. We show
that SCARECROW (SCR) blocks SHR movement by sequestering it
into the nucleus through protein-protein interaction and a
safeguard mechanism that relies on a SHR/SCR-dependent
positive feedback loop for SCR transcription. Our studies
with SHR and SCR homologs from rice suggest that this
mechanism is evolutionarily conserved, providing a plausible
explanation why nearly all plants have a single layer of
endodermis.},
Key = {fds140632}
}
@article{fds140633,
Author = {JS Weitz and PN Benfey and NS Wingreen},
Title = {Evolution, interactions, and biological networks.},
Journal = {PLoS biology, United States},
Volume = {5},
Number = {1},
Pages = {e11},
Year = {2007},
Month = {January},
ISSN = {1545-7885},
Keywords = {Bacteriophages • Ecology • Evolution, Molecular*
• Gene Regulatory Networks* • Host-Parasite
Interactions • Variation (Genetics) •
standards},
Key = {fds140633}
}
@article{fds140634,
Author = {SM Brady and S Song and KS Dhugga and JA Rafalski and PN
Benfey},
Title = {Combining expression and comparative evolutionary analysis.
The COBRA gene family.},
Journal = {Plant physiology, United States},
Volume = {143},
Number = {1},
Pages = {172-87},
Year = {2007},
Month = {January},
ISSN = {0032-0889},
Keywords = {Amino Acid Sequence • Arabidopsis • Arabidopsis
Proteins • Cell Wall • Cluster Analysis •
Evolution, Molecular* • Gene Expression Regulation,
Plant • Glucosyltransferases • Glucuronidase
• Membrane Glycoproteins • Molecular Sequence Data
• Multigene Family* • Phylogeny • Plant
Leaves • Plant Proteins • Plant Roots • Plant
Stems • Sequence Alignment • Zea mays •
analysis • classification • genetics •
genetics* • growth & development • metabolism
• physiology},
Abstract = {Plant cell shape is achieved through a combination of
oriented cell division and cell expansion and is defined by
the cell wall. One of the genes identified to influence cell
expansion in the Arabidopsis (Arabidopsis thaliana) root is
the COBRA (COB) gene that belongs to a multigene family.
Three members of the AtCOB gene family have been shown to
play a role in specific types of cell expansion or cell wall
biosynthesis. Functional orthologs of one of these genes
have been identified in maize (Zea mays) and rice (Oryza
sativa; Schindelman et al., 2001; Li et al., 2003; Brown et
al., 2005; Persson et al., 2005; Ching et al., 2006; Jones
et al., 2006). We present the maize counterpart of the COB
gene family and the COB gene superfamily phylogeny. Most of
the genes belong to a family with two main clades as
previously identified by analysis of the Arabidopsis family
alone. Within these clades, however, clear differences
between monocot and eudicot family members exist, and these
are analyzed in the context of Type I and Type II cell walls
in eudicots and monocots. In addition to changes at the
sequence level, gene regulation of this family in a eudicot,
Arabidopsis, and a monocot, maize, is also characterized.
Gene expression is analyzed in a multivariate approach,
using data from a number of sources, including massively
parallel signature sequencing libraries, transcriptional
reporter fusions, and microarray data. This analysis has
revealed that the expression of Arabidopsis and maize COB
gene family members is highly developmentally and spatially
regulated at the tissue and cell type-specific level, that
gene superfamily members show overlapping and unique
expression patterns, and that only a subset of gene
superfamily members act in response to environmental
stimuli. Regulation of expression of the Arabidopsis COB
gene family members has highly diversified in comparison to
that of the maize COB gene superfamily members. We also
identify BRITTLE STALK 2-LIKE 3 as a putative ortholog of
AtCOB.},
Key = {fds140634}
}
@article{fds52623,
Author = {TA Long and PN Benfey},
Title = {Transcription factors and hormones: new insights into plant
cell differentiation.},
Journal = {Curr Opin Cell Biol, United States},
Volume = {18},
Number = {6},
Pages = {710-4},
Year = {2006},
Month = {December},
Abstract = {Plant development is a continuous process, mainly due to the
presence of stem cell niches within the root and shoot. The
interplay between a host of transcription factors determines
whether the cells within the meristem maintain their stem
cell state, differentiate into leaves or form secondary
meristems, which develop into shoots and flowers. Several
recent studies provide new insight into how transcription
factors and phytohormones interact within meristems to
control cell proliferation and differentiation.},
Key = {fds52623}
}
@article{fds52624,
Author = {SM Brady and TA Long and PN Benfey},
Title = {Unraveling the dynamic transcriptome.},
Journal = {Plant Cell, United States},
Volume = {18},
Number = {9},
Pages = {2101-11},
Year = {2006},
Month = {September},
Key = {fds52624}
}
@article{fds52625,
Author = {DL Mace and JY Lee and RW Twigg and J Colinas and PN Benfey and U
Ohler},
Title = {Quantification of transcription factor expression from
Arabidopsis images.},
Journal = {Bioinformatics, England},
Volume = {22},
Number = {14},
Pages = {e323-31},
Year = {2006},
Month = {July},
Abstract = {MOTIVATION: Confocal microscopy has long provided
qualitative information for a variety of applications in
molecular biology. Recent advances have led to extensive
image datasets, which can now serve as new data sources to
obtain quantitative gene expression information. In contrast
to microarrays, which usually provide data for many genes at
one time point, these image data provide us with expression
information for only one gene, but with the advantage of
high spatial and/or temporal resolution, which is often
lostin microarray samples. RESULTS: We have developed a
prototype for the automatic analysis of Arabidopsis confocal
images, which show the expression of a single transcription
factor by means of GFP reporter constructs. Using techniques
from image registration, we are able to address inherent
problems of non-rigid transformation and partial mapping,
and obtain relative expression values for 13 different
tissues in Arabidopsis roots. This provides quantitative
information with high spatial resolution, which accurately
represents the underlying expression values within the
organism. We validate our approach on a data set of 122
images depicting expression patterns of 30 transcription
factors, both in terms of registration accuracy, as well as
correlation with cell-sorted microarray data. Approaches
like this will be useful to lay the groundwork to
reconstruct regulatory networks on the level of tissues or
even individual cells. AVAILABILITY: Upon request from the
authors.},
Key = {fds52625}
}
@article{fds52626,
Author = {MP Levesque and T Vernoux and W Busch and H Cui and JY Wang and I Blilou and H
Hassan, K Nakajima and N Matsumoto and JU Lohmann and B Scheres and PN
Benfey},
Title = {Whole-genome analysis of the SHORT-ROOT developmental
pathway in Arabidopsis.},
Journal = {PLoS Biol, United States},
Volume = {4},
Number = {5},
Pages = {e143},
Year = {2006},
Month = {May},
Abstract = {Stem cell function during organogenesis is a key issue in
developmental biology. The transcription factor SHORT-ROOT
(SHR) is a critical component in a developmental pathway
regulating both the specification of the root stem cell
niche and the differentiation potential of a subset of stem
cells in the Arabidopsis root. To obtain a comprehensive
view of the SHR pathway, we used a statistical method called
meta-analysis to combine the results of several microarray
experiments measuring the changes in global expression
profiles after modulating SHR activity. Meta-analysis was
first used to identify the direct targets of SHR by
combining results from an inducible form of SHR driven by
its endogenous promoter, ectopic expression, followed by
cell sorting and comparisons of mutant to wild-type roots.
Eight putative direct targets of SHR were identified, all
with expression patterns encompassing subsets of the native
SHR expression domain. Further evidence for direct
regulation by SHR came from binding of SHR in vivo to the
promoter regions of four of the eight putative targets. A
new role for SHR in the vascular cylinder was predicted from
the expression pattern of several direct targets and
confirmed with independent markers. The meta-analysis
approach was then used to perform a global survey of the SHR
indirect targets. Our analysis suggests that the SHR pathway
regulates root development not only through a large
transcription regulatory network but also through hormonal
pathways and signaling pathways using receptor-like kinases.
Taken together, our results not only identify the first
nodes in the SHR pathway and a new function for SHR in the
development of the vascular tissue but also reveal the
global architecture of this developmental
pathway.},
Key = {fds52626}
}
@article{fds52627,
Author = {JY Lee and J Colinas and JY Wang and D Mace and U Ohler and PN
Benfey},
Title = {Transcriptional and posttranscriptional regulation of
transcription factor expression in Arabidopsis
roots.},
Journal = {Proc Natl Acad Sci U S A, United States},
Volume = {103},
Number = {15},
Pages = {6055-60},
Year = {2006},
Month = {April},
Abstract = {Understanding how the expression of transcription factor
(TF) genes is modulated is essential for reconstructing gene
regulatory networks. There is increasing evidence that
sequences other than upstream noncoding can contribute to
modulating gene expression, but how frequently they do so
remains unclear. Here, we investigated the regulation of TFs
expressed in a tissue-enriched manner in Arabidopsis roots.
For 61 TFs, we created GFP reporter constructs driven by
each TF's upstream noncoding sequence (including the 5'UTR)
fused to the GFP reporter gene alone or together with the
TF's coding sequence. We compared the visually detectable
GFP patterns with endogenous mRNA expression patterns, as
defined by a genome-wide microarray root expression map. An
automated image analysis method for quantifying GFP signals
in different tissues was developed and used to validate our
visual comparison method. From these combined analyses, we
found that (i) the upstream noncoding sequence was
sufficient to recapitulate the mRNA expression pattern for
80% (35/44) of the TFs, and (ii) 25% of the TFs undergo
posttranscriptional regulation via microRNA-mediated mRNA
degradation (2/24) or via intercellular protein movement
(6/24). The results suggest that, for Arabidopsis TFs,
upstream noncoding sequences are major contributors to mRNA
expression pattern establishment, but modulation of
transcription factor protein expression pattern after
transcription is relatively frequent. This study provides a
systematic overview of regulation of TF expression at a
cellular level.},
Key = {fds52627}
}
@article{fds44171,
Author = {J Friml and P Benfey and E Benková and M Bennett and T Berleth and N
Geldner, M Grebe and M Heisler and J Hejátko and G Jürgens and T Laux and K Lindsey and W Lukowitz and C Luschnig and R Offringa and B Scheres and R
Swarup, R Torres-Ruiz and D Weijers and E Zazímalová},
Title = {Apical-basal polarity: why plant cells don't stand on their
heads.},
Journal = {Trends Plant Sci, England},
Volume = {11},
Number = {1},
Pages = {12-4},
Year = {2005},
Month = {December},
Key = {fds44171}
}
@article{fds44668,
Author = {JR Dinneny and PN Benfey},
Title = {Stem Cell Research Goes Underground: The
RETINOBLASTOMA-RELATED Gene in Root Development.},
Journal = {Cell},
Volume = {123},
Number = {7},
Pages = {1180-2},
Year = {2005},
Month = {December},
Abstract = {Both cellular differentiation and stem cell maintenance must
occur at the root apex in order to ensure the continuous
growth of plant roots. In this issue of Cell, reveal that a
canonical Retinoblastoma pathway plays a crucial role in
regulating the balance between differentiation and renewal
of plant root stem cells.},
Key = {fds44668}
}
@article{fds44172,
Author = {J Lim and JW Jung and CE Lim and MH Lee and BJ Kim and M Kim and WB Bruce and PN
Benfey},
Title = {Conservation and diversification of SCARECROW in
maize.},
Journal = {Plant Mol Biol, Netherlands},
Volume = {59},
Number = {4},
Pages = {619-30},
Year = {2005},
Month = {November},
Abstract = {The SCARECROW (SCR) gene in Arabidopsis is required for
asymmetric cell divisions responsible for ground tissue
formation in the root and shoot. Previously, we reported
that Zea mays SCARECROW (ZmSCR) is the likely maize ortholog
of SCR. Here we describe conserved and divergent aspects of
ZmSCR. Its ability to complement the Arabidopsis scr mutant
phenotype suggests conservation of function, yet its
expression pattern during embryogenesis and in the shoot
system indicates divergence. ZmSCR expression was detected
early during embryogenesis and localized to the endodermal
lineage in the root, showing a gradual regionalization of
expression. Expression of ZmSCR appeared to be analogous to
that of SCR during leaf formation. However, its absence from
the maize shoot meristem and its early expression pattern
during embryogenesis suggest a diversification of ZmSCR in
the patterning processes in maize. To further investigate
the evolutionary relationship of SCR and ZmSCR, we performed
a phylogenetic analysis using Arabidopsis, rice and maize
SCARECROW-LIKE genes (SCLs). We found SCL23 to be the most
closely related to SCR in both eudicots and monocots,
suggesting that a gene duplication resulting in SCR and
SCL23 predates the divergence of dicots and
monocots.},
Key = {fds44172}
}
@article{fds44173,
Author = {K Birnbaum and JW Jung and JY Wang and GM Lambert and JA Hirst and DW
Galbraith, PN Benfey},
Title = {Cell type-specific expression profiling in plants via cell
sorting of protoplasts from fluorescent reporter
lines.},
Journal = {Nat Methods, United States},
Volume = {2},
Number = {8},
Pages = {615-9},
Year = {2005},
Month = {August},
Key = {fds44173}
}
@article{fds44174,
Author = {T Vernoux and PN Benfey},
Title = {Signals that regulate stem cell activity during plant
development.},
Journal = {Curr Opin Genet Dev, England},
Volume = {15},
Number = {4},
Pages = {388-94},
Year = {2005},
Month = {August},
Abstract = {Plant stem cells are used continuously to generate new
structures during the entire life-span of the organism. In
the adult plant, stem cells are found in specialized
structures called meristems. The meristems contain the stem
cell niche together with rapidly dividing daughter cells
that will ultimately differentiate into specific cell types.
Some of the master genes that orchestrate the establishment
and maintenance of the stem cell niche have now been
identified in both the root and the shoot. Recent results
show that these genes also determine the fate of the stem
cells and that feedback signals from differentiated cells
are involved in stem cell specification. These advances have
provided a framework to understand how short-range and
long-range signals are integrated to specify and position
the stem cell niche in the meristems, and how the
differentiation potential of plant stem cells is
controlled.},
Key = {fds44174}
}
@article{fds44178,
Author = {T Nawy and JY Lee and J Colinas and JY Wang and SC Thongrod and JE Malamy and K Birnbaum and PN Benfey},
Title = {Transcriptional profile of the Arabidopsis root quiescent
center.},
Journal = {Plant Cell, United States},
Volume = {17},
Number = {7},
Pages = {1908-25},
Year = {2005},
Month = {July},
Abstract = {The self-renewal characteristics of stem cells render them
vital engines of development. To better understand the
molecular mechanisms that determine the properties of stem
cells, transcript profiling was conducted on quiescent
center (QC) cells from the Arabidopsis thaliana root
meristem. The AGAMOUS-LIKE 42 (AGL42) gene, which encodes a
MADS box transcription factor whose expression is enriched
in the QC, was used to mark these cells. RNA was isolated
from sorted cells, labeled, and hybridized to Affymetrix
microarrays. Comparisons with digital in situ expression
profiles of surrounding tissues identified a set of genes
enriched in the QC. Promoter regions from a subset of
transcription factors identified as enriched in the QC
conferred expression in the QC. These studies demonstrated
that it is possible to successfully isolate and profile a
rare cell type in the plant. Mutations in all enriched
transcription factor genes including AGL42 exhibited no
detectable root phenotype, raising the possibility of a high
degree of functional redundancy in the QC.},
Key = {fds44178}
}
@article{fds44175,
Author = {AJ Paquette and PN Benfey},
Title = {Maturation of the ground tissue of the root is regulated by
gibberellin and SCARECROW and requires SHORT-ROOT.},
Journal = {Plant Physiol, United States},
Volume = {138},
Number = {2},
Pages = {636-40},
Year = {2005},
Month = {June},
Key = {fds44175}
}
@article{fds44176,
Author = {JY Lee and M Levesque and PN Benfey},
Title = {High-throughput RNA isolation technologies. New tools for
high-resolution gene expression profiling in plant
systems.},
Journal = {Plant Physiol, United States},
Volume = {138},
Number = {2},
Pages = {585-90},
Year = {2005},
Month = {June},
Key = {fds44176}
}
@article{fds44177,
Author = {PN Benfey},
Title = {Developmental networks.},
Journal = {Plant Physiol, United States},
Volume = {138},
Number = {2},
Pages = {548-9},
Year = {2005},
Month = {June},
Key = {fds44177}
}
@article{fds44179,
Author = {F Roudier and AG Fernandez and M Fujita and R Himmelspach and GH Borner and G Schindelman and S Song and TI Baskin and P Dupree and GO Wasteneys and PN
Benfey},
Title = {COBRA, an Arabidopsis extracellular glycosyl-phosphatidyl
inositol-anchored protein, specifically controls highly
anisotropic expansion through its involvement in cellulose
microfibril orientation.},
Journal = {Plant Cell, United States},
Volume = {17},
Number = {6},
Pages = {1749-63},
Year = {2005},
Month = {June},
Abstract = {The orientation of cell expansion is a process at the heart
of plant morphogenesis. Cellulose microfibrils are the
primary anisotropic material in the cell wall and thus are
likely to be the main determinant of the orientation of cell
expansion. COBRA (COB) has been identified previously as a
potential regulator of cellulose biogenesis. In this study,
characterization of a null allele, cob-4, establishes the
key role of COB in controlling anisotropic expansion in most
developing organs. Quantitative polarized-light and
field-emission scanning electron microscopy reveal that loss
of anisotropic expansion in cob mutants is accompanied by
disorganization of the orientation of cellulose microfibrils
and subsequent reduction of crystalline cellulose. Analyses
of the conditional cob-1 allele suggested that COB is
primarily implicated in microfibril deposition during rapid
elongation. Immunodetection analysis in elongating root
cells revealed that, in agreement with its substitution by a
glycosylphosphatidylinositol anchor, COB was polarly
targeted to both the plasma membrane and the longitudinal
cell walls and was distributed in a banding pattern
perpendicular to the longitudinal axis via a
microtubule-dependent mechanism. Our observations suggest
that COB, through its involvement in cellulose microfibril
orientation, is an essential factor in highly anisotropic
expansion during plant morphogenesis.},
Key = {fds44179}
}
@article{fds44180,
Author = {KL Gallagher and PN Benfey},
Title = {Not just another hole in the wall: understanding
intercellular protein trafficking.},
Journal = {Genes Dev, United States},
Volume = {19},
Number = {2},
Pages = {189-95},
Year = {2005},
Month = {January},
Abstract = {Development and differentiation of multicellular organisms
requires cell-to-cell communication. In plants direct
signaling and exchange of macromolecules between cells is
possible through plasmodesmata. Recently direct exchange of
membrane-bound vesicles and organelles has been demonstrated
between animal cells through formation of cytoplasmic
bridges (tunneling nanotubes) in vitro. Here we review
recent developments in cell-to-cell trafficking of
macromolecules in plants and animals.},
Key = {fds44180}
}
@article{fds17046,
Author = {Birnbaum, K. and Shasha, D.E. and Wang, J.Y. and Jung, J. and Lambert, G.M. and Galbraith, D.W. and P.N. Benfey},
Title = {A gene expression map of the Arabidopsis
root},
Journal = {Science},
Volume = {302},
Pages = {1956-60},
Year = {2003},
Month = {December},
Key = {fds17046}
}
@article{fds17047,
Author = {Brenner ED and Stevenson DW and McCombie RW and Katari MS and Rudd SA and Mayer KF and Palenchar PM and Runko SJ and Twigg RW and Dai G and Martienssen RA and Benfey PN and Coruzzi GM},
Title = {Expressed sequence tag analysis in Cycas, the most primitive
living seed plant},
Journal = {Genome Biology},
Volume = {4},
Pages = {R78},
Year = {2003},
Key = {fds17047}
}
@article{fds17048,
Author = {P.N. Benfey},
Title = {Molecular biology: microRNA is here to stay},
Journal = {Nature},
Volume = {425(},
Pages = {244-245},
Year = {2003},
Key = {fds17048}
}
@article{fds17049,
Author = {Levesque M and Shasha D and Kim W and Surette MG and P.N.
Benfey},
Title = {Trait-to-gene: a computational method for predicting the
function of uncharacterized genes},
Journal = {Current Biology},
Volume = {13},
Pages = {129-133},
Year = {2003},
Key = {fds17049}
}
@article{fds29758,
Author = {Birnbaum, K. and DeSalle, R. and Peters, C.M. and P.N.
Benfey},
Title = {Integrating gene flow, crop biology, and farm management in
the on-farm conservation of avocado (Persea americana,
Lauraceae).},
Journal = {American Journal of Botany},
Volume = {90},
Pages = {1619-1627},
Year = {2003},
Key = {fds29758}
}
@article{fds4157,
Author = {Roudier, F. and Schindelman, G and DeSalle, R. and P.N.
Benfey},
Title = {The COBRA family of putative GPI-anchored proteins in
Arabidopsis: a new fellowship in expansion.},
Journal = {Plant Physiology},
Volume = {130},
Number = {2},
Pages = {538-48.},
Year = {2002},
Month = {December},
Key = {fds4157}
}
@article{fds4158,
Author = {Muller S and Fuchs E and Ovecka M and Wysocka-Diller J and Benfey P.N and MT Hauser},
Title = {Two new loci, PLEIADE and HYADE, implicate organ-specific
regulation of cytokinesis in Arabidopsis.},
Journal = {Plant Physiol.},
Volume = {130},
Number = {1},
Pages = {312-24},
Year = {2002},
Month = {December},
Key = {fds4158}
}
@article{fds4159,
Author = {Colinas J and Birnbaum K and P.N. Benfey},
Title = {Using cauliflower to find conserved non-coding regions in
Arabidopsis.},
Journal = {Plant Physiol.},
Volume = {129},
Number = {2},
Pages = {451-4},
Year = {2002},
Month = {December},
Key = {fds4159}
}
@article{fds4160,
Author = {P.N. Benfey},
Title = {Auxin action: slogging out of the swamp},
Journal = {Curr Biol.},
Volume = {12},
Number = {11},
Pages = {R389-90},
Year = {2002},
Month = {December},
Key = {fds4160}
}
@article{fds4161,
Author = {Nakajima, K and P.N. Benfey},
Title = {Signaling in and out: control of cell division and
differentiation in the shoot and root.},
Journal = {Plant Cell},
Volume = {14},
Pages = {S265-76},
Year = {2002},
Month = {December},
Key = {fds4161}
}
@article{fds5271,
Author = {Birnbaum, K. and Benfey, P.N. and Peters, C.M. and R.
DeSalle},
Title = {MANAGEDPOP: a computer simulation to project allelic
diversity in managed populations with overlapping
generations},
Journal = {Molecular Ecology Notes},
Volume = {2},
Pages = {615-617},
Year = {2002},
Month = {January},
Key = {fds5271}
}
%% Articles
@article{fds152723,
Author = {J Colinas and SC Schmidler and G Bohrer and B Iordanov and PN
Benfey},
Title = {Intergenic and genic sequence lengths have opposite
relationships with respect to gene expression.},
Journal = {PLoS ONE, United States},
Volume = {3},
Number = {11},
Pages = {e3670},
Year = {2008},
Abstract = {Eukaryotic genomes are mostly composed of noncoding DNA
whose role is still poorly understood. Studies in several
organisms have shown correlations between the length of the
intergenic and genic sequences of a gene and the expression
of its corresponding mRNA transcript. Some studies have
found a positive relationship between intergenic sequence
length and expression diversity between tissues, and
concluded that genes under greater regulatory control
require more regulatory information in their intergenic
sequences. Other reports found a negative relationship
between expression level and gene length and the
interpretation was that there is selection pressure for
highly expressed genes to remain small. However, a
correlation between gene sequence length and expression
diversity, opposite to that observed for intergenic
sequences, has also been reported, and to date there is no
testable explanation for this observation. To shed light on
these varied and sometimes conflicting results, we performed
a thorough study of the relationships between sequence
length and gene expression using cell-type (tissue) specific
microarray data in Arabidopsis thaliana. We measured median
gene expression across tissues (expression level),
expression variability between tissues (expression pattern
uniformity), and expression variability between replicates
(expression noise). We found that intergenic (upstream and
downstream) and genic (coding and noncoding) sequences have
generally opposite relationships with respect to expression,
whether it is tissue variability, median, or expression
noise. To explain these results we propose a model, in which
the lengths of the intergenic and genic sequences have
opposite effects on the ability of the transcribed region of
the gene to be epigenetically regulated for differential
expression. These findings could shed light on the role and
influence of noncoding sequences on gene
expression.},
Key = {fds152723}
}
%% Book Chapter
@article{fds52786,
Author = {Dinneny, J. and P.N. Benfey},
Title = {Studying root development using a genomic
approach},
Booktitle = {Root Development},
Year = {2006},
Key = {fds52786}
}
@article{fds52629,
Author = {Lee, J-Y and P.N. Benfey},
Title = {Root Apical Meristems},
Booktitle = {Encyclopedia of Life Sciences},
Year = {2006},
Key = {fds52629}
}
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