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% Generated by Paperpile. Check out http://paperpile.com for more information.
% BibTeX export options can be customized via Settings -> BibTeX.
@ARTICLE{Karlsson2017-wy,
title = "Single-cell {mRNA} isoform diversity in the mouse brain",
author = "Karlsson, Kasper and Linnarsson, Sten",
affiliation = "Departments of Medicine and Genetics, Stanford University,
94305, Stanford, CA, USA. Laboratory for Molecular
Neurobiology, Department of Medical Biochemistry and
Biophysics, Karolinska Institutet, Scheeles v{\"a}g 1, SE-171
77, Stockholm, Sweden. [email protected].",
abstract = "BACKGROUND: Alternative mRNA isoform usage is an important
source of protein diversity in mammalian cells. This
phenomenon has been extensively studied in bulk tissues,
however, it remains unclear how this diversity is reflected in
single cells. RESULTS: Here we use long-read sequencing
technology combined with unique molecular identifiers (UMIs)
to reveal patterns of alternative full-length isoform
expression in single cells from the mouse brain. We found a
surprising amount of isoform diversity, even after applying a
conservative definition of what constitutes an isoform. Genes
tend to have one or a few isoforms highly expressed and a
larger number of isoforms expressed at a low level. However,
for many genes, nearly every sequenced mRNA molecule was
unique, and many events affected coding regions suggesting
previously unknown protein diversity in single cells. Exon
junctions in coding regions were less prone to splicing errors
than those in non-coding regions, indicating purifying
selection on splice donor and acceptor efficiency.
CONCLUSIONS: Our findings indicate that mRNA isoform diversity
is an important source of biological variability also in
single cells.",
journal = "BMC Genomics",
volume = 18,
number = 1,
pages = "126",
month = "3~" # feb,
year = 2017,
keywords = "Alternative isoform usage; Long read sequencing;
Oligodendrocytes; PacBio; STRT; Single-cell RNA sequencing;
UMI",
language = "en"
}
@ARTICLE{Locke2011-tc,
title = "Stochastic pulse regulation in bacterial stress response",
author = "Locke, James C W and Young, Jonathan W and Fontes, Michelle
and Hern{\'a}ndez Jim{\'e}nez, Mar{\'\i}a Jes{\'u}s and
Elowitz, Michael B",
affiliation = "Howard Hughes Medical Institute, Division of Biology and
Bioengineering, Broad Center, California Institute of
Technology, 1200 East California Boulevard, Pasadena, CA
91125, USA.",
abstract = "Gene regulatory circuits can use dynamic, and even stochastic,
strategies to respond to environmental conditions. We examined
activation of the general stress response mediated by the
alternative sigma factor, $\sigma$(B), in individual Bacillus
subtilis cells. We observed that energy stress activates
$\sigma$(B) in discrete stochastic pulses, with increasing
levels of stress leading to higher pulse frequencies. By
perturbing and rewiring the endogenous system, we found that
this behavior results from three key features of the
$\sigma$(B) circuit: an ultrasensitive phosphorylation switch;
stochasticity (``noise''), which activates that switch; and a
mixed (positive and negative) transcriptional feedback, which
can both amplify a pulse and switch it off. Together, these
results show how prokaryotes encode signals using stochastic
pulse frequency modulation through a compact regulatory
architecture.",
journal = "Science",
volume = 334,
number = 6054,
pages = "366--369",
month = "21~" # oct,
year = 2011,
language = "en"
}
@ARTICLE{Brar2012-pj,
title = "{High-Resolution} View of the Yeast Meiotic Program Revealed by
Ribosome Profiling",
author = "Brar, G A and Yassour, M and Friedman, N and Regev, A and
Ingolia, N T and Weissman, J S",
abstract = "CTCs = circulating tumor cells, ie primary tumor cells found in
the blood/circulatory system. Have epithelial cell markers. DTCs
= disseminated tumor cells, ie tumor cells found in neighboring
tissues such as bone.",
journal = "Science",
volume = 335,
number = 6068,
pages = "552--557",
year = 2012
}
@ARTICLE{Saletore2012-fp,
title = "The birth of the Epitranscriptome: deciphering the function of
{RNA} modifications",
author = "Saletore, Yogesh and Meyer, Kate and Korlach, Jonas and Vilfan,
Igor D and Jaffrey, Samie and Mason, Christopher E",
abstract = "Recent studies have found methyl-6-adenosine in thousands of
mammalian genes, and this modification is most pronounced near
the beginning of the 3' UTR. We present a perspective on current
work and new single-molecule sequencing methods for detecting RNA
base modifications.",
journal = "Genome Biol.",
volume = 13,
number = 10,
pages = "175",
month = "31~" # oct,
year = 2012,
language = "en"
}
@ARTICLE{Itzkovitz2011-ex,
title = "Validating transcripts with probes and imaging technology",
author = "Itzkovitz, Shalev and van Oudenaarden, Alexander",
affiliation = "Department of Physics, Massachusetts Institute of Technology,
Cambridge, Massachusetts, USA.",
abstract = "High-throughput gene expression screens provide a quantitative
picture of the average expression signature of biological
samples. However, the analysis of spatial gene expression
patterns with single-cell resolution requires quantitative in
situ measurement techniques. Here we describe recent
technological advances in RNA fluorescence in situ
hybridization (FISH) techniques that facilitate detection of
individual fluorescently labeled mRNA molecules of practically
any endogenous gene. These methods, which are based on
advances in probe design, imaging technology and image
processing, enable the absolute measurement of transcript
abundance in individual cells with single-molecule resolution.",
journal = "Nat. Methods",
volume = 8,
number = "4 Suppl",
pages = "S12--9",
month = apr,
year = 2011,
language = "en"
}
@ARTICLE{Dueck2016-mr,
title = "Variation is function: Are single cell differences
functionally important?: Testing the hypothesis that single
cell variation is required for aggregate function",
author = "Dueck, Hannah and Eberwine, James and Kim, Junhyong",
affiliation = "Genomics and Computational Biology Graduate Group, University
of Pennsylvania, Philadelphia, PA, USA. Genomics and
Computational Biology Graduate Group, University of
Pennsylvania, Philadelphia, PA, USA. Department of Systems
Pharmacology and Translational Therapeutics, University of
Pennsylvania, Philadelphia, PA, USA. Penn Program in Single
Cell Biology, Perelman School of Medicine, University of
Pennsylvania, Philadelphia, PA, USA. Genomics and
Computational Biology Graduate Group, University of
Pennsylvania, Philadelphia, PA, USA. Department of Systems
Pharmacology and Translational Therapeutics, University of
Pennsylvania, Philadelphia, PA, USA. Penn Program in Single
Cell Biology, Perelman School of Medicine, University of
Pennsylvania, Philadelphia, PA, USA. Department of Biology,
University of Pennsylvania, Philadelphia, PA, USA. Department
of Computer and Information Science, University of
Pennsylvania, Philadelphia, PA, USA.",
abstract = "There is a growing appreciation of the extent of transcriptome
variation across individual cells of the same cell type. While
expression variation may be a byproduct of, for example,
dynamic or homeostatic processes, here we consider whether
single-cell molecular variation per se might be crucial for
population-level function. Under this hypothesis, molecular
variation indicates a diversity of hidden functional
capacities within an ensemble of identical cells, and this
functional diversity facilitates collective behavior that
would be inaccessible to a homogenous population. In reviewing
this topic, we explore possible functions that might be
carried by a heterogeneous ensemble of cells; however, this
question has proven difficult to test, both because methods to
manipulate molecular variation are limited and because it is
complicated to define, and measure, population-level function.
We consider several possible methods to further pursue the
hypothesis that variation is function through the use of
comparative analysis and novel experimental techniques.",
journal = "Bioessays",
volume = 38,
number = 2,
pages = "172--180",
month = feb,
year = 2016,
keywords = "bet-hedging; evolution of variation; fractional response;
functional variation; single cell transcriptome; single cell
variation",
language = "en"
}
@ARTICLE{Wilhelm2014-tt,
title = "Mass-spectrometry-based draft of the human proteome",
author = "Wilhelm, Mathias and Schlegl, Judith and Hahne, Hannes and
Gholami, Amin Moghaddas and Lieberenz, Marcus and Savitski,
Mikhail M and Ziegler, Emanuel and Butzmann, Lars and
Gessulat, Siegfried and Marx, Harald and Mathieson, Toby and
Lemeer, Simone and Schnatbaum, Karsten and Reimer, Ulf and
Wenschuh, Holger and Mollenhauer, Martin and Slotta-Huspenina,
Julia and Boese, Joos-Hendrik and Bantscheff, Marcus and
Gerstmair, Anja and Faerber, Franz and Kuster, Bernhard",
affiliation = "1] Chair of Proteomics and Bioanalytics, Technische
Universit{\"a}t M{\"u}nchen, Emil-Erlenmeyer Forum 5, 85354
Freising, Germany [2] SAP AG, Dietmar-Hopp-Allee 16, 69190
Walldorf, Germany [3]. 1] SAP AG, Dietmar-Hopp-Allee 16, 69190
Walldorf, Germany [2]. 1] Chair of Proteomics and
Bioanalytics, Technische Universit{\"a}t M{\"u}nchen,
Emil-Erlenmeyer Forum 5, 85354 Freising, Germany [2]. 1] Chair
of Proteomics and Bioanalytics, Technische Universit{\"a}t
M{\"u}nchen, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany
[2]. SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf, Germany.
Cellzome GmbH, Meyerhofstra{\ss}e 1, 69117 Heidelberg,
Germany. SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf,
Germany. SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf,
Germany. SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf,
Germany. Chair of Proteomics and Bioanalytics, Technische
Universit{\"a}t M{\"u}nchen, Emil-Erlenmeyer Forum 5, 85354
Freising, Germany. Cellzome GmbH, Meyerhofstra{\ss}e 1, 69117
Heidelberg, Germany. Chair of Proteomics and Bioanalytics,
Technische Universit{\"a}t M{\"u}nchen, Emil-Erlenmeyer Forum
5, 85354 Freising, Germany. JPT Peptide Technologies GmbH,
Volmerstra{\ss}e 5, 12489 Berlin, Germany. JPT Peptide
Technologies GmbH, Volmerstra{\ss}e 5, 12489 Berlin, Germany.
JPT Peptide Technologies GmbH, Volmerstra{\ss}e 5, 12489
Berlin, Germany. Institute of Pathology, Technische
Universit{\"a}t M{\"u}nchen, Trogerstra{\ss}e 18, 81675
M{\"u}nchen, Germany. Institute of Pathology, Technische
Universit{\"a}t M{\"u}nchen, Trogerstra{\ss}e 18, 81675
M{\"u}nchen, Germany. SAP AG, Dietmar-Hopp-Allee 16, 69190
Walldorf, Germany. Cellzome GmbH, Meyerhofstra{\ss}e 1, 69117
Heidelberg, Germany. SAP AG, Dietmar-Hopp-Allee 16, 69190
Walldorf, Germany. SAP AG, Dietmar-Hopp-Allee 16, 69190
Walldorf, Germany. 1] Chair of Proteomics and Bioanalytics,
Technische Universit{\"a}t M{\"u}nchen, Emil-Erlenmeyer Forum
5, 85354 Freising, Germany [2] Center for Integrated Protein
Science Munich, Germany.",
abstract = "Proteomes are characterized by large protein-abundance
differences, cell-type- and time-dependent expression patterns
and post-translational modifications, all of which carry
biological information that is not accessible by genomics or
transcriptomics. Here we present a mass-spectrometry-based
draft of the human proteome and a public, high-performance,
in-memory database for real-time analysis of terabytes of big
data, called ProteomicsDB. The information assembled from
human tissues, cell lines and body fluids enabled estimation
of the size of the protein-coding genome, and identified
organ-specific proteins and a large number of translated
lincRNAs (long intergenic non-coding RNAs). Analysis of
messenger RNA and protein-expression profiles of human tissues
revealed conserved control of protein abundance, and
integration of drug-sensitivity data enabled the
identification of proteins predicting resistance or
sensitivity. The proteome profiles also hold considerable
promise for analysing the composition and stoichiometry of
protein complexes. ProteomicsDB thus enables navigation of
proteomes, provides biological insight and fosters the
development of proteomic technology.",
journal = "Nature",
publisher = "nature.com",
volume = 509,
number = 7502,
pages = "582--587",
month = "29~" # may,
year = 2014,
language = "en"
}
@ARTICLE{Jangi2014-ww,
title = "Rbfox2 controls autoregulation in {RNA-binding} protein
networks",
author = "Jangi, Mohini and Boutz, Paul L and Paul, Prakriti and Sharp,
Phillip A",
affiliation = "David H. Koch Institute for Integrative Cancer Research.",
abstract = "The tight regulation of splicing networks is critical for
organismal development. To maintain robust splicing patterns,
many splicing factors autoregulate their expression through
alternative splicing-coupled nonsense-mediated decay (AS-NMD).
However, as negative autoregulation results in a self-limiting
window of splicing factor expression, it is unknown how
variations in steady-state protein levels can arise in
different physiological contexts. Here, we demonstrate that
Rbfox2 cross-regulates AS-NMD events within RNA-binding
proteins to alter their expression. Using individual
nucleotide-resolution cross-linking immunoprecipitation
coupled to high-throughput sequencing (iCLIP) and mRNA
sequencing, we identified >200 AS-NMD splicing events that are
bound by Rbfox2 in mouse embryonic stem cells. These
``silent'' events are characterized by minimal apparent
splicing changes but appreciable changes in gene expression
upon Rbfox2 knockdown due to degradation of the NMD-inducing
isoform. Nearly 70 of these AS-NMD events fall within genes
encoding RNA-binding proteins, many of which are
autoregulated. As with the coding splicing events that we
found to be regulated by Rbfox2, silent splicing events are
evolutionarily conserved and frequently contain the Rbfox2
consensus UGCAUG. Our findings uncover an unexpectedly broad
and multilayer regulatory network controlled by Rbfox2 and
offer an explanation for how autoregulatory splicing networks
are tuned.",
journal = "Genes Dev.",
volume = 28,
number = 6,
pages = "637--651",
month = "15~" # mar,
year = 2014,
keywords = "RNA-binding protein; Rbfox; alternative splicing; embryonic
stem cell; iCLIP; nonsense-mediated decay",
language = "en"
}
@ARTICLE{Hao2011-sp,
title = "Signal-dependent dynamics of transcription factor
translocation controls gene expression",
author = "Hao, Nan and O'Shea, Erin K",
affiliation = "Howard Hughes Medical Institute, Harvard University,
Cambridge, Massachusetts, USA.",
abstract = "Information about environmental stimuli is often transmitted
using common signaling molecules, but the mechanisms that
ensure signaling specificity are not entirely known. Here we
show that the identities and intensities of different stresses
are transmitted by modulation of the amplitude, duration or
frequency of nuclear translocation of the Saccharomyces
cerevisiae general stress response transcription factor Msn2.
Through artificial control of the dynamics of Msn2
translocation, we reveal how distinct dynamical schemes
differentially affect reporter gene expression. Using a simple
model, we predict stress-induced reporter gene expression from
single-cell translocation dynamics. We then demonstrate that
the response of natural target genes to dynamical modulation
of Msn2 translocation is influenced by differences in the
kinetics of promoter transitions and transcription factor
binding properties. Thus, multiple environmental signals can
trigger qualitatively different dynamics of a single
transcription factor and influence gene expression patterns.",
journal = "Nat. Struct. Mol. Biol.",
volume = 19,
number = 1,
pages = "31--39",
month = "18~" # dec,
year = 2011,
language = "en"
}
@ARTICLE{Wilson2012-zv,
title = "The structure and function of the eukaryotic ribosome",
author = "Wilson, Daniel N and Doudna Cate, Jamie H",
affiliation = "Center for Integrated Protein Science Munich, Germany.
abstract = "Structures of the bacterial ribosome have provided a framework
for understanding universal mechanisms of protein synthesis.
However, the eukaryotic ribosome is much larger than it is in
bacteria, and its activity is fundamentally different in many
key ways. Recent cryo-electron microscopy reconstructions and
X-ray crystal structures of eukaryotic ribosomes and ribosomal
subunits now provide an unprecedented opportunity to explore
mechanisms of eukaryotic translation and its regulation in
atomic detail. This review describes the X-ray crystal
structures of the Tetrahymena thermophila 40S and 60S subunits
and the Saccharomyces cerevisiae 80S ribosome, as well as
cryo-electron microscopy reconstructions of translating yeast
and plant 80S ribosomes. Mechanistic questions about
translation in eukaryotes that will require additional
structural insights to be resolved are also presented.",
journal = "Cold Spring Harb. Perspect. Biol.",
volume = 4,
number = 5,
month = "1~" # may,
year = 2012,
language = "en"
}
@ARTICLE{Shi2015-fh,
title = "Translating the genome in time and space: specialized
ribosomes, {RNA} regulons, and {RNA-binding} proteins",
author = "Shi, Zhen and Barna, Maria",
affiliation = "Department of Developmental Biology and Department of
Genetics, Stanford University, Stanford, California 94305;
email: [email protected]. Department of Developmental
Biology and Department of Genetics, Stanford University,
Stanford, California 94305; email: [email protected].",
abstract = "A central question in cell and developmental biology is how
the information encoded in the genome is differentially
interpreted to generate a diverse array of cell types. A
growing body of research on posttranscriptional gene
regulation is revealing that both global protein synthesis
rates and the translation of specific mRNAs are highly
specialized in different cell types. How this exquisite
translational regulation is achieved is the focus of this
review. Two levels of regulation are discussed: the
translation machinery and cis-acting elements within mRNAs.
Recent evidence shows that the ribosome itself directs how the
genome is translated in time and space and reveals surprising
functional specificity in individual components of the core
translation machinery. We are also just beginning to
appreciate the rich regulatory information embedded in the
untranslated regions of mRNAs, which direct the selective
translation of transcripts. These hidden RNA regulons may
interface with a myriad of RNA-binding proteins and
specialized translation machinery to provide an additional
layer of regulation to how transcripts are spatiotemporally
expressed. Understanding this largely unexplored world of
translational codes hardwired in the core translation
machinery is an exciting new research frontier fundamental to
our understanding of gene regulation, organismal development,
and evolution.",
journal = "Annu. Rev. Cell Dev. Biol.",
publisher = "annualreviews.org",
volume = 31,
pages = "31--54",
month = "5~" # oct,
year = 2015,
keywords = "RNA regulons; RNA-binding proteins; ribosomal proteins;
ribosome-centered regulation; specialized translation
machinery",
language = "en"
}
@ARTICLE{Gott2000-gr,
title = "Functions and mechanisms of {RNA} editing",
author = "Gott, J M and Emeson, R B",
affiliation = "Center for RNA Molecular Biology, Department of Molecular
Biology and Microbiology, Case Western Reserve University,
Cleveland, Ohio 44106, USA. [email protected]",
abstract = "RNA editing can be broadly defined as any site-specific
alteration in an RNA sequence that could have been copied from
the template, excluding changes due to processes such as RNA
splicing and polyadenylation. Changes in gene expression
attributed to editing have been described in organisms from
unicellular protozoa to man, and can affect the mRNAs, tRNAs,
and rRNAs present in all cellular compartments. These sequence
revisions, which include both the insertion and deletion of
nucleotides, and the conversion of one base to another,
involve a wide range of largely unrelated mechanisms. Recent
advances in the development of in vitro editing and transgenic
systems for these varied modifications have provided a better
understanding of similarities and differences between the
biochemical strategies, regulatory sequences, and cellular
factors responsible for such RNA processing events.",
journal = "Annu. Rev. Genet.",
publisher = "annualreviews.org",
volume = 34,
pages = "499--531",
year = 2000,
language = "en"
}
@ARTICLE{Liu2012-pu,
title = "Imaging protein synthesis in cells and tissues with an alkyne
analog of puromycin",
author = "Liu, Jing and Xu, Yangqing and Stoleru, Dan and Salic, Adrian",
affiliation = "Department of Cell Biology, Harvard Medical School, 240
Longwood Avenue, Boston, MA 02115, USA.",
abstract = "Synthesis of many proteins is tightly controlled at the level
of translation, and plays an essential role in fundamental
processes such as cell growth and proliferation, signaling,
differentiation, or death. Methods that allow imaging and
identification of nascent proteins are critical for dissecting
regulation of translation, both spatially and temporally,
particularly in whole organisms. We introduce a simple and
robust chemical method to image and affinity-purify nascent
proteins in cells and in animals, based on an alkyne analog of
puromycin, O-propargyl-puromycin (OP-puro). OP-puro forms
covalent conjugates with nascent polypeptide chains, which are
rapidly turned over by the proteasome and can be visualized or
captured by copper(I)-catalyzed azide-alkyne cycloaddition.
Unlike methionine analogs, OP-puro does not require
methionine-free conditions and, uniquely, can be used to label
and assay nascent proteins in whole organisms. This strategy
should have broad applicability for imaging protein synthesis
and for identifying proteins synthesized under various
physiological and pathological conditions in vivo.",
journal = "Proc. Natl. Acad. Sci. U. S. A.",
volume = 109,
number = 2,
pages = "413--418",
month = "10~" # jan,
year = 2012,
language = "en"
}
@ARTICLE{Bianconi2013-jr,
title = "An estimation of the number of cells in the human body",
author = "Bianconi, Eva and Piovesan, Allison and Facchin, Federica and
Beraudi, Alina and Casadei, Raffaella and Frabetti, Flavia and
Vitale, Lorenza and Pelleri, Maria Chiara and Tassani, Simone
and Piva, Francesco and Perez-Amodio, Soledad and Strippoli,
Pierluigi and Canaider, Silvia",
affiliation = "Department of Experimental, Diagnostic and Specialty Medicine,
University of Bologna , Bologna , Italy .",
abstract = "BACKGROUND: All living organisms are made of individual and
identifiable cells, whose number, together with their size and
type, ultimately defines the structure and functions of an
organism. While the total cell number of lower organisms is
often known, it has not yet been defined in higher organisms.
In particular, the reported total cell number of a human being
ranges between 10(12) and 10(16) and it is widely mentioned
without a proper reference. AIM: To study and discuss the
theoretical issue of the total number of cells that compose
the standard human adult organism. SUBJECTS AND METHODS: A
systematic calculation of the total cell number of the whole
human body and of the single organs was carried out using
bibliographical and/or mathematical approaches. RESULTS: A
current estimation of human total cell number calculated for a
variety of organs and cell types is presented. These partial
data correspond to a total number of 3.72 $\times$ 10(13).
CONCLUSIONS: Knowing the total cell number of the human body
as well as of individual organs is important from a cultural,
biological, medical and comparative modelling point of view.
The presented cell count could be a starting point for a
common effort to complete the total calculation.",
journal = "Ann. Hum. Biol.",
volume = 40,
number = 6,
pages = "463--471",
month = nov,
year = 2013,
language = "en"
}
% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Flynn2016-am,
title = "Transcriptome-wide interrogation of {RNA} secondary structure
in living cells with {icSHAPE}",
author = "Flynn, Ryan A and Zhang, Qiangfeng Cliff and Spitale, Robert C
and Lee, Byron and Mumbach, Maxwell R and Chang, Howard Y",
affiliation = "Center for Personal Dynamic Regulomes, Stanford University
School of Medicine, Stanford, California, USA. Center for
Personal Dynamic Regulomes, Stanford University School of
Medicine, Stanford, California, USA. Center for Personal
Dynamic Regulomes, Stanford University School of Medicine,
Stanford, California, USA. Center for Personal Dynamic
Regulomes, Stanford University School of Medicine, Stanford,
California, USA. Center for Personal Dynamic Regulomes,
Stanford University School of Medicine, Stanford, California,
USA. Center for Personal Dynamic Regulomes, Stanford
University School of Medicine, Stanford, California, USA.",
abstract = "icSHAPE (in vivo click selective 2-hydroxyl acylation and
profiling experiment) captures RNA secondary structure at a
transcriptome-wide level by measuring nucleotide flexibility
at base resolution. Living cells are treated with the icSHAPE
chemical NAI-N3 followed by selective chemical enrichment of
NAI-N3-modified RNA, which provides an improved
signal-to-noise ratio compared with similar methods leveraging
deep sequencing. Purified RNA is then reverse-transcribed to
produce cDNA, with SHAPE-modified bases leading to truncated
cDNA. After deep sequencing of cDNA, computational analysis
yields flexibility scores for every base across the starting
RNA population. The entire experimental procedure can be
completed in ∼5 d, and the sequencing and bioinformatics data
analysis take an additional 4-5 d with no extensive
computational skills required. Comparing in vivo and in vitro
icSHAPE measurements can reveal in vivo RNA-binding protein
imprints or facilitate the dissection of RNA
post-transcriptional modifications. icSHAPE reactivities can
additionally be used to constrain and improve RNA secondary
structure prediction models.",
journal = "Nat. Protoc.",
volume = 11,
number = 2,
pages = "273--290",
month = feb,
year = 2016,
language = "en"
}
@ARTICLE{Ocone2015-zy,
title = "Reconstructing gene regulatory dynamics from high-dimensional
single-cell snapshot data",
author = "Ocone, Andrea and Haghverdi, Laleh and Mueller, Nikola S and
Theis, Fabian J",
affiliation = "Institute of Computational Biology, Helmholtz Zentrum
M{\"u}nchen, 85764 Neuherberg, Germany and Department of
Mathematics, Technical University Munich, 85747 Garching,
Germany. Institute of Computational Biology, Helmholtz Zentrum
M{\"u}nchen, 85764 Neuherberg, Germany and Department of
Mathematics, Technical University Munich, 85747 Garching,
Germany. Institute of Computational Biology, Helmholtz Zentrum
M{\"u}nchen, 85764 Neuherberg, Germany and Department of
Mathematics, Technical University Munich, 85747 Garching,
Germany. Institute of Computational Biology, Helmholtz Zentrum
M{\"u}nchen, 85764 Neuherberg, Germany and Department of
Mathematics, Technical University Munich, 85747 Garching,
Germany Institute of Computational Biology, Helmholtz Zentrum
M{\"u}nchen, 85764 Neuherberg, Germany and Department of
Mathematics, Technical University Munich, 85747 Garching,
Germany.",
abstract = "MOTIVATION: High-dimensional single-cell snapshot data are
becoming widespread in the systems biology community, as a
mean to understand biological processes at the cellular level.
However, as temporal information is lost with such data,
mathematical models have been limited to capture only static
features of the underlying cellular mechanisms. RESULTS: Here,
we present a modular framework which allows to recover the
temporal behaviour from single-cell snapshot data and reverse
engineer the dynamics of gene expression. The framework
combines a dimensionality reduction method with a cell
time-ordering algorithm to generate pseudo time-series
observations. These are in turn used to learn transcriptional
ODE models and do model selection on structural network
features. We apply it on synthetic data and then on real
hematopoietic stem cells data, to reconstruct gene expression
dynamics during differentiation pathways and infer the
structure of a key gene regulatory network. AVAILABILITY AND
IMPLEMENTATION: C++ and Matlab code available at
https://www.helmholtz-muenchen.de/fileadmin/ICB/software/inferenceSnapshot.zip.",
journal = "Bioinformatics",
volume = 31,
number = 12,
pages = "i89--96",
month = "15~" # jun,
year = 2015,
language = "en"
}
@ARTICLE{Arya2014-po,
title = "{RBFOX2} protein domains and cellular activities",
author = "Arya, Anurada D and Wilson, David I and Baralle, Diana and
Raponi, Michaela",
affiliation = "*Human Development and Health Academic Unit, Faculty of
Medicine, University of Southampton, Institute of
Developmental Sciences Building, Southampton General Hospital,
Tremona Road, Southampton SO16 6YD, U.K. *Human Development
and Health Academic Unit, Faculty of Medicine, University of
Southampton, Institute of Developmental Sciences Building,
Southampton General Hospital, Tremona Road, Southampton SO16
6YD, U.K. *Human Development and Health Academic Unit, Faculty
of Medicine, University of Southampton, Institute of
Developmental Sciences Building, Southampton General Hospital,
Tremona Road, Southampton SO16 6YD, U.K. *Human Development
and Health Academic Unit, Faculty of Medicine, University of
Southampton, Institute of Developmental Sciences Building,
Southampton General Hospital, Tremona Road, Southampton SO16
6YD, U.K.",
abstract = "RBFOX2 (RNA-binding protein, Fox-1 homologue 2)/RBM9
(RNA-binding-motif protein 9)/RTA (repressor of tamoxifen
action)/HNRBP2 (hexaribonucleotide-binding protein 2) encodes
an RNA-binding protein involved in tissue specific alternative
splicing regulation and steroid receptors transcriptional
activity. Its ability to regulate specific splicing profiles
depending on context has been related to different expression
levels of the RBFOX2 protein itself and that of other splicing
regulatory proteins involved in the shared modulation of
specific genes splicing. However, this cannot be the sole
explanation as to why RBFOX2 plays a widespread role in
numerous cellular mechanisms from development to cell survival
dependent on cell/tissue type. RBFOX2 isoforms with altered
protein domains exist. In the present article, we describe the
main RBFOX2 protein domains, their importance in the context
of splicing and transcriptional regulation and we propose that
RBFOX2 isoform distribution may play a fundamental role in
RBFOX2-specific cellular effects.",
journal = "Biochem. Soc. Trans.",
volume = 42,
number = 4,
pages = "1180--1183",
month = aug,
year = 2014,
language = "en"
}
@ARTICLE{Buszczak2014-yq,
title = "Cellular differences in protein synthesis regulate tissue
homeostasis",
author = "Buszczak, Michael and Signer, Robert A J and Morrison, Sean J",
affiliation = "Department of Molecular Biology, Children's Research
Institute, Department of Pediatrics, University of Texas
Southwestern Medical Center, Dallas, TX 75390, USA. Howard
Hughes Medical Institute, Children's Research Institute,
Department of Pediatrics, University of Texas Southwestern
Medical Center, Dallas, TX 75390, USA. Howard Hughes Medical
Institute, Children's Research Institute, Department of
Pediatrics, University of Texas Southwestern Medical Center,
Dallas, TX 75390, USA. Electronic address:
abstract = "Although sometimes considered a ``house-keeping'' function,
multiple aspects of protein synthesis are regulated
differently among somatic cells, including stem cells, and can
be modulated in a cell-type-specific manner. These differences
are required to establish and maintain differences in cell
identity, cell function, tissue homeostasis, and tumor
suppression.",
journal = "Cell",
volume = 159,
number = 2,
pages = "242--251",
month = "9~" # oct,
year = 2014,
language = "en"
}
@ARTICLE{Knie2016-km,
title = "Reverse {U-to-C} editing exceeds {C-to-U} {RNA} editing in some
ferns -- a monilophyte-wide comparison of chloroplast and
mitochondrial {RNA} editing suggests independent evolution of the
two processes in both organelles",
author = "Knie, Nils and Grewe, Felix and Fischer, Simon and Knoop, Volker",
abstract = "RNA editing by C-to-U conversions is nearly omnipresent in land
plant chloroplasts and mitochondria, where it mainly serves to
reconstitute conserved codon identities in the organelle mRNAs.
Reverse U-to-C RNA editing in contrast appears to be restricted
to hornworts, some lycophytes, and ferns (monilophytes). A
well-resolved monilophyte phylogeny has recently emerged and now
allows to trace the side-by-side evolution of both types of
pyrimidine exchange editing in the two endosymbiotic organelles.",
journal = "BMC Evol. Biol.",
volume = 16,
number = 1,
pages = "134",
year = 2016
}
@UNPUBLISHED{Garalde2016-iw,
title = "Highly parallel direct {RNA} sequencing on an array of nanopores",
author = "Garalde, Daniel R and Snell, Elizabeth A and Jachimowicz, Daniel
and Heron, Andrew J and Bruce, Mark and Lloyd, Joseph and
Warland, Anthony and Pantic, Nadia and Admassu, Tigist and
Ciccone, Jonah and Serra, Sabrina and Keenan, Jemma and Martin,
Samuel and McNeill, Luke and Wallace, Jayne and Jayasinghe,
Lakmal and Wright, Chris and Blasco, Javier and Sipos, Botond and
Young, Stephen and Juul, Sissel and Clarke, James and Turner,
Daniel J",
abstract = "Ribonucleic acid sequencing can allow us to monitor the RNAs
present in a sample. This enables us to detect the presence and
nucleotide sequence of viruses, or to build a picture of how
active transcriptional processes are changing -- information that
is useful for understanding the status and function of a sample.
Nanopore-based sequencing technology is capable of electronically
analysing a sample's DNA directly, and in real-time. In this
manuscript we demonstrate the ability of an array of nanopores to
sequence RNA directly, and we apply it to a range of biological
situations. Nanopore technology is the only available sequencing
technology which can sequence RNA directly, rather than depending
on reverse transcription and PCR. There are several potential
advantages of this approach over other RNA-seq strategies,
including the absence of amplification and reverse transcription
biases, the ability to detect nucleotide analogues and the
ability to generate full-length, strand-specific RNA sequences.
This will improve the ease and speed of RNA analysis, while
yielding richer biological information.",
journal = "bioRxiv",
pages = "068809",
month = "12~" # aug,
year = 2016,
language = "en"
}
@ARTICLE{Kim2016-hn,
title = "Filling the Void: {Proximity-Based} Labeling of Proteins in
Living Cells",
author = "Kim, Dae In and Roux, Kyle J",
affiliation = "Sanford Children's Health Research Center, Sanford Research,
Sioux Falls, SD 57104, USA. Sanford Children's Health Research
Center, Sanford Research, Sioux Falls, SD 57104, USA;
Department of Pediatrics, Sanford School of Medicine,
University of South Dakota, Sioux Falls, SD 57105, USA.
Electronic address: [email protected].",
abstract = "There are inherent limitations with traditional methods to
study protein behavior or to determine the constituency of
proteins in discrete subcellular compartments. In response to
these limitations, several methods have recently been
developed that use proximity-dependent labeling. By fusing
proteins to enzymes that generate reactive molecules, most
commonly biotin, proximate proteins are covalently labeled to
enable their isolation and identification. In this review we
describe current methods for proximity-dependent labeling in
living cells and discuss their applications and future use in
the study of protein behavior.",
journal = "Trends Cell Biol.",
volume = 26,
number = 11,
pages = "804--817",
month = nov,
year = 2016,
keywords = "APEX; BioID; protein--protein interactions; proteomics;
proximity-dependent labeling; subcellular proteome",
language = "en"
}
@ARTICLE{Ellis1986-oz,
title = "Genetic control of programmed cell death in the nematode C.
elegans",
author = "Ellis, H M and Horvitz, H R",
abstract = "The wild-type functions of the genes ced-3 and ced-4 are required
for the initiation of programmed cell deaths in the nematode
Caenorhabditis elegans. The reduction or loss of ced-3 or ced-4
function results in a transformation in the fates of cells that
normally die; in ced-3 or ced-4 mutants, such cells instead
survive and differentiate, adopting fates that in the wild type
and associated with other cells. ced-3 and ced-4 mutants appear
grossly normal in morphology and behavior, indicating that
programmed cell death is not an essential aspect of nematode
development. The genes ced-3 and ced-4 define the first known
step of a developmental pathway for programmed cell death,
suggesting that these genes may be involved in determining which
cells die during C. elegans development.",
journal = "Cell",
volume = 44,
number = 6,
pages = "817--829",
month = "28~" # mar,
year = 1986,
language = "en"
}
% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Huppertz2014-jt,
title = "{iCLIP}: {Protein--RNA} interactions at nucleotide resolution",
author = "Huppertz, Ina and Attig, Jan and D’Ambrogio, Andrea and Easton,
Laura E and Sibley, Christopher R and Sugimoto, Yoichiro and
Tajnik, Mojca and K{\"o}nig, Julian and Ule, Jernej",
abstract = "Abstract RNA-binding proteins (RBPs) are key players in the
post-transcriptional regulation of gene expression. Precise
knowledge about their binding sites is therefore critical to
unravel their molecular function and to understand their role in
development and disease. Individual-nucleotide resolution UV
crosslinking and immunoprecipitation (iCLIP) identifies
protein--RNA crosslink sites on a genome-wide scale. The high
resolution and specificity of this method are achieved by an
intramolecular cDNA circularization step that enables analysis of
cDNAs that truncated at the protein--RNA crosslink sites. Here,
we describe the improved iCLIP protocol and discuss critical
optimization and control experiments that are required when
applying the method to new RBPs.",
journal = "Methods",
volume = 65,
number = 3,
pages = "274--287",
year = 2014,
keywords = "iCLIP; UV crosslinking and immunoprecipitation (CLIP);
Protein--RNA interaction; High-throughput sequencing; RNA-binding
protein; RNA; Post-transcriptional regulation"
}
@ARTICLE{Kaufmann2007-nh,
title = "Stochastic gene expression: from single molecules to the
proteome",
author = "Kaufmann, Benjamin B and van Oudenaarden, Alexander",
affiliation = "Department of Physics, Massachusetts Institute of Technology,
Cambridge, MA 02139, USA.",
abstract = "Protein production involves a series of stochastic chemical
steps. One consequence of this fact is that the copy number of
any given protein varies substantially from cell to cell, even
within isogenic populations. Recent experiments have measured
this variation for thousands of different proteins, revealing
a linear relationship between variance and mean level of
expression for much of the proteome. This simple relationship
is frequently thought to arise from the random production and
degradation of mRNAs, but several lines of evidence suggest
that infrequent gene activation events also bear
responsibility. In support of the latter hypothesis,
single-molecule experiments have demonstrated that mRNA
transcripts are often produced in large bursts. Moreover, the
temporal pattern of these bursts appears to be correlated for
chromosomally proximal genes, suggesting the existence of an
upstream player.",
journal = "Curr. Opin. Genet. Dev.",
publisher = "Elsevier",
volume = 17,
number = 2,
pages = "107--112",
month = apr,
year = 2007,
language = "en"
}
@ARTICLE{Kleinman2012-td,
title = "{RNA} editing of protein sequences: A rare event in human
transcriptomes",
author = "Kleinman, C L and {Adoue, V} and Majewski, J",
journal = "RNA",
volume = 18,
number = 9,
pages = "1586--1596",
year = 2012
}
@ARTICLE{Gal2011-mg,
title = "Nuclear localization sequence of {FUS} and induction of stress
granules by {ALS} mutants",
author = "Gal, Jozsef and Zhang, Jiayu and Kwinter, David M and Zhai,
Jianjun and Jia, Hongge and Jia, Jianhang and Zhu, Haining",
affiliation = "Department of Molecular and Cellular Biochemistry, College of
Medicine, University of Kentucky, Lexington, KY 40536, USA.",
abstract = "Mutations in fused in sarcoma (FUS) have been reported to
cause a subset of familial amyotrophic lateral sclerosis (ALS)
cases. Wild-type FUS is mostly localized in the nuclei of
neurons, but the ALS mutants are partly mislocalized in the
cytoplasm and can form inclusions. We demonstrate that the
C-terminal 32 amino acid residues of FUS constitute an
effective nuclear localization sequence (NLS) as it targeted
beta-galactosidase (LacZ, 116 kDa) to the nucleus. Deletion of
or the ALS mutations within the NLS caused cytoplasmic
mislocalization of FUS. Moreover, we identified the poly-A
binding protein (PABP1), a stress granule marker, as an
interacting partner of FUS. Large PABP1-positive cytoplasmic
foci (i.e. stress granules) colocalized with the mutant FUS
inclusions but were absent in wild-type FUS-expressing cells.
Processing bodies, which are functionally related to stress
granules, were adjacent to but not colocalized with the mutant
FUS inclusions. Our results suggest that the ALS mutations in
FUS NLS can impair FUS nuclear localization, induce
cytoplasmic inclusions and stress granules, and potentially
perturb RNA metabolism.",
journal = "Neurobiol. Aging",
volume = 32,
number = 12,
pages = "2323.e27--40",
month = dec,
year = 2011,
language = "en"
}
@ARTICLE{Siddiqui2012-mv,
title = "{mRNA} export and cancer",
author = "Siddiqui, Nadeem and Borden, Katherine L B",
affiliation = "Institute for Research in Immunology and Cancer,
Universit{\'e} de Montr{\'e}al, Montr{\'e}al, Quebec, Canada.",
abstract = "Studies in the past several years highlight important features
of the messenger RNA (mRNA) export process. For instance,
groups of mRNAs acting in the same biochemical processes can
be retained or exported in a coordinated manner thereby
impacting on specific biochemistries and ultimately on cell
physiology. mRNAs can be transported by either bulk export
pathways involving NXF1/TAP or more specialized pathways
involving chromosome region maintenance 1 (CRM1). Studies on
primary tumor specimens indicate that many common and
specialized mRNA export factors are dysregulated in cancer
including CRM1, eukaryotic translation initiation factor 4E
(eIF4E), HuR, nucleoporin 88, REF/Aly, and THO. This positions
these pathways as potential therapeutic targets. Recently,
specific targeting of the eIF4E-dependent mRNA export pathway
in a phase II proof-of-principle trial with ribavirin led to
impaired eIF4E-dependent mRNA export correlating with clinical
responses including remissions in leukemia patients. Here, we
provide an overview of these mRNA export pathways and
highlight their relationship to cancer.",
journal = "Wiley Interdiscip. Rev. RNA",
volume = 3,
number = 1,
pages = "13--25",
month = jan,
year = 2012,
language = "en"
}
@ARTICLE{Lee2015-fj,
title = "Fluorescent in situ sequencing ({FISSEQ}) of {RNA} for gene
expression profiling in intact cells and tissues",
author = "Lee, Je Hyuk and Daugharthy, Evan R and Scheiman, Jonathan and
Kalhor, Reza and Ferrante, Thomas C and Terry, Richard and
Turczyk, Brian M and Yang, Joyce L and Lee, Ho Suk and Aach,
John and Zhang, Kun and Church, George M",
affiliation = "Wyss Institute, Harvard Medical School, Boston, Massachusetts,
USA. 1] Wyss Institute, Harvard Medical School, Boston,
Massachusetts, USA. [2] Department of Genetics, Harvard
Medical School, Boston, Massachusetts, USA. [3] Department of
Systems Biology, Harvard Medical School, Boston,
Massachusetts, USA. 1] Wyss Institute, Harvard Medical School,
Boston, Massachusetts, USA. [2] Department of Genetics,
Harvard Medical School, Boston, Massachusetts, USA. Department
of Genetics, Harvard Medical School, Boston, Massachusetts,
USA. Wyss Institute, Harvard Medical School, Boston,
Massachusetts, USA. Wyss Institute, Harvard Medical School,
Boston, Massachusetts, USA. Wyss Institute, Harvard Medical
School, Boston, Massachusetts, USA. Department of Genetics,
Harvard Medical School, Boston, Massachusetts, USA. Department
of Electrical and Computer Engineering, University of
California San Diego, California, USA. Department of Genetics,
Harvard Medical School, Boston, Massachusetts, USA. Department
of Bioengineering, University of California San Diego, La
Jolla, California, USA. 1] Wyss Institute, Harvard Medical
School, Boston, Massachusetts, USA. [2] Department of
Genetics, Harvard Medical School, Boston, Massachusetts, USA.",
abstract = "RNA-sequencing (RNA-seq) measures the quantitative change in
gene expression over the whole transcriptome, but it lacks
spatial context. In contrast, in situ hybridization provides
the location of gene expression, but only for a small number
of genes. Here we detail a protocol for genome-wide profiling
of gene expression in situ in fixed cells and tissues, in
which RNA is converted into cross-linked cDNA amplicons and
sequenced manually on a confocal microscope. Unlike
traditional RNA-seq, our method enriches for context-specific
transcripts over housekeeping and/or structural RNA, and it
preserves the tissue architecture for RNA localization
studies. Our protocol is written for researchers experienced
in cell microscopy with minimal computing skills. Library
construction and sequencing can be completed within 14 d, with
image analysis requiring an additional 2 d.",
journal = "Nat. Protoc.",
publisher = "nature.com",
volume = 10,
number = 3,
pages = "442--458",
month = mar,
year = 2015,
language = "en"
}