9,910 research outputs found
Induction of microRNAs, mir-155, mir-222, mir-424 and mir-503, promotes monocytic differentiation through combinatorial regulation
Acute myeloid leukemia (AML) involves a block in terminal differentiation of
the myeloid lineage and uncontrolled proliferation of a progenitor state. Using
phorbol myristate acetate (PMA), it is possible to overcome this block in THP-1
cells (an M5-AML containing the MLL-MLLT3 fusion), resulting in differentiation
to an adherent monocytic phenotype. As part of FANTOM4, we used microarrays to
identify 23 microRNAs that are regulated by PMA. We identify four PMA-induced
micro- RNAs (mir-155, mir-222, mir-424 and mir-503) that when overexpressed
cause cell-cycle arrest and partial differentiation and when used in
combination induce additional changes not seen by any individual microRNA. We
further characterize these prodifferentiative microRNAs and show that mir-155
and mir-222 induce G2 arrest and apoptosis, respectively. We find mir-424 and
mir-503 are derived from a polycistronic precursor mir-424-503 that is under
repression by the MLL-MLLT3 leukemogenic fusion. Both of these microRNAs
directly target cell-cycle regulators and induce G1 cell-cycle arrest when
overexpressed in THP-1. We also find that the pro-differentiative mir-424 and
mir-503 downregulate the anti-differentiative mir-9 by targeting a site in its
primary transcript. Our study highlights the combinatorial effects of multiple
microRNAs within cellular systems.Comment: 45 pages 5 figure
Mechanisms underlying the exquisite sensitivity of Candida albicans to combinatorial cationic and oxidative stress that enhances the potent fungicidal activity of phagocytes
Copyright © 2014 Kaloriti et al.Peer reviewedPublisher PD
Transcriptional Regulation: a Genomic Overview
The availability of the Arabidopsis thaliana genome sequence allows a comprehensive analysis of transcriptional regulation in plants using novel genomic approaches and methodologies. Such a genomic view of transcription first necessitates the compilation of lists of elements. Transcription factors are the most numerous of the different types of proteins involved in transcription in eukaryotes, and the Arabidopsis genome codes for more than 1,500 of them, or approximately 6% of its total number of genes. A genome-wide comparison of transcription factors across the three eukaryotic kingdoms reveals the evolutionary generation of diversity in the components of the regulatory machinery of transcription. However, as illustrated by Arabidopsis, transcription in plants follows similar basic principles and logic to those in animals and fungi. A global view and understanding of transcription at a cellular and organismal level requires the characterization of the Arabidopsis transcriptome and promoterome, as well as of the interactome, the localizome, and the phenome of the proteins involved in transcription
Algebraic Comparison of Partial Lists in Bioinformatics
The outcome of a functional genomics pipeline is usually a partial list of
genomic features, ranked by their relevance in modelling biological phenotype
in terms of a classification or regression model. Due to resampling protocols
or just within a meta-analysis comparison, instead of one list it is often the
case that sets of alternative feature lists (possibly of different lengths) are
obtained. Here we introduce a method, based on the algebraic theory of
symmetric groups, for studying the variability between lists ("list stability")
in the case of lists of unequal length. We provide algorithms evaluating
stability for lists embedded in the full feature set or just limited to the
features occurring in the partial lists. The method is demonstrated first on
synthetic data in a gene filtering task and then for finding gene profiles on a
recent prostate cancer dataset
How to understand the cell by breaking it: network analysis of gene perturbation screens
Modern high-throughput gene perturbation screens are key technologies at the
forefront of genetic research. Combined with rich phenotypic descriptors they
enable researchers to observe detailed cellular reactions to experimental
perturbations on a genome-wide scale. This review surveys the current
state-of-the-art in analyzing perturbation screens from a network point of
view. We describe approaches to make the step from the parts list to the wiring
diagram by using phenotypes for network inference and integrating them with
complementary data sources. The first part of the review describes methods to
analyze one- or low-dimensional phenotypes like viability or reporter activity;
the second part concentrates on high-dimensional phenotypes showing global
changes in cell morphology, transcriptome or proteome.Comment: Review based on ISMB 2009 tutorial; after two rounds of revisio
Biases in the Experimental Annotations of Protein Function and their Effect on Our Understanding of Protein Function Space
The ongoing functional annotation of proteins relies upon the work of
curators to capture experimental findings from scientific literature and apply
them to protein sequence and structure data. However, with the increasing use
of high-throughput experimental assays, a small number of experimental studies
dominate the functional protein annotations collected in databases. Here we
investigate just how prevalent is the "few articles -- many proteins"
phenomenon. We examine the experimentally validated annotation of proteins
provided by several groups in the GO Consortium, and show that the distribution
of proteins per published study is exponential, with 0.14% of articles
providing the source of annotations for 25% of the proteins in the UniProt-GOA
compilation. Since each of the dominant articles describes the use of an assay
that can find only one function or a small group of functions, this leads to
substantial biases in what we know about the function of many proteins.
Mass-spectrometry, microscopy and RNAi experiments dominate high throughput
experiments. Consequently, the functional information derived from these
experiments is mostly of the subcellular location of proteins, and of the
participation of proteins in embryonic developmental pathways. For some
organisms, the information provided by different studies overlap by a large
amount. We also show that the information provided by high throughput
experiments is less specific than those provided by low throughput experiments.
Given the experimental techniques available, certain biases in protein function
annotation due to high-throughput experiments are unavoidable. Knowing that
these biases exist and understanding their characteristics and extent is
important for database curators, developers of function annotation programs,
and anyone who uses protein function annotation data to plan experiments.Comment: Accepted to PLoS Computational Biology. Press embargo applies. v4:
text corrected for style and supplementary material inserte
An Integrated Strategy for Analyzing the Unique Developmental Programs of Different Myoblast Subtypes
An important but largely unmet challenge in understanding the mechanisms that govern the formation of specific organs is to decipher the complex and dynamic genetic programs exhibited by the diversity of cell types within the tissue of interest. Here, we use an integrated genetic, genomic, and computational strategy to comprehensively determine the molecular identities of distinct myoblast subpopulations within the Drosophila embryonic mesoderm at the time that cell fates are initially specified. A compendium of gene expression profiles was generated for primary mesodermal cells purified by flow cytometry from appropriately staged wild-type embryos and from 12 genotypes in which myogenesis was selectively and predictably perturbed. A statistical meta-analysis of these pooled datasets—based on expected trends in gene expression and on the relative contribution of each genotype to the detection of known muscle genes—provisionally assigned hundreds of differentially expressed genes to particular myoblast subtypes. Whole embryo in situ hybridizations were then used to validate the majority of these predictions, thereby enabling true-positive detection rates to be estimated for the microarray data. This combined analysis reveals that myoblasts exhibit much greater gene expression heterogeneity and overall complexity than was previously appreciated. Moreover, it implicates the involvement of large numbers of uncharacterized, differentially expressed genes in myogenic specification and subsequent morphogenesis. These findings also underscore a requirement for considerable regulatory specificity for generating diverse myoblast identities. Finally, to illustrate how the developmental functions of newly identified myoblast genes can be efficiently surveyed, a rapid RNA interference assay that can be scored in living embryos was developed and applied to selected genes. This integrated strategy for examining embryonic gene expression and function provides a substantially expanded framework for further studies of this model developmental system
Combinatorial stress response of the fungal pathogen Candida glabrata
Candida glabrata is an opportunistic human fungal pathogen, with an increasing incidence of infection, as well as an innate resistance to antifungal drug therapies. It is more closely related to the model and non-pathogenic yeast, Saccharomyces cerevisiae, than other Candida spp. Previous studies have only focused on the response to independent stressors therefore little is known about the adaptive response to simultaneous stresses, even though this is likely to be more relevant in an ecological and pathophysiological setting e.g. upon macrophage engulfment. This study was conducted with the hypothesis that the response of C. glabrata to stressors applied simultaneously could not be explained by simply combining the response to single stresses. To investigate this hypothesis, the response of C. glabrata to hyperosmotic and oxidative stressors applied singly and in combination were examined by timecourse microarray analysis and functional genomics.
While genes involved in a HOG-like (High Osmolarity Glycerol) response were regulated by C. glabrata under hyperosmotic stress, many homologous genes are not observed to be regulated by S. cerevisiae. The phenotypes displayed by null mutants of the HOG pathway implicate this MAPK signalling pathway in not only hyperosmotic stress, but also cell wall integrity and metal ion resistance. Microarray analysis revealed a prolonged transcriptional regulation over time with increasing concentration of oxidative stress and other genes with a similar pattern of expression were identified and studied. Transcript profiling of a strain lacking the key oxidative stress regulator Yap1, along with bioinformatic analysis of its binding sites, identified possible targets of this transcription factor in C. glabrata under oxidative stress. This study has identified differentially regulated transcript profiles unique to simultaneous stress and not seen under single stress conditions, indicating that a specific transcriptional response is required for C. glabrata to respond and adapt to combinatorial stress; it is not simply the addition of two individual responses. Comparisons of the transcriptional analysis presented here with that of published macrophage engulfed C. glabrata cells revealed that combinatorial stress elicits a similar response as the host environment.
Combining functional genomics and transcript profiling under stress has allowed the identification and characterisation of genes involved in stress response as well as the construction of diagrams specific to the response of C. glabrata to stress
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