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  • 1
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 16, No. 5 ( 2006-05), p. 656-668
    Abstract: The identification of regulatory regions is one of the most important and challenging problems toward the functional annotation of the human genome. In higher eukaryotes, transcription-factor (TF) binding sites are often organized in clusters called cis -regulatory modules (CRM). While the prediction of individual TF-binding sites is a notoriously difficult problem, CRM prediction has proven to be somewhat more reliable. Starting from a set of predicted binding sites for more than 200 TF families documented in Transfac, we describe an algorithm relying on the principle that CRMs generally contain several phylogenetically conserved binding sites for a few different TFs. The method allows the prediction of more than 118,000 CRMs within the human genome. A subset of these is shown to be bound in vivo by TFs using ChIP-chip. Their analysis reveals, among other things, that CRM density varies widely across the genome, with CRM-rich regions often being located near genes encoding transcription factors involved in development. Predicted CRMs show a surprising enrichment near the 3′ end of genes and in regions far from genes. We document the tendency for certain TFs to bind modules located in specific regions with respect to their target genes and identify TFs likely to be involved in tissue-specific regulation. The set of predicted CRMs, which is made available as a public database called PReMod (http://genomequebec.mcgill.ca/PReMod), will help analyze regulatory mechanisms in specific biological systems.
    Type of Medium: Online Resource
    ISSN: 1088-9051
    RVK:
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2006
    detail.hit.zdb_id: 1483456-X
    SSG: 12
    Location Call Number Limitation Availability
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  • 2
    In: Genes & Development, Cold Spring Harbor Laboratory, Vol. 21, No. 15 ( 2007-08-01), p. 1909-1920
    Abstract: Macrophage activation by the proinflammatory cytokine interferon-γ (IFN-γ) is a critical component of the host innate response to bacterial pathogenesis. However, the precise nature of the IFN-γ-induced activation pathway is not known. Here we show using genome-wide expression and chromatin-binding profiling that IFN-γ induces the expression of many nuclear genes encoding mitochondrial respiratory chain machinery via activation of the nuclear receptor ERRα (estrogen-related receptor α, NR3B1). Studies with macrophages lacking ERRα demonstrate that it is required for induction of mitochondrial reactive oxygen species (ROS) production and efficient clearance of Listeria monocytogenes (LM) in response to IFN-γ. As a result, mice lacking ERRα are susceptible to LM infection, a phenotype that is localized to bone marrow-derived cells. Furthermore, we found that IFN-γ-induced activation of ERRα depends on coactivator PGC-1β (peroxisome proliferator-activated receptor γ coactivator-1β), which appears to be a direct target for the IFN-γ/STAT-1 signaling cascade. Thus, ERRα and PGC-1β act together as a key effector of IFN-γ-induced mitochondrial ROS production and host defense.
    Type of Medium: Online Resource
    ISSN: 0890-9369 , 1549-5477
    RVK:
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2007
    detail.hit.zdb_id: 1467414-2
    SSG: 12
    Location Call Number Limitation Availability
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