1,720,976 research outputs found
bHLH and bHLH-LZ factor exchange at promoters
Get PDFMammalian promoters often contain DNA-elements that can be bound by a number of closely related transcription factors (TFs) that cannot bind to the same DNA-element simultaneously. It is possible that each TF responds to distinct cues, allowing the gene to be activated in response to multiple stimuli. An alternative possibility is that each TF binds sequentially, each contributing to the pre-initiation events leading up to transcription. Here, we explore the exchange of basic-Helix-Loop-Helix-Leucine-Zipper (bHLH-LZ) factors, USF1, USF2 and MITF at the TYROSINASE promoter following induction by UVB-irradiation and methotrexate-administration. We demonstrate, for the first time in human melanoma, differential induction kinetics of TYROSINASE gene in response to an initial or re-induction, a phenomenon akin to "transcription memory" previously described in yeast. We also show that USF2, specifically detected by two different antibodies targeting the N-terminal region, is largely cytoplasmic, at least in the cell lines we have investigated. We also showed that nucleo-cytoplasmic shuttling of these USF2 species is partly regulated by glucose. Using deletion mutants, we demonstrated the requirement of the amino-acids surrounding the USF-specific region and the basic domain in nuclear localisation of USF2, and that amino-acids 1−193 appear to enhance dimerization of USF2 in addition to the classical HLH-LZ dimerization domain. We will further investigate the role(s) played by MYC, MITF, HIF and USF exchange at common targets (which we identified through our ChIP-seq analysis) in gene activation and the effect on the (re)activation potential of these genes when DNA-binding by one or more of these factors are abolished, as well as when the promoter is monopolised by one of these factors through overexpression using cell lines expressing one of the bHLH-TFs under a tet-inducible promoter. In the long run, we aim to understand the potential differences in the role(s) of each bHLH-factors co-occupying E-box elements
Post-translational regulation of TFEB/3 activity
Get PDFThe ability of cells to sense and adapt to changes in their environment is critical for their survival. Cancer cells acquire the ability to promote cell growth and proliferation independently of growth factors, whilst retaining the ability to sense and adapt to changes in nutrient availability. During tumorigenesis, poor vascularisation results in the promotion of catabolic processes, such as autophagy. Transcription factor EB (TFEB), a member of the microphthalmia/transcription factor E (MiT/TFE) family has been coined as the master regulator of autophagy and lysosomal biogenesis. In response to nutrient deprivation, TFEB is dephosphorylated and rapidly accumulates in the nucleus to promote expression of the CLEAR network. In tumours that exhibit high levels of TFEB/3-dependent autophagy, TFEB is constitutively nuclear and hyperactivated, contributing to cancer pathogenesis. Conversely, in neurodegenerative diseases, such as Alzheimer’s disease, lysosomal function and autophagy are often impaired. Over-expression or activation of TFEB can ameliorate disease pathogenesis through promoting intracellular clearance. In this study, we show that TFEB accumulates in the nucleus in response to both amino acid and glucose depletion which is readily reversed upon nutrient replenishment. Furthermore, glucose deprivation does not inhibit mTORC1 but instead, activates the mTORC2-AKT signalling pathway. We demonstrated that GSK3β can phosphorylate TFEB/MITF on Ser138/Ser69 but only when Ser142/Ser73 is first phosphorylated by ERK2 or mTORC1, highlighting that this dual phosphorylation event is required for nuclear export of TFEB. Additionally, we performed two reciprocal, high-throughput image-based screens to explore the regulatory mechanisms which govern TFEB subcellular localisation. The first screen allowed us to identify 50 FDA-approved drugs that could promote nuclear accumulation of TFEB as well as increase lysosomal staining. We identified pimozide as a potential candidate for drug re-purposing for neurodegenerative diseases as it displayed neuroprotection in cell-based models of neurodegenerative disease. The second screen identified 10 kinase inhibitors from the PKISI/II library (GSK) that may have cancer therapeutic potential, being able to attenuate nuclear accumulation of TFEB in response to glucose and/or amino acid deprivation. GW869516X was able to partially rescue mTORC1 activity whilst inhibiting mTORC2 signalling in response to amino acid and glucose starvation respectively. Additionally, GW869516X inhibited AMPK signalling and can directly bind to AMPK. Overall, this work contributes to our understanding of how TFEB activity is regulated through dynamic phosphorylation events. The results obtained from our screens provide a reservoir of drugs that can modulate TFEB subcellular localisation, warranting further investigation
bHLH and bHLH-LZ factor exchange at promoters
No full textMammalian promoters often contain DNA-elements that can be bound by a number of closely related transcription factors (TFs) that cannot bind to the same DNA-element simultaneously. It is possible that each TF responds to distinct cues, allowing the gene to be activated in response to multiple stimuli. An alternative possibility is that each TF binds sequentially, each contributing to the pre-initiation events leading up to transcription.
Here, we explore the exchange of basic-Helix-Loop-Helix-Leucine-Zipper (bHLH-LZ) factors, USF1, USF2 and MITF at the TYROSINASE promoter following induction by UVB-irradiation and methotrexate-administration. We demonstrate, for the first time in human melanoma, differential induction kinetics of TYROSINASE gene in response to an initial or re-induction, a phenomenon akin to "transcription memory" previously described in yeast.
We also show that USF2, specifically detected by two different antibodies targeting the N-terminal region, is largely cytoplasmic, at least in the cell lines we have investigated. We also showed that nucleo-cytoplasmic shuttling of these USF2 species is partly regulated by glucose. Using deletion mutants, we demonstrated the requirement of the amino-acids surrounding the USF-specific region and the basic domain in nuclear localisation of USF2, and that amino-acids 1−193 appear to enhance dimerization of USF2 in addition to the classical HLH-LZ dimerization domain.
We will further investigate the role(s) played by MYC, MITF, HIF and USF exchange at common targets (which we identified through our ChIP-seq analysis) in gene activation and the effect on the (re)activation potential of these genes when DNA-binding by one or more of these factors are abolished, as well as when the promoter is monopolised by one of these factors through overexpression using cell lines expressing one of the bHLH-TFs under a tet-inducible promoter. In the long run, we aim to understand the potential differences in the role(s) of each bHLH-factors co-occupying E-box elements.</p
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
- …
