Three-Dimensional Multiphoton Imaging of Transcription Factor by ClearSee

2018 ◽  
pp. 257-268 ◽  
Author(s):  
Yoko Mizuta ◽  
Katsutoshi Tsuda
Keyword(s):  
Transcription Factor ◽  
Three Dimensional ◽  
Multiphoton Imaging

scholarly journals Multi-Funnel Landscape of the Fold-Switching Protein RfaH-CTD

2017 ◽  
Author(s):  
Nathan A. Bernhardt ◽  
Ulrich H.E. Hansmann
Keyword(s):  
Free Energy ◽  
Transcription Factor ◽  
Biological Function ◽  
Double Helix ◽  
Energy Landscape ◽  
Three Dimensional ◽  
Conversion Process ◽  
Free Energy Landscape ◽  
Enhanced Sampling ◽  
Helix Bundle

AbstractProteins such as the transcription factor RfaH can change biological function by switching between distinct three-dimensional folds. RfaH regulates transcription if the C-terminal domain folds into a double helix bundle, and promotes translation when this domain assumes a β-barrel form. This fold-switch has been also observed for the isolated domain, dubbed by us RfaH-CTD, and is studied here with a variant of the RET approach recently introduced by us. We use the enhanced sampling properties of this technique to map the free energy landscape of RfaH-CTD and to propose a mechanism for the conversion process.TOC Image

scholarly journals Evolutionary conservation of the intrinsic disorder-based Radical-Induced Cell Death1 hub interactome

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Lise Friis Christensen ◽  
Lasse Staby ◽  
Katrine Bugge ◽  
Charlotte O’Shea ◽  
Birthe B. Kragelund ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Stress Responses ◽  
Plant Stress ◽  
Three Dimensional ◽  
Intrinsic Disorder ◽  
Dimensional Structure ◽  
Linear Motif ◽  
Intrinsically Disordered ◽  
Helix Formation ◽  
Α Helix

AbstractRadical-Induced Cell Death1 (RCD1) functions as a cellular hub interacting with intrinsically disordered transcription factor regions, which lack a well-defined three-dimensional structure, to regulate plant stress. Here, we address the molecular evolution of the RCD1-interactome. Using bioinformatics, its history was traced back more than 480 million years to the emergence of land plants with the RCD1-binding short linear motif (SLiM) identified from mosses to flowering plants. SLiM variants were biophysically verified to be functional and to depend on the same RCD1 residues as the DREB2A transcription factor. Based on this, numerous additional members may be assigned to the RCD1-interactome. Conservation was further strengthened by similar intrinsic disorder profiles of the transcription factor homologs. The unique structural plasticity of the RCD1-interactome, with RCD1-binding induced α-helix formation in DREB2A, but not detectable in ANAC046 or ANAC013, is apparently conserved. Thermodynamic analysis also indicated conservation with interchangeability between Arabidopsis and soybean RCD1 and DREB2A, although with fine-tuned co-evolved binding interfaces. Interruption of conservation was observed, as moss DREB2 lacked the SLiM, likely reflecting differences in plant stress responses. This whole-interactome study uncovers principles of the evolution of SLiM:hub-interactions, such as conservation of α-helix propensities, which may be paradigmatic for disorder-based interactomes in eukaryotes.

scholarly journals Video-rate multimodal multiphoton imaging and three-dimensional characterization of cellular dynamics in wounded skin

2020 ◽  
Vol 13 (02) ◽  
pp. 2050007
Author(s):  
Joanne Li ◽  
Madison N. Wilson ◽  
Andrew J. Bower ◽  
Marina Marjanovic ◽  
Eric J. Chaney ◽  
...  
Keyword(s):  
Cell Tracking ◽  
Skin Diseases ◽  
Ex Vivo ◽  
Three Dimensional ◽  
Biological Information ◽  
Cellular Dynamics ◽  
Multiphoton Imaging ◽  
Cellular Events ◽  
Analysis Platform

To date, numerous studies have been performed to elucidate the complex cellular dynamics in skin diseases, but few have attempted to characterize these cellular events under conditions similar to the native environment. To address this challenge, a three-dimensional (3D) multimodal analysis platform was developed for characterizing in vivo cellular dynamics in skin, which was then utilized to process in vivo wound healing data to demonstrate its applicability. Special attention is focused on in vivo biological parameters that are difficult to study with ex vivo analysis, including 3D cell tracking and techniques to connect biological information obtained from different imaging modalities. These results here open new possibilities for evaluating 3D cellular dynamics in vivo, and can potentially provide new tools for characterizing the skin microenvironment and pathologies in the future.

scholarly journals Grainyhead-like 2 regulates epithelial morphogenesis by establishing functional tight junctions through the organization of a molecular network among claudin3, claudin4, and Rab25

2012 ◽  
Vol 23 (15) ◽  
pp. 2845-2855 ◽  
Author(s):  
Kazunori Senga ◽  
Keith E. Mostov ◽  
Toshihiro Mitaka ◽  
Atsushi Miyajima ◽  
Naoki Tanimizu
Keyword(s):  
Transcription Factor ◽  
Tight Junctions ◽  
Progenitor Cell ◽  
Three Dimensional ◽  
Intercellular Junctions ◽  
Molecular Network ◽  
Epithelial Morphogenesis ◽  
Lumen Formation ◽  
Liver Progenitor Cell ◽  
Progenitor Cell Line

During development, epithelial progenitors establish intercellular junctions, including tight junctions (TJs), and form three-dimensional (3D) tissue structures, which are often associated with luminal structures. Here we identify grainyhead-like 2 (Grhl2) as a transcription factor that regulates the size of luminal space surrounded by polarized epithelial cells. We show that HPPL, a liver progenitor cell line, transfected with Grhl2 cDNA forms remarkably larger cysts than the control cells in 3D cultures. We find that Grhl2 up-regulates claudin (Cldn) 3 and Cldn4, and their functions are necessary for the formation of large cysts. Overexpression of Cldn3 alone induces the cyst expansion. In contrast, expression of Cldn4 alone does not induce expansion, as it is not localized at TJs. Of interest, Rab25, another Grhl2 target, not only increases the Cldn4 protein, but also enhances its localization at TJs. Taken together, the results indicate that Grhl2 regulates epithelial morphogenesis through transcriptional up-regulation of Cldn3 and Cldn4, as well as of Rab25, which increases the Cldn4 protein and its localization at TJs. The results reveal a molecular network regulating epithelial lumen formation organized by Grhl2.

scholarly journals Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements

2013 ◽  
Vol 368 (1632) ◽  
pp. 20130029 ◽  
Author(s):  
Harendra Guturu ◽  
Andrew C. Doxey ◽  
Aaron M. Wenger ◽  
Gill Bejerano
Keyword(s):  
Transcription Factor ◽  
Binding Site ◽  
Protein Interactions ◽  
Binding Sites ◽  
Three Dimensional ◽  
Structural Data ◽  
Regulatory Elements ◽  
Computational Method ◽  
Web Resource ◽  
Three Dimensional Models

Mapping the DNA-binding preferences of transcription factor (TF) complexes is critical for deciphering the functions of cis -regulatory elements. Here, we developed a computational method that compares co-occurring motif spacings in conserved versus unconserved regions of the human genome to detect evolutionarily constrained binding sites of rigid TF complexes. Structural data were used to estimate TF complex physical plausibility, explore overlapping motif arrangements seldom tackled by non-structure-aware methods, and generate and analyse three-dimensional models of the predicted complexes bound to DNA. Using this approach, we predicted 422 physically realistic TF complex motifs at 18% false discovery rate, the majority of which (326, 77%) contain some sequence overlap between binding sites. The set of mostly novel complexes is enriched in known composite motifs, predictive of binding site configurations in TF–TF–DNA crystal structures, and supported by ChIP-seq datasets. Structural modelling revealed three cooperativity mechanisms: direct protein–protein interactions, potentially indirect interactions and ‘through-DNA’ interactions. Indeed, 38% of the predicted complexes were found to contain four or more bases in which TF pairs appear to synergize through overlapping binding to the same DNA base pairs in opposite grooves or strands. Our TF complex and associated binding site predictions are available as a web resource at http://bejerano.stanford.edu/complex .

scholarly journals Nucleus-cytoskeleton communication impacts on OCT4-chromatin interactions in embryonic stem cells

BMC Biology ◽  
2022 ◽  
Vol 20 (1) ◽  
Author(s):  
Juan José Romero ◽  
María Cecilia De Rossi ◽  
Camila Oses ◽  
Camila Vázquez Echegaray ◽  
Paula Verneri ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Cell Fate ◽  
Opposite Effect ◽  
Es Cells ◽  
Three Dimensional ◽  
Embryonic Stem ◽  
Cytoskeleton Organization ◽  
Chromatin Interactions ◽  
Cellular Environment ◽  
Dimensional Distribution

Abstract Background The cytoskeleton is a key component of the system responsible for transmitting mechanical cues from the cellular environment to the nucleus, where they trigger downstream responses. This communication is particularly relevant in embryonic stem (ES) cells since forces can regulate cell fate and guide developmental processes. However, little is known regarding cytoskeleton organization in ES cells, and thus, relevant aspects of nuclear-cytoskeletal interactions remain elusive. Results We explored the three-dimensional distribution of the cytoskeleton in live ES cells and show that these filaments affect the shape of the nucleus. Next, we evaluated if cytoskeletal components indirectly modulate the binding of the pluripotency transcription factor OCT4 to chromatin targets. We show that actin depolymerization triggers OCT4 binding to chromatin sites whereas vimentin disruption produces the opposite effect. In contrast to actin, vimentin contributes to the preservation of OCT4-chromatin interactions and, consequently, may have a pro-stemness role. Conclusions Our results suggest roles of components of the cytoskeleton in shaping the nucleus of ES cells, influencing the interactions of the transcription factor OCT4 with the chromatin and potentially affecting pluripotency and cell fate.

Marchantia TCP transcription factor activity correlates with three-dimensional chromatin structure

Nature Plants ◽  
2020 ◽  
Vol 6 (10) ◽  
pp. 1250-1261 ◽  
Author(s):  
Ezgi Süheyla Karaaslan ◽  
Nan Wang ◽  
Natalie Faiß ◽  
Yuyu Liang ◽  
Sean A. Montgomery ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Chromatin Structure ◽  
Three Dimensional ◽  
Transcription Factor Activity ◽  
Factor Activity
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