Faculty Opinions recommendation of Three-dimensional macronutrient-associated Fos expression patterns in the mouse brainstem.

: HOX genes belong to the highly conserved homeobox superfamily, responsible for the regulation of various cellular processes that control cell homeostasis, from embryogenesis to carcinogenesis. The abnormal expression of HOX genes is observed in various cancers, including breast cancer; they act as oncogenes or as suppressors of cancer, according to context. In this review, we analyze HOX gene expression patterns in breast cancer and examine their relationship, based on the three-dimensional genome structure of the HOX locus. The presence of non-coding RNAs, embedded within the HOX cluster, and the role of these molecules in breast cancer have been reviewed. We further evaluate the characteristic activity of HOX protein in breast cancer and its therapeutic potential.

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HiCRes: a computational method to estimate and predict the resolution of HiC libraries

10.1101/2020.09.22.307967 ◽

2020 ◽

Author(s):

Claire Marchal ◽

Nivedita Singh ◽

Ximena Corso-Díaz ◽

Anand Swaroop

Keyword(s):

Expression Patterns ◽

Three Dimensional ◽

Computational Method ◽

Mathematical Concepts ◽

Regulate Gene Expression ◽

Chromatin Interactions ◽

Genome Wide ◽

A Cell ◽

Cell Type Specific ◽

Human And Mouse

AbstractThree-dimensional (3D) conformation of the chromatin is crucial to stringently regulate gene expression patterns and DNA replication in a cell-type specific manner. HiC is a key technique for measuring 3D chromatin interactions genome wide. Estimating and predicting the resolution of a library is an essential step in any HiC experimental design. Here, we present the mathematical concepts to estimate the resolution of a library and predict whether deeper sequencing would enhance the resolution. We have developed HiCRes, a docker pipeline, by applying these concepts to human and mouse HiC libraries.

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Structure and Location Studies on Key Enzymes in Saponins Biosynthesis of Panax notoginseng

International Journal of Molecular Sciences ◽

10.3390/ijms20246121 ◽

2019 ◽

Vol 20 (24) ◽

pp. 6121

Author(s):

Pengguo Xia ◽

Yujie Zheng ◽

Zongsuo Liang

Keyword(s):

Subcellular Localization ◽

Fluorescent Protein ◽

Expression Patterns ◽

Three Dimensional ◽

Panax Notoginseng ◽

Squalene Epoxidase ◽

Protein Fusion ◽

Active Components ◽

Key Enzymes ◽

Saponin Biosynthesis

Panax notoginseng is one of the most widely used traditional herbs for the treatment of various diseases, in which saponins were the main active components. At present, the research of P. notoginseng mainly focused on the discovery of new compounds and pharmacology. However, there were few studies on the molecular mechanism of the synthesis of secondary metabolites of P. notoginseng. In our study, four coding sequences (CDS) encoding the key enzymes involved in saponin biosynthesis were cloned, namely farnesyl diphosphate synthase (FPS), squalene synthase (SS), squalene epoxidase (SE), and dammarenediol-II synthase (DS), which contained open reading frame (ORF) of 1029 bp, 1248 bp, 1614 bp, and 2310 bp, and coded 342, 415, 537, and 769 amino acids, respectively. At the same time, their domains, secondary structures, three-dimensional structures, and phylogenetics trees were analyzed by kinds of bioinformatics tools. Their phylogenetics relationships were also analyzed. In addition, GFP (Green fluorescent protein) fusion genes were constructed by the plasmid transformation system to determine the subcellular localization. The results of subcellular localization showed that FPS, SE, and DS were mainly located in cytomembrane and its surrounding, while SS was located both in cytoplasm and cytomembrane. Our findings provided data demonstrating the expression patterns of genes involved in saponin biosynthesis and would facilitate efforts to further elucidate the biosynthesis of the bioactive components in P. notoginseng.

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Mutant p53 Disrupts MCF-10A Cell Polarity in Three-dimensional Culture via Epithelial-to-mesenchymal Transitions

Journal of Biological Chemistry ◽

10.1074/jbc.m110.214585 ◽

2011 ◽

Vol 286 (18) ◽

pp. 16218-16228 ◽

Cited By ~ 60

Author(s):

Yanhong Zhang ◽

Wensheng Yan ◽

Xinbin Chen

Keyword(s):

Cell Polarity ◽

Expression Patterns ◽

Ectopic Expression ◽

Three Dimensional ◽

Mutant P53 ◽

Wild Type ◽

Gain Of Function ◽

Three Dimensional Culture ◽

Wild Type P53 ◽

E Cadherin

Mutant p53 is not only deficient in tumor suppression but also acquires additional activity, called gain of function. Mutant p53 gain of function is recapitulated in knock-in mice that carry one null allele and one mutant allele of the p53 gene. These knock-in mice develop aggressive tumors compared with p53-null mice. Recently, we and others showed that tumor cells carrying a mutant p53 are addicted to the mutant for cell survival and resistance to DNA damage. To further define mutant p53 gain of function, we used the MCF-10A three-dimensional model of mammary morphogenesis. MCF-10A cells in three-dimensional culture undergo a series of morphological changes and form polarized and growth-arrested spheroids with hollow lumen, which resembles normal glandular architectures in vivo. Here, we found that endogenous wild-type p53 in MCF-10A cells was not required for acinus formation, but knockdown of endogenous wild-type p53 (p53-KD) led to partial clearance of cells in the lumen due to decreased apoptosis. Consistent with this, p53-KD altered expression patterns of the cell adhesion molecule E-cadherin, the cytoskeletal marker β-catenin, and the extracellular matrix protein laminin V. We also found that ectopic expression of the mutant G245S led to a phenotype similar to p53-KD, whereas a combination of ectopic expression of siRNA-resistant G245S with p53-KD led to a less cleared lumen. In contrast, ectopic expression of mutant R248W, R175H, and R273H disrupted normal acinus architectures with filled lumen and led to formation of irregular and multiacinus structures regardless of p53-KD. In addition, these mutants altered normal expression patterns and/or levels of E-cadherin, β-catenin, laminin V, and tight junction marker ZO-1. Furthermore, epithelial-to-mesenchymal transitions (EMT) markers, Snail, Slug, and Twist, were highly induced by mutant p53 and/or p53-KD. Together, we postulate that EMT represents a mutant p53 gain of function and mutant p53 alters cell polarity via EMT.

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Combined subunit-specific and unspecific inhibition of NMDA receptors triggers distinct cortical c-fos expression patterns

Synapse ◽

10.1002/syn.21562 ◽

2012 ◽

Vol 66 (8) ◽

pp. 752-754 ◽

Cited By ~ 5

Author(s):

Dragos Inta ◽

Juan M. Lima-Ojeda ◽

Christof Dormann ◽

Georg KÖHr ◽

Rolf Sprengel ◽

...

Keyword(s):

Nmda Receptors ◽

Expression Patterns ◽

Fos Expression

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Dexamethasone Inhibits Spheroid Formation of Thyroid Cancer Cells Exposed to Simulated Microgravity

Cells ◽

10.3390/cells9020367 ◽

2020 ◽

Vol 9 (2) ◽

pp. 367 ◽

Cited By ~ 3

Author(s):

Melnik ◽

Sahana ◽

Corydon ◽

Kopp ◽

Nassef ◽

...

Keyword(s):

Thyroid Cancer ◽

Cancer Cells ◽

Cancer Progression ◽

Cancer Biology ◽

Expression Patterns ◽

Three Dimensional ◽

Signal Pathways ◽

Dependent Manner ◽

Spheroid Formation ◽

Mesenchymal Transition

Detachment and the formation of spheroids under microgravity conditions can be observed with various types of intrinsically adherent human cells. In particular, for cancer cells this process mimics metastasis and may provide insights into cancer biology and progression that can be used to identify new drug/target combinations for future therapies. By using the synthetic glucocorticoid dexamethasone (DEX), we were able to suppress spheroid formation in a culture of follicular thyroid cancer (FTC)-133 cells that were exposed to altered gravity conditions on a random positioning machine. DEX inhibited the growth of three-dimensional cell aggregates in a dose-dependent manner. In the first approach, we analyzed the expression of several factors that are known to be involved in key processes of cancer progression such as autocrine signaling, proliferation, epithelial–mesenchymal transition, and anoikis. Wnt/β-catenin signaling and expression patterns of important genes in cancer cell growth and survival, which were further suggested to play a role in three-dimensional aggregation, such as NFKB2, VEGFA, CTGF, CAV1, BCL2(L1), or SNAI1, were clearly affected by DEX. Our data suggest the presence of a more complex regulation network of tumor spheroid formation involving additional signal pathways or individual key players that are also influenced by DEX.

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Functional Internal Complexity of Amygdala: Focus on Gene Activity Mapping After Behavioral Training and Drugs of Abuse

Physiological Reviews ◽

10.1152/physrev.00037.2006 ◽

2007 ◽

Vol 87 (4) ◽

pp. 1113-1173 ◽

Cited By ~ 84

Author(s):

Ewelina Knapska ◽

Kasia Radwanska ◽

Tomasz Werka ◽

Leszek Kaczmarek

Keyword(s):

Basolateral Amygdala ◽

Drugs Of Abuse ◽

Experimental Situation ◽

Expression Patterns ◽

Gene Activity ◽

The Other ◽

Central Amygdala ◽

Behavioral Training ◽

Specific Expression ◽

Fos Expression

The amygdala is a heterogeneous brain structure implicated in processing of emotions and storing the emotional aspects of memories. Gene activity markers such as c-Fos have been shown to reflect both neuronal activation and neuronal plasticity. Herein, we analyze the expression patterns of gene activity markers in the amygdala in response to either behavioral training or treatment with drugs of abuse and then we confront the results with data on other approaches to internal complexity of the amygdala. c-Fos has been the most often studied in the amygdala, showing specific expression patterns in response to various treatments, most probably reflecting functional specializations among amygdala subdivisions. In the basolateral amygdala, c-Fos expression appears to be consistent with the proposed role of this nucleus in a plasticity of the current stimulus-value associations. Within the medial part of the central amygdala, c-Fos correlates with acquisition of alimentary/gustatory behaviors. On the other hand, in the lateral subdivision of the central amygdala, c-Fos expression relates to attention and vigilance. In the medial amygdala, c-Fos appears to be evoked by emotional novelty of the experimental situation. The data on the other major subdivisions of the amygdala are scarce. In conclusion, the studies on the gene activity markers, confronted with other approaches involving neuroanatomy, physiology, and the lesion method, have revealed novel aspects of the amygdala, especially pointing to functional heterogeneity of this brain region that does not fit very well into contemporarily active debate on serial versus parallel information processing within the amygdala.

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Global Analysis of Cell Type-Specific Gene Expression

Comparative and Functional Genomics ◽

10.1002/cfg.281 ◽

2003 ◽

Vol 4 (2) ◽

pp. 208-215 ◽

Cited By ~ 16

Author(s):

David W. Galbraith

Keyword(s):

Gene Expression ◽

Fluorescent Protein ◽

Global Analysis ◽

Expression Patterns ◽

Three Dimensional ◽

Global Gene Expression ◽

Cell Types ◽

Reasonable Assumption ◽

Specific Gene ◽

Different Cell Types

The tissues and organs of multicellular eukaryotes are frequently observed to comprise complex three-dimensional interspersions of different cell types. It is a reasonable assumption that different global patterns of gene expression are found within these different cell types. This review outlines general experimental strategies designed to characterize these global gene expression patterns, based on a combination of methods of transgenic fluorescent protein (FP) expression and targeting, of flow cytometry and sorting and of high-throughput gene expression analysis.

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Spatial organization of different sigma factor activities and c-di-GMP signalling within the three-dimensional landscape of a bacterial biofilm

Open Biology ◽

10.1098/rsob.180066 ◽

2018 ◽

Vol 8 (8) ◽

pp. 180066 ◽

Cited By ~ 24

Author(s):

Gisela Klauck ◽

Diego O. Serra ◽

Alexandra Possling ◽

Regine Hengge

Keyword(s):

Gene Expression ◽

Extracellular Matrix ◽

Stationary Phase ◽

Sigma Factor ◽

Spatial Organization ◽

Expression Patterns ◽

Three Dimensional ◽

Biomechanical Properties ◽

Ribosomal Gene ◽

Bacterial Biofilm

Bacterial biofilms are large aggregates of cells embedded in an extracellular matrix of self-produced polymers. In macrocolony biofilms of Escherichia coli , this matrix is generated in the upper biofilm layer only and shows a surprisingly complex supracellular architecture. Stratified matrix production follows the vertical nutrient gradient and requires the stationary phase σ S (RpoS) subunit of RNA polymerase and the second messenger c-di-GMP. By visualizing global gene expression patterns with a newly designed fingerprint set of Gfp reporter fusions, our study reveals the spatial order of differential sigma factor activities, stringent control of ribosomal gene expression and c-di-GMP signalling in vertically cryosectioned macrocolony biofilms. Long-range physiological stratification shows a duplication of the growth-to-stationary phase pattern that integrates nutrient and oxygen gradients. In addition, distinct short-range heterogeneity occurs within specific biofilm strata and correlates with visually different zones of the refined matrix architecture. These results introduce a new conceptual framework for the control of biofilm formation and demonstrate that the intriguing extracellular matrix architecture, which determines the emergent physiological and biomechanical properties of biofilms, results from the spatial interplay of global gene regulation and microenvironmental conditions. Overall, mature bacterial macrocolony biofilms thus resemble the highly organized tissues of multicellular organisms.

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