Three‐dimensional reconstruction of Prdm family gene expression patterns during mouse development stage by tissue clearing technique

The integration of genetic and environmental factors that regulate the gene expression patterns associated with exercise adaptation is mediated by epigenetic mechanisms. The organisation of the human genome within three-dimensional space, known as chromosome conformation, has recently been shown as a dynamic epigenetic regulator of gene expression, facilitating the interaction of distal genomic regions due to tight and regulated packaging of chromosomes in the cell nucleus. Technological advances in the study of chromosome conformation mean a new class of biomarker—the chromosome conformation signature (CCS)—can identify chromosomal interactions across several genomic loci as a collective marker of an epigenomic state. Investigative use of CCSs in biological and medical research shows promise in identifying the likelihood that a disease state is present or absent, as well as an ability to prospectively stratify individuals according to their likely response to medical intervention. The association of CCSs with gene expression patterns suggests that there are likely to be CCSs that respond, or regulate the response, to exercise and related stimuli. The present review provides a contextual background to CCS research and a theoretical framework discussing the potential uses of this novel epigenomic biomarker within sport and exercise science and medicine.

Download Full-text

ZebraFISH: Fluorescent In Situ Hybridization Protocol and Three-Dimensional Imaging of Gene Expression Patterns

Zebrafish ◽

10.1089/zeb.2006.3.465 ◽

2006 ◽

Vol 3 (4) ◽

pp. 465-476 ◽

Cited By ~ 37

Author(s):

Monique C.M. Welten ◽

Simon B. de Haan ◽

Niels van den Boogert ◽

Jasprien N. Noordermeer ◽

Gerda E.M. Lamers ◽

...

Keyword(s):

Gene Expression ◽

In Situ Hybridization ◽

Fluorescent In Situ Hybridization ◽

Expression Patterns ◽

Three Dimensional ◽

Gene Expression Patterns ◽

Three Dimensional Imaging ◽

Hybridization Protocol

Download Full-text

Three-dimensional reconstruction of gene expression patterns during cardiac development

Physiological Genomics ◽

10.1152/physiolgenomics.00182.2002 ◽

2003 ◽

Vol 13 (3) ◽

pp. 187-195 ◽

Cited By ~ 61

Author(s):

Alexandre T. Soufan ◽

Jan M. Ruijter ◽

Maurice J. B. van den Hoff ◽

Piet A. J. de Boer ◽

Jaco Hagoort ◽

...

Keyword(s):

Gene Expression ◽

3D Reconstruction ◽

Cardiac Development ◽

3D Visualization ◽

Expression Patterns ◽

Genetic Regulation ◽

Three Dimensional ◽

Specific Staining ◽

Dimensional Reconstruction

The study of the genetic regulation of embryonic development requires the three-dimensional (3D) mapping of gene expression at the microscopic level. Despite the recent burst in the number of methods focusing on 3D reconstruction of embryonic specimens, an adequate and accessible 3D reconstruction protocol for the visualization of patterns of gene expression is lacking. In this communication we describe a protocol that was developed for the 3D visualization of patterns of gene expression determined by in situ hybridization (ISH) on serial sections. The method still requires tissue sectioning, due to penetration limits of the specific staining agents into whole embryo preparations. With regard to expenditure of resources, i.e., hardware, software, and time, the protocol is relatively undemanding. Because the variation between specimens requires the visualization of multiple specimens per stage, it was decided to “do more, less well.” The current protocol, therefore, results in reconstructions of sufficient, but not the highest, quality. The use of the protocol is demonstrated on a series of serially sectioned mouse hearts, ranging from embryonic day 8.5 to 14.5. The myocardium of the hearts was identified by ISH using a mixture of specific mRNA probes and reconstructed.

Download Full-text

Zinc Finger Protein Sall2 Is Not Essential for Embryonic and Kidney Development

Molecular and Cellular Biology ◽

10.1128/mcb.23.1.62-69.2003 ◽

2003 ◽

Vol 23 (1) ◽

pp. 62-69 ◽

Cited By ~ 25

Author(s):

Akira Sato ◽

Yuko Matsumoto ◽

Urara Koide ◽

Yuki Kataoka ◽

Nobuaki Yoshida ◽

...

Keyword(s):

Gene Expression ◽

Kidney Development ◽

Zinc Finger Protein ◽

Expression Patterns ◽

Perinatal Period ◽

Gene Expression Patterns ◽

Homeotic Gene ◽

Finger Protein ◽

Family Gene ◽

Deficient Mice

ABSTRACT SALL/Sall is a mammalian homolog of the Drosophila region-specific homeotic gene spalt (sal), and heterozygous mutations in SALL1 in humans lead to Townes-Brocks syndrome. We earlier reported that mice deficient in Sall1 die in the perinatal period and that kidney agenesis or severe dysgenesis are present. We have now generated mice lacking Sall2, another Sall family gene. Although Sall2 is expressed mostly in an overlapping fashion versus that of Sall1, Sall2-deficient mice show no apparent abnormal phenotypes. Morphology and gene expression patterns of the mutant kidney were not affected. Mice lacking both Sall1 and Sall2 show kidney phenotypes comparable to those of Sall1 knockout, thereby demonstrating the dispensable roles of Sall2 in embryonic and kidney development.

Download Full-text

Analysis of Tachykinin Peptide Family Gene Expression Patterns by Combined High-Performance Liquid Chromatography–Radioimmunoassay

Methods in Neurosciences - Neuropeptide Technology - Synthesis, Assay, Purification, and Processing ◽

10.1016/b978-0-12-185261-0.50013-7 ◽

1991 ◽

pp. 119-130 ◽

Cited By ~ 3

Author(s):

Y. Takeda ◽

J.D. Cremins ◽

J. Takeda ◽

J.E. Krause

Keyword(s):

Gene Expression ◽

High Performance Liquid Chromatography ◽

Liquid Chromatography ◽

High Performance ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Peptide Family ◽

Family Gene

Download Full-text

Orientation and repositioning of chromosomes correlate with cell geometry–dependent gene expression

Molecular Biology of the Cell ◽

10.1091/mbc.e16-12-0825 ◽

2017 ◽

Vol 28 (14) ◽

pp. 1997-2009 ◽

Cited By ~ 47

Author(s):

Yejun Wang ◽

Mallika Nagarajan ◽

Caroline Uhler ◽

G. V. Shivashankar

Keyword(s):

Gene Expression ◽

Expression Patterns ◽

Three Dimensional ◽

Gene Expression Patterns ◽

Cell Behavior ◽

Global Changes ◽

Cell Geometry ◽

Transcription Inhibition ◽

Regulate Gene Expression

Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries. Experiments combined with ellipsoid packing models revealed that the mechanosensitivity of chromosomes was correlated with their orientation in the nucleus. Transcription inhibition experiments suggested that the intermingling degree was more sensitive to global changes in transcription than to chromosome radial positioning and its orientations. These results suggested that cell geometry modulated 3D chromosome arrangement, and their neighborhoods correlated with gene expression patterns in a predictable manner. This is central to understanding geometric control of genetic programs involved in cellular homeostasis and the associated diseases.

Download Full-text