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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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An analytical methodology can be divided into four sequential steps: technique, method, procedure, and protocol. A technique is a scientific principle that rationalizes a specific phenomenon through chemical measurements. Adapting a technique for analyzing a sample of interest is termed a method. The procedure outlines the directions for performing the analysis via an analytical method. The protocol is the detailed guidelines on the procedure, which should be strictly followed to obtain the...
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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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As the human population continues to grow and use resources, we must be mindful of our planet’s natural limits. Sustainable development provides a pathway to maintain and improve human life now while also ensuring that future generations will have the resources that they need. The long-term success of sustainability efforts rests on understanding the interplay between human actions and ecological systems.
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A Semi-high-throughput Imaging Method and Data Visualization Toolkit to Analyze C. elegans Embryonic Development
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Developing novel methods to image and visualize 3D genomes.

Tszshan Ma1, Long Chen2,3, Maoxiang Shi4

  • 1School of Medicine, Tsinghua University, Beijing, 100084, China.

Cell Biology and Toxicology
|March 27, 2018
PubMed
Summary
This summary is machine-generated.

Investigating 3D genome organization involves proximity ligation, imaging, and computational methods. This review highlights novel imaging and visualization techniques for exploring gene regulation and transcription in cell nuclei.

Keywords:
3D genomesChromatinsFISH method

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Area of Science:

  • Molecular Biology
  • Genomics
  • Cell Biology

Background:

  • Three-dimensional (3D) genome organization is crucial for cellular functions.
  • Understanding spatial genome arrangements requires advanced methodologies.
  • Existing methods include proximity ligation, imaging, and computational approaches.

Purpose of the Study:

  • To review novel imaging and visualization methods for studying 3D genome organization.
  • To highlight recent advancements in 3D genome imaging and data visualization.
  • To emphasize the complementary nature of different 3D genome analysis strategies.

Main Methods:

  • Focuses on novel imaging techniques: long-probe labeling, short-probe labeling, RNA FISH, and CRISPR system.
  • Introduces advanced microscopy: Super-resolution Distance Optics Microscopy (SDOM) and low-power super-resolution STED.
  • Discusses computational and visualization tools for proximity ligation data.

Main Results:

  • Recent progress in 3D genome imaging for fixed and live cells is presented.
  • Novel super-resolution microscopy methods offer enhanced sensitivity for live-cell imaging.
  • Software tools for visualizing proximity ligation data have been developed.

Conclusions:

  • Imaging and visualization methods are powerful, complementary tools for 3D genome studies.
  • These techniques aid in exploring mechanisms of gene regulation and transcription.
  • Integrated approaches provide comprehensive insights into genome organization.