Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Genomics02:02

Genomics

41.6K
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...
41.6K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

7.2K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
7.2K
Synthetic Biology02:55

Synthetic Biology

5.8K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
5.8K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

21.4K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
21.4K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

823
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
823
Evolution of Microbial Genome01:08

Evolution of Microbial Genome

2
Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.
2

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Higher order assembly: folding the chromosome.

Current opinion in structural biology·2017
Same author

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.

Cell·2016
Same author

An integrated model of transcription factor diffusion shows the importance of intersegmental transfer and quaternary protein structure for target site finding.

PloS one·2014
Same author

Targeting the c-Kit Promoter G-quadruplexes with 6-Substituted Indenoisoquinolines.

ACS medicinal chemistry letters·2014
Same author

The autoregulation of a eukaryotic DNA transposon.

eLife·2013
Same author

A complex network framework for unbiased statistical analyses of DNA-DNA contact maps.

Nucleic acids research·2012

Related Experiment Video

Updated: Mar 19, 2026

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

412.2K

Systems Biology Approaches for Understanding Genome Architecture.

Sven Sewitz1, Karen Lipkow2,3

  • 1Babraham Institute, Nuclear Dynamics Programme, Cambridge, CB22 3AT, UK.

Methods in Molecular Biology (Clifton, N.J.)
|June 11, 2016
PubMed
Summary

Understanding chromatin organization is key to gene regulation. This study integrates genome-wide data and 3D simulations to explore how protein movement influences chromatin states and genome dynamics.

Keywords:
Chromatin statesGenome organizationHidden Markov modelsStochastic spatial simulationsSystems biology

More Related Videos

3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells
11:25

3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells

Published on: January 25, 2020

11.0K
Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
11:36

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Published on: April 21, 2023

3.1K

Related Experiment Videos

Last Updated: Mar 19, 2026

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

412.2K
3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells
11:25

3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells

Published on: January 25, 2020

11.0K
Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
11:36

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Published on: April 21, 2023

3.1K

Area of Science:

  • Genomics and molecular biology
  • Computational biology and bioinformatics

Background:

  • Gene regulation is governed by the linear and 3D organization of chromatin in eukaryotic genomes.
  • Comprehensive understanding necessitates integrating diverse data types and experimental findings.

Purpose of the Study:

  • To present a method for determining chromatin states by integrating genome-wide protein-DNA binding data.
  • To describe stochastic simulations for analyzing 3D genome organization and protein movement within a nucleus.
  • To facilitate a systems-level approach for investigating genome dynamics and regulatory mechanisms.

Main Methods:

  • Integration of genome-wide protein-DNA binding data to define chromatin states.
  • Development and application of stochastic simulations to model protein dynamics in a 3D nuclear environment.
  • Systems-level analysis integrating computational modeling with experimental data.

Main Results:

  • A framework for determining chromatin states through integrated data analysis.
  • A detailed protocol for performing 3D stochastic simulations of protein movement.
  • Demonstration of how spatial genome organization impacts gene regulation.

Conclusions:

  • The integration of diverse data types and advanced simulation techniques provides novel insights into genome organization.
  • This systems-level approach enables the formulation of new research questions regarding genome dynamics and gene regulation.
  • Understanding chromatin spatial arrangement is crucial for deciphering regulatory mechanisms.