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

DNA Microarrays02:34

DNA Microarrays

18.4K
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
18.4K
Ribosome Profiling02:24

Ribosome Profiling

3.6K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.6K
Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

47.6K
Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
47.6K
Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

11.2K
Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
11.2K
Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

23.7K
Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the...
23.7K
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

8.5K
The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer...
8.5K

You might also read

Related Articles

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

Sort by
Same author

Topical resiquimod elicits systemic protection and improves anti-PD1 therapy in melanoma via priming of CD8+ T cells.

Cancer immunology research·2026
Same author

OmicGlaze: Spatial Multi-Omic Mapping of Traumatic Brain Injury.

bioRxiv : the preprint server for biology·2026
Same author

A theoretical and experimental framework enables low-coverage sequencing for accurate quantification of genome-wide cytosine modification levels.

bioRxiv : the preprint server for biology·2026
Same author

Toward Computationally Complete Spatial Omics.

bioRxiv : the preprint server for biology·2026
Same author

DNA Methylation-Based Risk Stratification and Classification of Pediatric Thyroid Carcinoma.

Clinical cancer research : an official journal of the American Association for Cancer Research·2026
Same author

KnowYourCG: Facilitating base-level sparse methylome interpretation.

Science advances·2025

Related Experiment Video

Updated: Sep 9, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

5.0K

Spatial joint profiling of DNA methylome and transcriptome in tissues.

Chin Nien Lee1,2, Hongxiang Fu3,4,5, Angelysia Cardilla3,5

  • 1Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA. chinnien.lee@pennmedicine.upenn.edu.

Nature
|September 3, 2025
PubMed
Summary

Researchers developed a new method for whole-genome spatial co-profiling of DNA methylation and transcriptome. This technique maps epigenetic marks and gene expression in the same tissue section, advancing spatial omics for developmental and brain studies.

More Related Videos

Methyl-binding DNA capture Sequencing for Patient Tissues
08:40

Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

8.7K
Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics
07:43

Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics

Published on: May 3, 2024

3.2K

Related Experiment Videos

Last Updated: Sep 9, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

5.0K
Methyl-binding DNA capture Sequencing for Patient Tissues
08:40

Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

8.7K
Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics
07:43

Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics

Published on: May 3, 2024

3.2K

Area of Science:

  • Epigenetics and Genomics
  • Developmental Biology
  • Neuroscience

Background:

  • Spatial resolution is crucial for understanding tissue biology and cellular functions.
  • Existing spatial omics methods lack the capacity to profile DNA methylation alongside other omics data.
  • DNA methylation is a key epigenetic mark regulating gene expression.

Purpose of the Study:

  • To introduce a novel method for whole-genome spatial co-profiling of DNA methylation and transcriptome.
  • To enable near single-cell resolution mapping of both DNA methylation and RNA expression in the same tissue section.
  • To explore the interplay between DNA methylation and gene expression in mammalian development and brain function.

Main Methods:

  • Development of a new technology for simultaneous spatial profiling of DNA methylation and transcriptome.
  • Application of the method to mouse embryos during development and the postnatal mouse brain.
  • Generation of DNA-RNA bimodal tissue maps at near single-cell resolution.

Main Results:

  • Creation of detailed spatial maps revealing the interplay between DNA methylation and gene expression.
  • Identification of synergistic molecular definitions of cell identity through spatial patterns of methylation and transcriptome.
  • Reconstruction of developmental dynamics in mouse embryogenesis, highlighting methylation-mediated transcriptional regulation.

Conclusions:

  • The developed method successfully extends spatial omics to include DNA cytosine methylation.
  • This technology provides a comprehensive understanding of tissue biology, development, and disease.
  • The findings offer new insights into spatial programming, cell identity, and epigenetic regulation in mammals.