Related Experiment Video
Updated: Mar 14, 2026

Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization
Published on: February 3, 2013
Regulated large-scale nucleosome density patterns and precise nucleosome positioning correlate with V(D)J
Sandhya R Pulivarthy1, Mattia Lion1, Guray Kuzu2
1Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114; Department of Genetics, Harvard Medical School, Boston, MA 02115.
Nucleosome positioning at antigen receptor loci is cell type-specific, regulating gene accessibility for V(D)J recombination. This chromatin organization controls access for the recombination activating gene (RAG) recombinase during development.
Area of Science:
- Immunology
- Epigenetics
- Molecular Biology
Background:
- Nucleosome positioning influences DNA accessibility and gene regulation.
- Antigen receptor loci undergo complex rearrangements essential for adaptive immunity.
Purpose of the Study:
- To investigate the role of nucleosome positioning in regulating V(D)J recombination at antigen receptor loci.
- To determine how cell type-specific chromatin organization impacts gene accessibility.
Main Methods:
- Analysis of nucleosome occupancy and positioning at the Ig heavy chain locus (IgH) in different cell types (pro-B cells, pro-T cells, mouse embryonic fibroblasts).
- Assessment of the correlation between nucleosome positioning and the accessibility of recombination signal sequences (RSS) to the recombination activating gene (RAG) recombinase.
Main Results:
- Pro-B cells exhibit nucleosome positioning that enhances RSS accessibility for RAG recombinase.
- Mouse embryonic fibroblasts show nucleosome positioning that hinders RSS accessibility.
- Cell type-specific, large-scale variations in nucleosome density delineate chromosomal domains within IgH.
Conclusions:
- Developmentally regulated nucleosome positioning is a fundamental mechanism controlling V(D)J recombination.
- Nucleosome positioning acts as a general mechanism for regulating genome accessibility during development across various scales.
More Related Videos
15:07VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
Published on: December 28, 2015
10:40Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA
Published on: September 10, 2013
Related Concept Videos
Chromatin Position Affects Gene Expression
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the...
Nucleosome Remodeling
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
Position-effect Variegation
Histone Variants at the Centromere
Crossing Over
Homologous Recombination