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Updated: Sep 18, 2025
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VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
Published on: December 28, 2015
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Building a neural network model to define DNA sequence specificity in V(D)J recombination
Justin C Harris1, Jennifer N Byrum2, Cooper B McKinney2
1Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences, Oklahoma City, OK 73104, United States.
Nucleic Acids Research
|June 23, 2025
Summary
V(D)J recombination uses specific DNA sequences called recombination signal sequences (RSSs) to assemble antigen receptor genes. Our study reveals how nucleotide changes in RSS heptamer and nonamer regions influence this crucial gene assembly process.
Area of Science:
- Immunology
- Molecular Biology
- Genetics
Background:
- V(D)J recombination assembles antigen receptor genes in developing lymphocytes.
- Recombination Signal Sequences (RSSs) guide this process, but their precise selection mechanism remains unclear.
- RSSs consist of heptamer and nonamer motifs separated by a spacer, flanking gene segments targeted for rearrangement.
Purpose of the Study:
- To elucidate the sequence-based rules governing RSS selection in V(D)J recombination.
- To understand how specific nucleotide positions within RSSs impact recombination efficiency.
- To investigate synergistic and interdependent effects between RSS heptamer and nonamer regions.
Main Methods:
- Developed a neural network model using V(D)J recombination efficiency data on randomized 12-RSSs.
- Applied SHapley Additive exPlanations (SHAP) to interpret the neural network's predictions.
- Trained a second neural network incorporating nonamer sequences to analyze heptamer-nonamer interactions.
Main Results:
- Identified specific nucleotide positions in the RSS heptamer that significantly affect recombination efficiency.
- SHAP analysis revealed synergistic contributions of nucleotide pairs within the heptamer.
- Discovered interdependent effects between heptamer and nonamer regions on V(D)J recombination efficiency.
Conclusions:
- Sequence variations at specific positions within the RSS heptamer are critical for V(D)J recombination efficiency.
- Nucleotide interactions within the RSS heptamer and between the heptamer and nonamer contribute to the regulation of V(D)J recombination.
- This study provides a deeper mechanistic understanding of RSS selection during adaptive immune receptor gene assembly.
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