Skip to content
DraconiticResearch
Search Sources API
190,869 studies31 sourcesUpdated 8 min ago
Peer-reviewedCC BY 4.0International Journal of Molecular Sciences

Barcoded Sleeping Beauty Transposons as Mobile Reporters of Chromatin Architecture

  • Anna Khabarova1
  • Miroslav Nuriddinov1,2
  • Alexander Smirnov1
  • Nariman Battulin1,3
  1. 1Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
  2. 2Department of Genetics and Life Sciences, Sirius University of Science and Technology, 354340 Sochi, Russia
  3. 3Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
Open at sourceDOICite

Abstract

Transposon integration is influenced by genomic context, but the contribution of three-dimensional genome organization to transposon mobility remains poorly understood. Here, we developed T7-Mediated Unique-barcode Recovery sequencing (TMUR-seq), combining T7-based junction enrichment with uniquely barcoded Sleeping Beauty (SB) transposons to track secondary transposition events and their relationships to individual donor sites. Using this approach, we characterized genome-wide secondary SB transposition in human cells and analyzed the effects of genomic distance, donor-specific directionality, and chromatin organization on target selection. Secondary transposition was strongly dependent on linear genomic distance but showed pronounced donor-specific directional asymmetries, including recurrent mirror-image patterns at neighboring donor sites. Secondary integratiotes also showed enrichment for Hi-C contacts with their donor loci within approximately 50 kb after accounting for genomic distance, consistent with a contribution of local three-dimensional chromatin organization to target selection. An extended chromosome 2 donor cluster further illustrated how donor distribution, chromatin state, domain organization, and local three-dimensional connectivity can coincide with highly asymmetric integration patterns and regions of pronounced integration depletion. Together, these findings indicate that secondary SB transposition is not entirely random and is shaped by the combined effects of genomic distance and local genomic context. TMUR-seq provides a framework for tracking donor–recipient relationships and investigating the genomic determinants of transposon mobility.

Related

  1. Chromosomal inversions modulate 3D chromatin interactions and regulatory architecture in Anopheles gambiae
    Kathryn S. Taquet, Cameron E. Anderson, Kenneth D. Vernick +1
    BMC BiologyPeer-reviewedCC BY-NC-ND 4.0Molecular biology & gene regulationCrossref
  2. A generalizable Hi-C foundation model for chromatin architecture, single-cell and multiomics analysis across species
    Xiao Wang, Yuanyuan Zhang, Suhita Ray +6
    Nature MethodsPeer-reviewedLicence not stated9 citedMolecular biology & gene regulationOpenAlex
  3. Multiomics analysis reveals the enhancer landscapes and 3D chromatin architecture in esophageal squamous cell carcinoma
    Haoqiang Sun, Yongjie Wang, Wenwen Xu +9
    Communications BiologyPeer-reviewedCC BY-NC-ND 4.0Full textMolecular biology & gene regulationCrossref
  4. H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs
    Brian Krug, Bo Hu, Haifeng Chen +34
    Nature GeneticsPeer-reviewedLicence not statedFull text9 citedMolecular biology & gene regulationOpenAlex
  5. Three-dimensional chromatin architecture is rapidly restored after DNA replication.
    Tyler K Fenstermaker, Svetlana Petruk, Alexander Mazo
    Nature communicationsPeer-reviewedCC BY-NC-NDFull textMolecular biology & gene regulationEurope PMC

Cite

BibTeXRIS
BibTeX
@article{khabarova2026barcoded,
  title = {{Barcoded Sleeping Beauty Transposons as Mobile Reporters of Chromatin Architecture}},
  author = {Anna Khabarova and Miroslav Nuriddinov and Alexander Smirnov and Nariman Battulin},
  journal = {International Journal of Molecular Sciences},
  year = {2026},
  month = sep,
  doi = {10.3390/ijms27188348},
  url = {https://www.mdpi.com/1422-0067/27/18/8348},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Barcoded Sleeping Beauty Transposons as Mobile Reporters of Chromatin Architecture
AU  - Anna Khabarova
AU  - Miroslav Nuriddinov
AU  - Alexander Smirnov
AU  - Nariman Battulin
PY  - 2026
DA  - 2026/09/19
JO  - International Journal of Molecular Sciences
DO  - 10.3390/ijms27188348
UR  - https://www.mdpi.com/1422-0067/27/18/8348
AB  - Transposon integration is influenced by genomic context, but the contribution of three-dimensional genome organization to transposon mobility remains poorly understood. Here, we developed T7-Mediated Unique-barcode Recovery sequencing (TMUR-seq), combining T7-based junction enrichment with uniquely barcoded Sleeping Beauty (SB) transposons to track secondary transposition events and their relationships to individual donor sites. Using this approach, we characterized genome-wide secondary SB transposition in human cells and analyzed the effects of genomic distance, donor-specific directionality, and chromatin organization on target selection. Secondary transposition was strongly dependent on linear genomic distance but showed pronounced donor-specific directional asymmetries, including recurrent mirror-image patterns at neighboring donor sites. Secondary integratiotes also showed enrichment for Hi-C contacts with their donor loci within approximately 50 kb after accounting for genomic distance, consistent with a contribution of local three-dimensional chromatin organization to target selection. An extended chromosome 2 donor cluster further illustrated how donor distribution, chromatin state, domain organization, and local three-dimensional connectivity can coincide with highly asymmetric integration patterns and regions of pronounced integration depletion. Together, these findings indicate that secondary SB transposition is not entirely random and is shaped by the combined effects of genomic distance and local genomic context. TMUR-seq provides a framework for tracking donor–recipient relationships and investigating the genomic determinants of transposon mobility.
SN  - 1422-0067
ER  -