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Updated: Jun 30, 2026
High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
Published on: October 5, 2018
Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM
Wataru Kobayashi1, Alicia K Michael2, Siwat Ruangroengkulrith1
1Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Munich, Germany.
None:
Pioneer transcription factors (TFs) possess the ability to read out DNA motifs embedded within nucleosomes, driving changes in gene expression during cellular differentiation and reprogramming. Here, we present selected engagement on nucleosome sequencing (SeEN-seq), a protocol designed to systematically identify potential TF-binding sites on the nucleosome. We describe steps for nucleosome library assembly, SeEN-seq assay, and cryoelectron microscopy (cryo-EM) sample preparation. This protocol facilitates the preparation of homogeneous pioneer TF-nucleosome complexes for cryo-EM structure determination using single-particle analysis. For complete details on the use and execution of this protocol, please refer to Michael et al.1.
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