---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20924'
abstract:
- lang: eng
  text: "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.\r\nFor complete
    details on the use and execution of this protocol, please refer to Michael et
    al.1"
acknowledgement: We thank R.H. Kim, A. Casper, and R. Gautsch for sequencing at the
  NGS facility (RRID:SCR_025746). K.T. is an Honorary Professor at the Department
  of Biology, Ludwig-Maximilians-University, Munich, Germany. This study was funded
  by European Research Council grant ERC-CoG-818556 TotipotentZygotChrom (K.T.), Max
  Planck Society (K.T.), and ERC Starting Grant “ChromaChrono” 101162145 (A.K.M.).
article_number: '104295'
article_processing_charge: Yes
article_type: original
author:
- first_name: Wataru
  full_name: Kobayashi, Wataru
  last_name: Kobayashi
- first_name: Alicia
  full_name: Michael, Alicia
  id: 6437c950-2a03-11ee-914d-d6476dd7b75c
  last_name: Michael
  orcid: 0000-0002-6080-839X
- first_name: Siwat
  full_name: Ruangroengkulrith, Siwat
  last_name: Ruangroengkulrith
- first_name: Maximilian
  full_name: Kümmecke, Maximilian
  last_name: Kümmecke
- first_name: Kikuë
  full_name: Tachibana, Kikuë
  last_name: Tachibana
citation:
  ama: Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K. Protocol
    for integrative analysis of transcription factor-nucleosome interactions using
    SeEN-seq and cryo-EM structure determination. <i>STAR Protocols</i>. 2025;7. doi:<a
    href="https://doi.org/10.1016/j.xpro.2025.104295">10.1016/j.xpro.2025.104295</a>
  apa: Kobayashi, W., Michael, A. K., Ruangroengkulrith, S., Kümmecke, M., &#38; Tachibana,
    K. (2025). Protocol for integrative analysis of transcription factor-nucleosome
    interactions using SeEN-seq and cryo-EM structure determination. <i>STAR Protocols</i>.
    Elsevier. <a href="https://doi.org/10.1016/j.xpro.2025.104295">https://doi.org/10.1016/j.xpro.2025.104295</a>
  chicago: Kobayashi, Wataru, Alicia K. Michael, Siwat Ruangroengkulrith, Maximilian
    Kümmecke, and Kikuë Tachibana. “Protocol for Integrative Analysis of Transcription
    Factor-Nucleosome Interactions Using SeEN-Seq and Cryo-EM Structure Determination.”
    <i>STAR Protocols</i>. Elsevier, 2025. <a href="https://doi.org/10.1016/j.xpro.2025.104295">https://doi.org/10.1016/j.xpro.2025.104295</a>.
  ieee: W. Kobayashi, A. K. Michael, S. Ruangroengkulrith, M. Kümmecke, and K. Tachibana,
    “Protocol for integrative analysis of transcription factor-nucleosome interactions
    using SeEN-seq and cryo-EM structure determination,” <i>STAR Protocols</i>, vol.
    7. Elsevier, 2025.
  ista: Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K. 2025.
    Protocol for integrative analysis of transcription factor-nucleosome interactions
    using SeEN-seq and cryo-EM structure determination. STAR Protocols. 7, 104295.
  mla: Kobayashi, Wataru, et al. “Protocol for Integrative Analysis of Transcription
    Factor-Nucleosome Interactions Using SeEN-Seq and Cryo-EM Structure Determination.”
    <i>STAR Protocols</i>, vol. 7, 104295, Elsevier, 2025, doi:<a href="https://doi.org/10.1016/j.xpro.2025.104295">10.1016/j.xpro.2025.104295</a>.
  short: W. Kobayashi, A.K. Michael, S. Ruangroengkulrith, M. Kümmecke, K. Tachibana,
    STAR Protocols 7 (2025).
corr_author: '1'
date_created: 2026-01-04T23:01:33Z
date_published: 2025-12-26T00:00:00Z
date_updated: 2026-06-18T18:27:57Z
day: '26'
ddc:
- '570'
department:
- _id: AlMi
doi: 10.1016/j.xpro.2025.104295
external_id:
  pmid:
  - '41455105'
has_accepted_license: '1'
intvolume: '         7'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1016/j.xpro.2025.104295
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9136c684-16d5-11f0-9cad-91c0177b365f
  grant_number: '101162145'
  name: Circadian structural transitions of chromatin
publication: STAR Protocols
publication_identifier:
  eissn:
  - 2666-1667
publication_status: epub_ahead
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protocol for integrative analysis of transcription factor-nucleosome interactions
  using SeEN-seq and cryo-EM structure determination
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2025'
...