iNOME-seq: in vivo simultaneous genome-wide mapping of chromatin accessibility, nucleosome positioning, DNA-binding protein sites, and DNA methylation in Arabidopsis
We present iNOMe-seq, a novel method for in vivo simultaneous profiling of chromatin accessibility, nucleosome occupancy, DNA-binding protein sites, and DNA methylation in living tissues. iNOMe-seq utilizes an <sup>m5</sup>C methyltransferase to mark accessible cytosines in a GpC context, bypassing nucleosome-restricted regions. Using Arabidopsis thaliana, we demonstrate that iNOMe-seq improves chromatin accessibility quantification compared to existing methods. Furthermore, it allows for the spatial and temporal analysis of chromatin dynamics, transcription factor binding, and DNA methylation, offering insight into the role of epigenetic components in transcriptional regulation across tissues and genetic variations in natural populations.
Authors
- Javier Antunez-Sanchez (ORCID: https://orcid.org/0000-0003-1865-2341)
- Detlef Weigel (ORCID: https://orcid.org/0000-0002-2114-7963)
- Anjar Tri Wibowo (ORCID: https://orcid.org/0000-0003-3961-0263)
- Julia Engelhorn (ORCID: https://orcid.org/0000-0002-6680-3012)
- David Latrasse (ORCID: https://orcid.org/0000-0003-2149-0128)
- Ilja Bezrukov (ORCID: https://orcid.org/0000-0003-0420-4329)
- Nicolae Radu Zabet (ORCID: https://orcid.org/0000-0001-9964-6271)
- Maximilian Collenberg (ORCID: https://orcid.org/0000-0003-1573-1888)
- Jose Gutierrez‐Marcos (ORCID: https://orcid.org/0000-0002-5441-9080)
- Moussa Benhamed (ORCID: https://orcid.org/0000-0002-4181-1702)
- E. Carrasco
- Travis Wrightsman (ORCID: https://orcid.org/0000-0002-0904-6473)
- Nosheen Hussain
- Hind Alotaibi (ORCID: https://orcid.org/0000-0003-1150-9788)
- Ryan Merrit
Institutions
- Princess Nourah bint Abdulrahman University (SA)
- University of Essex (GB)
- Centre National de la Recherche Scientifique (FR)
- European Bioinformatics Institute (GB)
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (FR)
- Queen Mary University of London (GB)
- Université Paris-Saclay (FR)
- University of Warwick (GB)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Institut des Sciences des Plantes de Paris Saclay (FR)
- Diversité, adaptation et développement des plantes (FR)
- Max Planck Institute for Biology (DE)
- Institut de Recherche pour le Développement (FR)
Publication Details
- Journal
- Genome biology
- Published
- 2025-10-22
- DOI
- https://doi.org/10.1186/s13059-025-03760-x
- Citations
- 1
- Primary Topic
- Plant Molecular Biology Research
- Type
- article
- Field-Weighted Citation Impact
- 1.75