iNOME-seq: in vivo simultaneous genome-wide mapping of chromatin accessibility, nucleosome positioning, DNA-binding protein sites, and DNA methylation in Arabidopsis

Nosheen Hussain; Ryan Merrit; Julia Engelhorn; Javier Antunez-Sanchez; Anjar Wibowo; David Latrasse; Travis Wrightsman; Maximillian Collenberg; Ilja Bezrukov; Hidayah Alotaibi; Elsa Carrasco; Moussa Benhamed; Detlef Weigel; Nicolae Radu Zabet; Jose Gutierrez-Marcos

doi:10.1186/s13059-025-03760-x

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iNOME-seq: in vivo simultaneous genome-wide mapping of chromatin accessibility, nucleosome positioning, DNA-binding protein sites, and DNA methylation in Arabidopsis

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iNOME-seq: in vivo simultaneous genome-wide mapping of chromatin accessibility, nucleosome positioning, DNA-binding protein sites, and DNA methylation in Arabidopsis

Nosheen Hussain, Ryan Merrit, Julia Engelhorn, Javier Antunez-Sanchez, Anjar Wibowo, David Latrasse, Travis Wrightsman, Maximillian Collenberg, Ilja Bezrukov, Hidayah Alotaibi, …

Genome biology, Vol.26(1), pp.361-19

22/10/2025

DOI: https://doi.org/10.1186/s13059-025-03760-x

PMID: 41126326

Résumé

Arabidopsis - genetics

Arabidopsis - metabolism

Arabidopsis Proteins - genetics

Arabidopsis Proteins - metabolism

Binding Sites

Chromatin - genetics

Chromatin - metabolism

Chromosome Mapping - methods

DNA Methylation

DNA-Binding Proteins - metabolism

Genome, Plant

Nucleosomes - genetics

Nucleosomes - metabolism

Sequence Analysis, DNA - methods

Transcription Factors - metabolism

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 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.

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Titre: iNOME-seq: in vivo simultaneous genome-wide mapping of chromatin accessibility, nucleosome positioning, DNA-binding protein sites, and DNA methylation in Arabidopsis
Créateurs - sans rôle: Nosheen Hussain - School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
Ryan Merrit - European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Julia Engelhorn - Agropolis International
Javier Antunez-Sanchez - School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
Anjar Wibowo - Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
David Latrasse - Institute of Plant Sciences, Université Paris-Saclay, CNRS, INRAE, University Evry, Paris-Saclay (IPS2), Orsay, 91405, France
Travis Wrightsman - Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
Maximillian Collenberg - Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
Ilja Bezrukov - Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
Hidayah Alotaibi - Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, 11671, Saudi Arabia
Elsa Carrasco - School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
Moussa Benhamed - Université Paris-Saclay
Detlef Weigel - Max Planck Institute for Biology
Nicolae Radu Zabet - The London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, Bartsand , London, E1 2AT, UK. r.zabet@qmul.ac.uk
Jose Gutierrez-Marcos - School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK. j.f.gutierrez-marcos@warwick.ac.uk
Détails de publication: Genome biology, Vol.26(1), pp.361-19
Identifiants: 99136716909311
Unité académique: Diversité, Adaptation et Développement des plantes - DIADE
Langue: English
Type de ressource: Journal article