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 Merritt; 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

PubMed · 41126326

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 Merritt·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

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Abstract

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 m5C 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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Arabidopsis DNA Methylation Nucleosomes Chromatin DNA-Binding Proteins Genome, Plant Binding Sites Chromosome Mapping Transcription Factors Arabidopsis Proteins Sequence Analysis, DNA Metabolic gene cluster Nucleosome Transcription Journal Article

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Nosheen Hussain, Ryan Merritt, 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. 2025-10-22. iNOME-seq: in vivo simultaneous genome-wide mapping of chromatin accessibility, nucleosome positioning, DNA-binding protein sites, and DNA methylation in Arabidopsis.. https://doi.org/10.1186/s13059-025-03760-x

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