David Latrasse | Search PubMed

PubMed2025

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 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.

Arabidopsis↗

PubMed2025

HiChIP for Plant Tissues.

While most epigenomics studies are based on a linear view of genome organization, the necessity to take the three-dimensional chromatin folding into account to understand transcriptional regulation is now clearly recognized. In the past years, approaches combining proximity-based ligation with high-throughput sequencing have opened the way to study long/short-range chromatin interactions and, thus, to analyze 3D chromatin organization. Among them, HiChIP, a protein-based method to capture chromatin interactions, gave rise to the most comprehensive view of the chromatin contacts involving specific chromatin components in a given system. Here, we describe a detailed procedure to produce HiChIP libraries starting from plant tissues.

Chromatin↗