10.1371/journal.pgen.1007819.g004 Florian Jupe Florian Jupe Angeline C. Rivkin Angeline C. Rivkin Todd P. Michael Todd P. Michael Mark Zander Mark Zander S. Timothy Motley S. Timothy Motley Justin P. Sandoval Justin P. Sandoval R. Keith Slotkin R. Keith Slotkin Huaming Chen Huaming Chen Rosa Castanon Rosa Castanon Joseph R. Nery Joseph R. Nery Joseph R. Ecker Joseph R. Ecker T-DNA insertions alter the chromatin landscape. Public Library of Science 2019 plant T-DNA insertions H 2A chromatin environments Arabidopsis thaliana lines T-DNA integration sites chromosome arm ends bacterium Agrobacterium tumefaciens WISC TAIR 10 reference genome plant genome engineering H 3K T-DNA lines RNA-directed DNA methylation pathway cytosine DNA methylation nanopore sequencing-based assemblies SALK H 3K H 3K T-DNA insertion sites T-DNA insertion collections 2019-01-18 21:03:36 Figure https://plos.figshare.com/articles/figure/T-DNA_insertions_alter_the_chromatin_landscape_/7607288 <p>(a) AnnoJ genome browser visualization of ChIP-seq reads derived from H3K4me3, H2A.Z and H3K27me3 occupancy in Col-0 and SALK_059379 seedlings around the T-DNA-induced deletion on the chromosome 2. Histone domains that are adjacent to the T-DNA deletion are indicated as domain 1 and 2. (b) Annoj genome browser visualization of H3K4me3, H2A.Z and H3K27me3 occupancy in Col-0 and SALK_069537 seedlings around the T-DNA insertion at <i>At5g23110</i>. Schematic illustration shows the gene structure of <i>At5g23110</i> and the approximate location of the corresponding T-DNA insertion. (c) Quantification of H3K4me3, H2A.Z and H3K27me3 around the T-DNA insertion site at <i>At5g23110</i> (SALK_069537). (d) Visualization of H3K4me3, H2A.Z and H3K27me3 occupancy in Col-0 and SALK_117411 seedlings indicates <i>de novo</i> trimethylation of H3K27 around the T-DNA insertion in <i>At3g53680</i>. Scheme of gene structure of <i>At3g53680</i> shows the approximate location of the T-DNA insertion into the genome of SALK_117411 plants. (b) Levels of H3K4me3, H2A.Z and H3K27me3 around the T-DNA insertion at <i>At3g53680</i> in SALK_117411 seedlings are shown. A red arrow marks the approximate location of the T-DNA integration site in the Annoj genome browser screenshots. The respective occupancies were identified with ChIP-seq and all shown AnnoJ genome browser tracks were normalized to the respective sequencing depth. The Col-0 IgG track serves as a control. The occupancy of the respective domains was calculated as the ratio between the respective ChIP-seq sample and the Col-0 IgG control.</p>