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>