RT Journal
A1 Wang, Congmao
A1 Liu, Chang
A1 Roqueiro, Damian
A1 Grimm, Dominik
A1 Schwab, Rebecca
A1 Becker, Claude
A1 Lanz, Christa
A1 Weigel, Detlef
T1 Genome-wide analysis of local chromatin packing in Arabidopsis thaliana
JF Genome Research 
JO Genome Research 
YR 2015 
FD February 01 
VO 25 
IS 2 
SP 246 
OP 256 
DO 10.1101/gr.170332.113 
UL http://genome.cshlp.org/content/25/2/246.abstract 
AB The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana. We find that local chromatin packing differs from the patterns seen in animals, with kilobasepair-sized segments that have much higher intrachromosome interaction rates than neighboring regions, representing a dominant local structural feature of genome conformation in A. thaliana. These regions, which appear as positive strips on two-dimensional representations of chromatin interaction, are enriched in epigenetic marks H3K27me3, H3.1, and H3.3. We also identify more than 400 insulator-like regions. Furthermore, although topologically associating domains (TADs), which are prominent in animals, are not an obvious feature of A. thaliana genome packing, we found more than 1000 regions that have properties of TAD boundaries, and a similar number of regions analogous to the interior of TADs. The insulator-like, TAD-boundary-like, and TAD-interior-like regions are each enriched for distinct epigenetic marks and are each correlated with different gene expression levels. We conclude that epigenetic modifications, gene density, and transcriptional activity combine to shape the local packing of the A. thaliana nuclear genome.