Genome Modality

Review "Mitotic genome folding" by Dr. Tatsuya Hirano

rupress.org/jcb/article/...

Replication-dependent histone labeling dissects the physical properties of euchromatin/heterochromatin in living human cells New labeling shows that dynamic nucleosome motion in euchromatin and heterochromatin can influence genome-wide replication timing.

Replication-dependent histone labeling dissects the physical properties of euchromatin/heterochromatin in living human cells | Science Advances www.science.org/doi/10.1126/...

Biophysical aspect of assembly and regulation of nuclear bodies scaffolded by architectural RNA A growing body of evidence suggests that nuclear bodies, condensates of RNAs and proteins within the nucleus, are assembled through liquid-liquid phas…

www.sciencedirect.com/science/arti...
#publication

Chromatin domains in the cell: Phase separation and condensation Negatively charged genomic DNA wraps around positively charged core histone octamers to form nucleosomes, which, along with proteins and RNAs, self-or…

Chromatin domains in the cell: Phase separation and condensation
www.sciencedirect.com/science/arti...
#publication

A common molecular mechanism underlying Cornelia de Lange and CHOPS syndromes The cohesin protein complex is essential for the formation of topologically associating domains (TADs) and chromatin loops on interphase chromosomes.1…

From Prof. Shirahige's group
A common molecular mechanism underlying Cornelia de Lange and CHOPS syndromes
www.sciencedirect.com/science/arti...
#publication

Simpler ABC browser
gmsuite.hgc.jp/jbrowse2/ind...
#GMSuite

SMC-mediated chromosome organization: Does loop extrusion explain it all? In recent years, loop extrusion has attracted much attention as a general mechanism of chromosome organization mediated by structural maintenance of c…

www.sciencedirect.com/science/arti...

#publication

Loop annotation (GMS Loops)
1. "hicCpus" generates "merged_loops.bedpe"
2. "hicDetecLoops" generated bedgraph files with different bins
3. "hicMergeLoops -r 25000" merges all the bedpe file and bedgraph files

#GMSuite

Domain annotation (GMS Domains)

1. Strong boundaries found by 4DN insulation scores are merged by "hicMergeDomains -v 5000" (A)

2. ArrowHead blocks overlapping with (A), "intersectBed -a awh -b (A) -F 0.5 -u", are generated as "GMS_domains.bedpe"

#GMSuite

Genome modality Grant-in-Aid for Transformative Research Areas (A) “Genome Modality: Understanding physical properties of the genome”

www.genome-modality.com/en/