Genome Modality
@genomemodality.bsky.social
Accelerating progress toward
the understanding of multi-dimensional genome properties
the understanding of multi-dimensional genome properties
Replication-dependent histone labeling dissects the physical properties of euchromatin/heterochromatin in living human cells | Science Advances www.science.org/doi/10.1126/...
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.
www.science.org
March 31, 2025 at 8:18 AM
Replication-dependent histone labeling dissects the physical properties of euchromatin/heterochromatin in living human cells | Science Advances www.science.org/doi/10.1126/...
Chromatin domains in the cell: Phase separation and condensation
www.sciencedirect.com/science/arti...
#publication
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…
www.sciencedirect.com
February 21, 2025 at 5:08 AM
Chromatin domains in the cell: Phase separation and condensation
www.sciencedirect.com/science/arti...
#publication
www.sciencedirect.com/science/arti...
#publication
From Prof. Shirahige's group
A common molecular mechanism underlying Cornelia de Lange and CHOPS syndromes
www.sciencedirect.com/science/arti...
#publication
A common molecular mechanism underlying Cornelia de Lange and CHOPS syndromes
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…
www.sciencedirect.com
February 21, 2025 at 1:35 AM
From Prof. Shirahige's group
A common molecular mechanism underlying Cornelia de Lange and CHOPS syndromes
www.sciencedirect.com/science/arti...
#publication
A common molecular mechanism underlying Cornelia de Lange and CHOPS syndromes
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
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
November 24, 2024 at 4:33 AM
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
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
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
November 24, 2024 at 4:30 AM
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
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
