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Speciesgenome coordinates (assembly, chromosome, start and end)notable features in the regionsreasons for analysismost appropriate cell types for analysiswhich cell lines to use?Suggester
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mousemm10, chr3:34,478,608-34,971,807Sox2previous work has established a Sox2 enhancer located 130kb downsteam of the gene; mESCF123/F129Bing
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mousemm10, chr16:45479887-50879887Dppa2, Dppa4This is a pluripotency specific locus that is an early replicating inter-lad in the A compartment in stem cells, flanked by large swaths of LAD/compartment B/late replicating chromatin. It is switched to late replication and compartment B upon differentiation to any germ layer. A series of deletion/inversions are made in this locus for analysis the effect on TADs/RT. FISH data have been published, as have time courses of expression, RT, RNA, 4C and DNA FISH during differentiation.mESCF121Gilbert
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humanhg19, chr8:55,370,494Sox17A marker for commitment to definitive endoderm. This RD/TAD switches from late to early during differentiation within 2 cell cycles in vitro.
hESC stem cell and differentiated
H1-hESCGilbert
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humanhg19 chr6:31,132,114POU5F1Oct4 gene locus has been well characterized with a high throughput CRISPR-screening and other toolshESCH1-hESCBing
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human/mousehg19, chrX:
DXZ4-FIRRE-G6PD loci, paternal specific
Paternal specific, evidence in ChIA-PET, Hi-C, and DNA FISHGM12878GM12878Noble/Yijun
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mouse/humanbeta-actin (actb)live cell imaging work from Bob SingerAll cellsallibrahim cissé
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human/mousehg19 chr8:128,748,315MYCdisease related; long-range regulation; gene desertAll cellsallBing Ren
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humanhg19: chr11:5,187,243-5,540,775LCR bGlobinENM0009, promoter enhancer interaction benchmark; a lot of existing work; but enhancer is only 40kb away - challenging for imaging. K562/GM12878Belmonthttp://higlass.io/app/?config=ZG6aNa1OTlu7jgkfnn_JTA
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humanhg19: chr4:89,941,945-96,939,600GRID2changing TADs in ES vs differentited cellsES vs HFF
H1-hESC/HFFc6
Dekker
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humanhg19: chr7:26,014,078-28,335,154HoxA, Hottip, ENm010changing TADs in ES vs differentited cellsES vs HFF
H1-hESC/HFFc6
Dekker
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humanchr3:180,357,788-182,632,351Sox2, Sox2-OTTAD border, changing TADs in ES vs differentited cellsES vs HFF
H1-hESC/HFFc6
Dekkerhttp://higlass.io/app/?config=P1cKrjuKQymp7OA4baJTzA
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humanhg19: chr17:37,800,000-38,200,000Ikzf3, Ormdl3Asthma and other autoimmune disorders :: TAD border, changing in GM12878 vs IMR90GM vs IMR90GM/IMR90Mirnyhttp://higlass.io/app/?config=L-HP--GoTFatsJGBsu_Dmw
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humanhg19: chr3:106744135-112046738Dppa2, Dppa4
Syntenic with mouse and as with mouse, this is a pluripotency specific locus that is an early replicating inter-lad in the A compartment in stem cells, flanked by large swaths of LAD/compartment B/late replicating chromatin. It is switched to late replication and compartment B upon differentiation to any germ layer.
stem cell and any differentiated cell type
H9/H1-hESCGilbert
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human hg19 (chr7:136,912,092-137,028,546)PtnChanging TADs in ES vs differentited cells
stem cell and NPCs
H9/H1-hESCGilbert
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mousemm10, chr6:34,000,000-39,000,000PtnThe Pleiotropin gene is induced upon differentiation to NPCs, is over-expressed in 80% of glioblastomas, the RD/TAD switches from late to early replication. Also a series of deletion/inversions are made in this locus for analysis the effect on TADs/RT. FISH data have been published, as have time courses of expression, RT, RNA, 4C and DNA FISH during differentiation. Promoter has been replaced with a Rheo-switch promoter.
mESC and differentiated to mNPCs
F121-9 and F123Gilbert
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MUC4:http://higlass.io/app/?config=YTNBiN7gTU-z-Z0RU24-2g
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ACTB:
http://higlass.io/app/?config=BV-T8JQfTqOa3ePElODsgA
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