Schema for Hi-C Domains (Embryos) (R5) - Topological Domains Defined by Hi-C in Late Embryos (R5)

Database: dm6 Primary Table: HiC_LE Row Count: 1,168

field	example	SQL type	info
`bin`	73	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	67150	`int(10) unsigned`	range
`chromEnd`	156849	`int(10) unsigned`	range
`name`	Active_0	`varchar(255)`	values
`score`	0	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	67150	`int(10) unsigned`	range
`thickEnd`	156849	`int(10) unsigned`	range
`itemRgb`	16711680	`int(10) unsigned`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	strand	thickStart	thickEnd	itemRgb
73	chr2L	67150	156849	Active_0	+	67150	156849	255,0,0
586	chr2L	156850	250149	Null_0	+	156850	250149	211,211,211
73	chr2L	250150	295749	Active_1	+	250150	295749	255,0,0
73	chr2L	295750	421449	HP1_centromeric_0	+	295750	421449	0,0,139
588	chr2L	421450	472049	HP1_centromeric_1	+	421450	472049	0,0,139
588	chr2L	472050	488649	Active_2	+	472050	488649	255,0,0
73	chr2L	488650	542149	PcG_0	+	488650	542149	128,128,128
73	chr2L	542150	809749	PcG_1	+	542150	809749	128,128,128
591	chr2L	809750	821449	Active_3	+	809750	821449	255,0,0
591	chr2L	821450	852449	Active_4	+	821450	852449	255,0,0

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Hi-C Domains (Embryos) (R5) (HiC_LE) Track Description

Description

This track shows the topological domains defined by Hi-C analysis of Drosophila embryonic nuclei. The Hi-C technique is based on Chromosome Conformation Capture (3C) and it provides an overview of the three dimensional organization of the genome.

The Hi-C results were obtained from the Comparative modENCODE / ENCODE web site. The analysis results were lifted from the D. melanogaster Release 5 assembly over to the Release 6 assembly.

The Hi-C analysis partitioned the genome into four discrete domains:

State	Description	Color
Null	Null domains: weak enrichment of the insulator protein Su(Hw)
Active	Transcriptionally active: enriched in H3K4me3, H3K36me3, hyperacetylation
PcG	Polycomb: enriched in H3K27me3
HP1_Centromere	Classical heterochromatin: enriched in HP1, Su(var)3-9, H3K9me2

References

Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, Parrinello H, Tanay A, Cavalli G. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell. 2012 Feb 3;148(3):458-72.

Ho JW et al. Comparative analysis of metazoan chromatin organization. Nature. 2014 Aug 28;512(7515):449-52.