A chromosome is not a straight line in the nucleus. It is folded so that some parts touch each other far more often than others, and the regions of preferential contact are called topologically associating domains. Domain boundaries matter for gene regulation, because an enhancer usually acts on genes inside its own domain and rarely across a boundary. Hi-C measures which parts of the genome are in contact by crosslinking, cutting and religating chromatin, then sequencing the resulting pairs.
This track does not show the contact matrix itself but two summary scores computed from it along the genome. The insulation index is low where few contacts cross a position, so its local minima mark domain boundaries. The directionality index measures whether the contacts at a position point mostly upstream or mostly downstream, and it flips sign at a boundary. Both are shown for 4 samples at 4 developmental stages (256-cell, Dome, 75% epiboly and Prim-5) and at three window sizes, 50 kb, 500 kb and 1 Mb.
This track is part of the DANIO-CODE collection.
Each combination of sample, index type and window size is a separate auto-scaled graph. Positive values are drawn in red and negative values in blue. The window size sets the scale at which the index is computed, so the 50 kb tracks respond to local boundaries and the 1 Mb tracks to large-scale compartments.
Nothing is displayed until tracks are selected on the configuration page, where they can be filtered by developmental stage, window size, index type and sample.
The DANIO-CODE consortium assembled 1,802 zebrafish developmental genomics datasets, 1,438 of them already published and 366 generated by consortium members, and reprocessed all of them from the raw sequencing reads so that samples from different laboratories and different protocols can be compared with each other. ChIP-seq and ATAC-seq were run through the ENCODE pipelines, CAGE-seq through the FANTOM pipeline, and Hi-C and 4C-seq through the pipelines of the groups that produced them. The pipelines are published at gitlab.com/danio-code, and samples were assigned to developmental stages using ZFIN and ENCODE nomenclature. See Baranasic et al. 2022 for details.
The Hi-C data were processed by the group that produced them, and the insulation and directionality indices were computed from the resulting contact matrices at 50 kb, 500 kb and 1 Mb windows. The samples come from the de Wit laboratory and were originally deposited under GSE105015.
At UCSC the tracks were converted from the consortium's public track hub at trackhub2.genereg.net/DANIO-CODE with the script danioCodeHubToRa.py, and the data files were copied from the same server. The data themselves were not modified. The steps are documented in our makeDoc.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our API, track=dcHiC_Composite.
For automated download and analysis, the annotations are stored in bigWig files that can be downloaded from our download server. Files are named after the sample, the window size and the index type, for example DCD003008SQ_DCD017502DT_50000_di.bigWig for the directionality index at 50 kb and ..._ii.bigWig for the insulation index. Individual regions or the whole genome annotation can be obtained using our tool bigWigToBedGraph, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain features within a given range, for example
bigWigToBedGraph http://hgdownload.soe.ucsc.edu/gbdb/danRer11/danioCode/DCD003008SQ_DCD017502DT_50000_di.bigWig \
-chrom=chr1 -start=20000000 -end=21000000 stdout
The original data files, and the sample and protocol metadata behind them, are available from the DANIO-CODE data coordination center at danio-code.zfin.org and from the consortium's track hub at trackhub2.genereg.net/DANIO-CODE.
Thanks to the DANIO-CODE consortium for collecting, reprocessing and publishing these data, and to the laboratories that produced the original datasets.
Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, Jimenez-Gonzalez A, Li N et al. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis- regulatory elements. Nat Genet. 2022 Jul;54(7):1037-1050. PMID: 35789323; PMC: PMC9279159