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Description
These tracks provide heatmaps of chromatin folding data from in situ Hi-C and Micro-C XL
experiments on the H1-hESC (embryonic stem cells) and HFFc6 (foreskin fibroblasts) cell lines
(Krietenstein et al., 2020).
The data indicate how many interactions were detected between regions of the genome.
A high score between two regions suggests that they are
probably in close proximity in 3D space within the nucleus of a cell. In the track display, this is
shown by a more intense color in the heatmap.
Display Conventions
This is a composite track with data from experiments that compare two protocols on each of two cell
lines. Individual subtrack settings can be adjusted by clicking the wrench next to the subtrack
name, and all subtracks can be configured simultaneously using the track controls at the top of the
page. Note that some controls (specifically, resolution and normalization options) are only
available in the subtrack-specific configuration. The proximity data in these tracks are displayed
as heatmaps, with high scores (and more intense colors) corresponding to closer proximity.
Draw modes
There are three display methods available for Hi-C tracks: square, triangle, and arc.
Square mode provides a traditional Hi-C display in which chromosome positions are mapped along the
top-left-to-bottom-right diagonal, and interaction values are plotted on both sides of that diagonal
to form a square. The upper-left corner of the square corresponds to the left-most position of the
window in view, while the bottom-right corner corresponds to the right-most position of the window.
The color shade at any point within the square shows the proximity score for two genomic regions:
the region where a vertical line drawn from that point intersects with the diagonal, and the region
where a horizontal line from that point intersects with the diagonal. A point directly on the
diagonal shows the score for how proximal a region is to itself (scores on the diagonal are usually
quite high unless no data are available). A point at the extreme bottom left of the square shows the
score for how proximal the left-most position within the window is to the right-most position within
the window.
In triangle mode, the display is quite similar to square except that only the top half of the square
is drawn (eliminating the redundancy), and the image is rotated so that the diagonal of the square
now lies on the horizontal axis. This display consumes less vertical space in the image, although it
may be more difficult to ascertain exactly which positions correspond to a point within the
triangle.
In arc mode, simple arcs are drawn between the centers of interacting regions. The color of each arc
corresponds to the proximity score. Self-interactions are not displayed.
Score normalization settings
Score values for this type of display correspond to how close two genomic regions are in 3D space.
A high score indicates more links were formed between them in the experiment, which suggests that
the regions are near to each other. A low score suggests that the regions are farther apart. High
scores are displayed with a more intense color value; low scores are displayed in paler shades.
There are four score values available in this display: NONE, VC, VC_SQRT, and KR. NONE provides raw,
un-normalized counts for the number of interactions between regions. VC, or Vanilla Coverage,
normalization (Lieberman-Aiden et al., 2009) and the VC_SQRT variant normalize these count
values based on the overall count values for each of the two interacting regions. Knight-Ruiz, or
KR, matrix balancing (Knight and Ruiz, 2013) provides an alternative normalization method where the
row and column sums of the contact matrix equal 1.
Color intensity in the heatmap goes up to indicate higher scores, but eventually saturates at a
maximum beyond which all scores share the same color intensity. The value of this maximum score for
saturation can be set manually by un-checking the "Auto-scale" box. When the
"Auto-scale" box is checked, it automatically sets the saturation maximum to be double
(2x) the median score in the current display window.
Resolution settings
The resolution for each track is measured in base pairs and represents the size of the bins into
which proximity data are gathered. The list of available resolutions ranges from 1kb to 10MB. There
is also an "Auto" setting, which attempts to use the coarsest resolution that still
displays at least 500 bins in the current window.
Methods
Cells from the H1-hESC and HFFc6 cell lines were processed using two protocols and submitted to
the 4D Nucleome Data Coordination and Integration Center (4D Nucleome). The data from the experimental replicates were then combined
to create a contact matrix for each cell line, which was then processed to create binary
heatmap files like the .hic files used by this track.
The first protocol, in situ Hi-C, was published in 2014 as a technique for obtaining full-genome
proximity data while keeping the cell nucleus intact (Rao et al., 2014). This method uses a
restriction enzyme to cleave DNA before linking. The second protocol, Micro-C XL, is an update to
the Micro-C method of obtaining chromatin conformation data (Hsieh et al., 2016, Hsieh
et al., 2015), and has largely supplanted the original. Both the original Micro-C and the
updated version are variants of Hi-C chromatin conformation capture that use micrococcal nuclease to
segment the genome before linking. This results in data sets with resolution down to the nucleosome
level. The original Micro-C method had difficulty recovering higher order interactions, and the
updated protocol makes use of additional cross-linking chemicals to address that issue.
We downloaded the .hic contact matrix files with the following accessions from the 4D Nucleome
Data Portal:
4DNFI18Q799K,
4DNFI2TK7L2F,
4DNFIFLJLIS5, and
4DNFIQYQWPF5.
The files are parsed for display using the Straw library from the Aiden lab at Baylor College
of Medicine.
Data Access
The data for this track can be explored interactively with the Table Browser in the
interact format. Direct access to the raw data files
in .hic format can be obtained from the 4D Nucleome Data Portal at the URL provided in the Methods
section or from our own download server. The following files for this track can be found in the
/gbdb/hg38/hic/
subdirectory: 4DNFI18Q799K.hic, 4DNFI2TK7L2F.hic, 4DNFIFLJLIS5.hic, 4DNFIQYQWPF5.hic. The name
of each file corresponds to its identifier at the Data Portal. Details on working with .hic files
can be found at https://www.aidenlab.org/documentation.html.
References
Hsieh TS, Fudenberg G, Goloborodko A, Rando OJ.
Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome.
Nat Methods. 2016 Dec;13(12):1009-1011.
PMID: 27723753
Knight P, Ruiz D.
A fast algorithm for matrix balancing.
IMA J Numer Anal. 2013 Jul;33(3):1029-1047.
Krietenstein N, Abraham S, Venev SV, Abdennur N, Gibcus J, Hsieh TS, Parsi KM, Yang L, Maehr R,
Mirny LA et al.
Ultrastructural Details of Mammalian Chromosome Architecture.
Mol Cell. 2020 May 7;78(3):554-565.e7.
PMID: 32213324
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR,
Sabo PJ, Dorschner MO et al.
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Science. 2009 Oct 9;326(5950):289-93.
PMID: 19815776; PMC: PMC2858594
Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD,
Lander ES et al.
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
Cell. 2014 Dec 18;159(7):1665-80.
PMID: 25497547; PMC: PMC5635824
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