Hi-C and Micro-C Track Settings
 
Comparison of Micro-C and In situ Hi-C protocols in H1-hESC and HFFc6   (All Regulation tracks)

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Items are drawn in shades of the chosen color depending on score - scores above the chosen maximum are drawn at full intensity.

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Subtracks below have additional file-specific configuration options for resolution and normalization.

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 H1-hESC In situ  In situ Hi-C Chromatin Structure on H1-hESC   schema 
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 H1-hESC Micro-C  Micro-C Chromatin Structure on H1-hESC   schema 
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 HFFc6 In situ  In situ Hi-C Chromatin Structure on HFFc6   schema 
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 HFFc6 Micro-C  Micro-C Chromatin Structure on HFFc6   schema 

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., 2019). 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. bioRxiv 639922 [Preprint]. 2019

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