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 areprobably in close proximity in 3D space within the nucleus of a cell. In the track display, this isshown 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 celllines. Individual subtrack settings can be adjusted by clicking the wrench next to the subtrackname, and all subtracks can be configured simultaneously using the track controls at the top of thepage. Note that some controls (specifically, resolution and normalization options) are onlyavailable in the subtrack-specific configuration. The proximity data in these tracks are displayedas 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 thetop-left-to-bottom-right diagonal, and interaction values are plotted on both sides of that diagonalto form a square. The upper-left corner of the square corresponds to the left-most position of thewindow 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 regionwhere a horizontal line from that point intersects with the diagonal. A point directly on thediagonal shows the score for how proximal a region is to itself (scores on the diagonal are usuallyquite high unless no data are available). A point at the extreme bottom left of the square shows thescore for how proximal the left-most position within the window is to the right-most position withinthe window.
In triangle mode, the display is quite similar to square except that only the top half of the squareis drawn (eliminating the redundancy), and the image is rotated so that the diagonal of the squarenow lies on the horizontal axis. This display consumes less vertical space in the image, although itmay be more difficult to ascertain exactly which positions correspond to a point within thetriangle.
In arc mode, simple arcs are drawn between the centers of interacting regions. The color of each arccorresponds 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 thatthe regions are near to each other. A low score suggests that the regions are farther apart. Highscores 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 countvalues based on the overall count values for each of the two interacting regions. Knight-Ruiz, orKR, matrix balancing (Knight and Ruiz, 2013) provides an alternative normalization method where therow and column sums of the contact matrix equal 1.
Color intensity in the heatmap goes up to indicate higher scores, but eventually saturates at amaximum beyond which all scores share the same color intensity. The value of this maximum score forsaturation 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 intowhich proximity data are gathered. The list of available resolutions ranges from 1kb to 10MB. Thereis also an "Auto" setting, which attempts to use the coarsest resolution that stilldisplays 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 tothe 4D Nucleome Data Coordination and Integration Center (4D Nucleome). The data from the experimental replicates were then combinedto create a contact matrix for each cell line, which was then processed to create binaryheatmap 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-genomeproximity data while keeping the cell nucleus intact (Rao et al., 2014). This method uses arestriction enzyme to cleave DNA before linking. The second protocol, Micro-C XL, is an update tothe Micro-C method of obtaining chromatin conformation data (Hsieh et al., 2016, Hsiehet al., 2015), and has largely supplanted the original. Both the original Micro-C and theupdated version are variants of Hi-C chromatin conformation capture that use micrococcal nuclease tosegment the genome before linking. This results in data sets with resolution down to the nucleosomelevel. The original Micro-C method had difficulty recovering higher order interactions, and theupdated 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 NucleomeData Portal:4DNFI18Q799K,4DNFI2TK7L2F,4DNFIFLJLIS5, and4DNFIQYQWPF5.The files are parsed for display using the Straw library from the Aiden lab at Baylor Collegeof Medicine.
Data Access
The data for this track can be explored interactively with the Table Browser in theinteract format. Direct access to the raw data filesin .hic format can be obtained from the 4D Nucleome Data Portal at the URL provided in the Methodssection 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 nameof each file corresponds to its identifier at the Data Portal. Details on working with .hic filescan 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: 27723753Knight 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
