Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver
- Boston University, United States
Figures
Figure 1 with 2 supplements
Features of TAD boundaries and TAD insulator function.
Profiles in A-E represent a normalized aggregate count of peaks or features along the length of all TADs, sub-divided into 100 equally-sized bins per TAD, where bin #1 is the 5’ start of the TAD and …
Figure 1—figure supplement 1
Additional Features of TAD boundaries.
(A) CTCF binding orientations are divergent at TAD boundaries. The top plot indicates bin enrichment relative to the TAD center, as in Figure 1A. The X-axis begins at the midpoint of one TAD, …
Figure 1—figure supplement 2
Additional Features of TAD boundaries, continued.
(A) Intra-CTCF-motif CpGs are highly hypomethylated compared to the genome-wide average and to neighboring CpGs within 10 kb (‘CpG <10 kb Away’). This is most pronounced for TAD and intra-TAD …
Figure 2 with 7 supplements
Predicted intra-TAD loop anchors share many properties of TAD anchors.
(A) Diagram illustrating intra-TAD loop prediction based on CTCF motif orientation and CTCF and cohesin (Rad21) ChIP-seq binding strength data. Iteration was conducted until 20,000 loops were …
Figure 2—figure supplement 1
Comparison of CTCF Features within TADs and Loop Prediction Improvements.
(A) Fewer than 25% of CTCF, CAC, and tissue ubiquitous CTCF sites are within 25 kb of a TAD boundary. While these features are strongly enriched at TAD boundaries (Figure 1A), the vast majority of …
Figure 2—figure supplement 2
Example Screenshots of Predicted intra-TAD Loops with Observable Interactions in CH12-LX (Mouse B-Cells).
(A-C) Many of the intra-TAD loop structures that we predicted for mouse liver can be seen in the high resolution Hi-C data from the mouse B-cell lymphoma cell line CH12-LX (12). TADs are marked in …
Figure 2—figure supplement 3
Subclasses of CTCF binding events in relation to predicted loops.
(A) Summary of CTCF sites, CAC sites, TAD loop anchors, and intra-TAD loop anchors in mouse liver based on lists in Supplementary file 1C. (1) CTCF peaks found in at least two biological replicate …
Figure 2—figure supplement 4
Intra-TAD loop prediction in two other mouse cell types: mESC and NPC.
(A) Comparison of CAC-mediated intra-TAD loop predicted for mouse embryonic stem cells (mESCs) and neural progenitor cells (NPCs) with those predicted in mouse liver. The number of loops present …
Figure 2—figure supplement 5
Example Screenshots for intra-TAD Loops in mESC and NPC (Mouse).
(A-C) Screenshots of intra-TAD loops predicted in mESC and NPC cells are shown below high-resolution Hi-C data for each cell type. These data provide support for both tissue-specific and …
Figure 2—figure supplement 6
Intra-TAD loop predictions in human cell lines GM12878 and K562.
(A) Comparison of CAC-mediated intra-TAD loop predicted in human lymphoblastoid-derived cells (GM12878 cells) and in human chronic myelogenous leukemic cells (K562 cells). The number of loops …
Figure 2—figure supplement 7
Example Screenshots for intra-TAD Loops in K562 and GM12878 (Human).
(A-C) Screenshots of intra-TAD loops predicted in K562 and GM12878 cells are shown below high-resolution Hi-C data for each cell line. The same genomic region is shown on the left and on the right …
Figure 3 with 2 supplements
Intra-TAD loops show directional interactions and insulate chromatin marks.
(A) TADs and intra-TAD loops both show a stronger orientation of interactions downstream of the motif than other CTCF-bound regions. TAD anchors also show higher inward bias than intra-TAD loops (p<0…
Figure 3—figure supplement 1
Direct evidence of insulation from the asymmetric read distributions for virtual 4C viewpoints anchored at intra-TAD loop anchors or adjacent upstream regions.
(A) Shown is the distribution of Hi-C sequence reads for three intra-TADs referred to in the main text, which provides evidence of directional interactions and insulation in mESCs. For all plots, …
Figure 3—figure supplement 2
Additional features of intra-TADs and their insulation.
(A) TAD anchors are more proximal to divergently-oriented upstream loop anchors, which may explain their elevated local insulation of chromatin contacts and the more diffuse bidirectional contact …
Figure 4 with 2 supplements
Categorization of DHS-based regulatory elements in mouse liver.
(A) Classification of set of ~70,000 open chromatin regions (DHS) identified in adult male mouse liver, based on relative intensities for a combination of H3K4me1 and H3K4me3 marks, and CTCF …
Figure 4—figure supplement 1
Characteristics of five classes of DHS in mouse liver.
(A) Schematic for the classification of open chromatin regions (DHS) in mouse liver based on their H3K4me1, H3K4me3, and CTCF ChIP-seq signals. DHS with >4 rpm for either H3K4me3 or H3K4me1 were …
Figure 4—figure supplement 2
Features of super-enhancers and single-TSS intra-TAD loops.
(A) Shown is the overlap of super-enhancers (SE) for all 19 liver H3K27ac ChIP-seq replicates (see Materials and methods). 503 of the super-enhancers were identified in all 19 liver samples, and are …
Figure 5
Impact of intra-TAD loops on gene expression.
(A) Two possible gene targets were assigned for each super-enhancer within an intra-TAD loop, one target gene for which the TSS is within the intra-TAD loop and another target gene for which the TSS …
Figure 6 with 1 supplement
Alb 4C-seq exemplifies intra-TAD insulation and super-enhancer interaction.
(A) The Alb promoter makes multiple directional contacts with the adjacent super-enhancer region in both male and female mouse liver, as determined by 4C-seq with a viewpoint at the Alb promoter. …
Figure 6—figure supplement 1
Alb 4C-seq replicates and cis/trans 4C-seq signal distribution.
(A) UCSC genome browser screenshots for all biological replicates. The proximal view shows a 150 kb window around the Alb TSS, while the distal view shows a 400 kb view around the Alb TSS. For each …
Additional files
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Source Code 1
All code used for the prediction of intra-TAD loops and additional custom scripts.
- https://doi.org/10.7554/eLife.34077.023
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Supplementary file 1
Intra-TAD loop and CTCF coordinates relevant to Figures 1–3.
- https://doi.org/10.7554/eLife.34077.024
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Supplementary file 2
Mouse liver DHS and Super-enhancer information relevant to Figure 4.
- https://doi.org/10.7554/eLife.34077.025
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Supplementary file 3
Genes and GO term enrichments for genes at refined TAD boundaries and in intra-TADs.
- https://doi.org/10.7554/eLife.34077.026
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Supplementary file 4
Publicly available datasets used and qPCR primers used to validate CTCF/Rad21 ChIPs.
- https://doi.org/10.7554/eLife.34077.027
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Transparent reporting form
- https://doi.org/10.7554/eLife.34077.028
