Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells
- Babraham Institute, United Kingdom
- University of Cambridge, United Kingdom
- King's College London School of Medicine, United Kingdom
Figures
Figure 1 with 4 supplements
A resource of high-resolution promoter interactions in human embryonic stem cells (ESCs) and ESC-derived neuroectodermal cells (NECs).
(A) Overview of the experimental design. Human embryonic stem cells (ESCs) and ESC-derived neuroectodermal progenitors (1) were analysed with Promoter Capture Hi-C to profile interactions involving …
Figure 1—figure supplement 1
Characterisation of ESCs and NECs.
(A) Phase contrast images of undifferentiated ESC colonies (left) and day 7 NEC spheres (right). (B) Flow cytometry analysis of ESCs (blue) and NECs (red) using lineage-specific cell surface …
Figure 1—figure supplement 2
PAX6 promoter interactome and CTCF enrichment at PIRs.
(A) Genome browser representation of the PAX6 promoter interactome in ESCs (upper) and NECs (lower). Significant interactions are shown as purple arcs. ChIP-seq (H3K27me3, H3K27ac, H3K4me1, H3K4me3; …
Figure 1—figure supplement 3
Integrated view of chromatin states and PCHi–C data.
(A) Definition of 16 ChromHMM emission states based on the relative presence or absence of signals from H3K27me3, H3K4me1, H3K27ac and H3K4me3 ChIP-seq data. Similar states were pooled to form six …
Figure 1—figure supplement 4
Read-count interaction profiles for baited promoters presented in Figures 1–3.
Plots show the read counts corresponding to the interactions of baited promoter fragments (grey line) with other HindIII fragments. Significant interactions detected by CHiCAGO (score ≥12) are shown …
Figure 2 with 1 supplement
Promoter-interacting regions can function as tissue-restricted developmental enhancers and identify associated target genes.
(A) A genome browser representation of the POU3F2 promoter interactome in NECs. Genome coordinates are shown underneath. Chromatin states are indicated (active chromatin, green; poised chromatin, …
Figure 2—figure supplement 1
Active PIRs are enriched for enhancers with neural-specific activity.
(A) In ESCs and NECs, PIRs are significantly enriched for VISTA-validated enhancer regions, compared to promoter distance-matched regions (p-value<0.001 for all six permutation tests based on 100 …
Figure 3 with 1 supplement
Characterisation of cis-regulatory units (CRUs).
(A) Boxplot shows the distributions of the number of PIRs per interacting promoter in ESCs (n = 17955) and NECs (n = 18146). Promoters with no detected PIRs are not shown (4121 in ESCs; 3930 in …
Figure 3—figure supplement 1
Additional CRU characterisation.
(A) Boxplots showing the number of PIRs per promoter in ESCs (left) and NECs (right), separated by gene expression quartiles. (B) Number of PIRs per promoter in ESCs (left) and NECs (right), …
Figure 4 with 3 supplements
Clustering of CRUs according to chromatin state of each PIR in ESCs.
(A) CRUs from ESCs were clustered hierarchically according to the distribution and fractions of their PIRs that correspond to each chromatin state. Boxplots show the distribution of PIR fractions …
Figure 4—figure supplement 1
Clustering of CRUs according to chromatin state of each PIR in NECs.
CRUs were hierarchically clustered according to their fractions of PIRs from different chromatin states in NECs. Boxplots depict the distribution of PIR fractions for each chromatin state (Act, …
Figure 4—figure supplement 2
Additional examples of CRUs in ESCs.
Genome browser representations of CRUs in ESCs. Interaction arcs are coloured according to PIR chromatin state (active, green; poised, orange; Polycomb-associated, red; background, grey).
Figure 4—figure supplement 3
Read-count interaction profiles for baited promoters presented in Figures 4 and 5.
Plots show the read counts corresponding to the interactions of baited promoter fragments (grey line) with other HindIII fragments. Significant interactions detected by CHiCAGO (score ≥12) are shown …
Figure 5
CRU state transitions occur during ESC differentiation and are associated with changes in gene transcription.
(A) Pie chart summarising CRU state transitions that occur upon ESC to NEC differentiation. The number of CRUs within each transition category are shown. Transitions that involve dual-state to …
Figure 6 with 1 supplement
Interaction Dynamics: ‘recolouring’ versus ‘rewiring’.
(A) A schematic of interaction dynamics during cell differentiation. In a ‘recolouring’ interaction (left)the PIR undergoes a change in chromatin colour (reflecting a change in chromatin state) …
Figure 6—figure supplement 1
Interaction dynamics involving recolouring and rewiring.
Genome browser representations of interaction dynamics upon ESC to NEC differentiation. Note that only one interaction is shown for each example. Arcs are coloured according to PIR chromatin state …
Author response image 1
CHiCAGO detection of cross-TAD and within-TAD interactions.
(A) The effect of TAD boundary crossing on background levels. In line with the CHiCAGO background estimation procedure (see Additional file 1, Cairns et al., 2016), we used 20kb distance bins to …
Author response image 2
Tuning a signal threshold for TAD detection with HOMER.
(A) Box plots show TAD length distributions for TADs called by HOMER using a range of TAD ∆Z score thresholds (blue to red boxes), as well as for the published TADs from Dixon et al., 2015 detected …
Author response image 3
Properties of CHiCAGO interactions called at different score thresholds in ESCs and NECs.
(A and B) The relative difference between observed and expected numbers of PIRs overlapping with the ChIP-seq peaks of histone modifications and CTCF, detected at a range of CHiCAGO score thresholds …
Additional files
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Supplementary file 1
The detected interactions and the chromatin states of the corresponding promoters and PIRs.
The table shows the IDs and genomic coordinates (based on GRCh37 assembly) of the baited promoter fragments (protein-coding genes only) and their respective PIRs for interactions detected in either ESCs (ESConly), NECs (NEConly), or both cell types (Both). The chromatin states of promoters and PIRs in each cell type are listed in the corresponding BaitState and PIRState columns. See Materials and methods for details on the thresholding approach used. CHiCAGO objects containing read-count and score information for all sequenced fragment pairs in ESCs and NECs are available through Open Science Framework (http://osf.io/sdbg4).
- https://doi.org/10.7554/eLife.21926.019
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Supplementary file 2
PCHi-C candidate genes for enhancer regions annotated in the VISTA Enhancer Browser.
The genomic coordinates (based on GRCh37 assembly) of enhancers annotated in the VISTA Enhancer Browser that map to PIRs detected in either ESCs, NECs, or both (ESConly, NEConly and Both), their reported tissue-specificities, and the associated PCHi-C-identified putative target genes. The columns ActiveESC and ActiveNEC list whether the corresponding VISTA enhancers overlap with active chromatin marks in ESCs and NECs, respectively.
- https://doi.org/10.7554/eLife.21926.020
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Supplementary file 3
The properties of the identified CRUs in ESCs and NECs.
The table lists the following CRU information: associated gene name, gene expression (processed with DESeq2), number of PIRs, the promoter (bait) chromatin state, single/dual-state annotation, CRU cluster ID and CRU chromatin state transitions between ESCs and NECs. Only CRUs which have been assigned to clusters in both ESC and NEC are listed.
- https://doi.org/10.7554/eLife.21926.021
