The human leukemia virus HTLV-1 alters the structure and transcription of host chromatin in cis
- Imperial College London, United Kingdom
- The European Bioinformatics Institute (EMBL-EBI), United Kingdom
Figures
Figure 1 with 11 supplements
HTLV-1 forms distant contacts with the host genome.
(A) Upper line: the HTLV-1 genome (green), with a long terminal repeat (LTR) at each end, is integrated into a clone-specific site in the human genome (grey). The q4C viewpoint (blue rectangle) is …
Figure 1—figure supplement 1
q4C and RNASeq data aligned – clone 6.25.
The distance from the integration site was chosen such that all called peaks are shown. For each clone, the top panel depicts q4C profile in the infected chromosome in duplicate (normalized …
Figure 1—figure supplement 2
q4C and RNASeq data aligned – clone 10.1.
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Figure 1—figure supplement 3
q4C and RNASeq data aligned – clone 8.8.
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Figure 1—figure supplement 4
q4C and RNASeq data aligned – clone 3.83.
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Figure 1—figure supplement 5
q4C and RNASeq data aligned – clone 8.13.
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Figure 1—figure supplement 6
q4C and RNASeq data aligned – clone 11.50.
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Figure 1—figure supplement 7
q4C and RNASeq data aligned – clone 11.63.
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Figure 1—figure supplement 8
q4C and RNASeq data aligned – clone TBX4B.
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Figure 1—figure supplement 9
q4C and RNASeq data aligned – clone 11.65.
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Figure 1—figure supplement 10
q4C and RNASeq data aligned – clone 3.60.
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Figure 1—figure supplement 11
Position of q4C peaks relative to the HTLV-1 provirus. We defined 'upstream' peaks as q4C peaks that lie on the 5′ side of the 5′ LTR of the HTLV-1 provirus, and 'downstream' peaks as those which lie 3′ to the 3′ LTR.
(A) significantly fewer peaks were found upstream of the integration site than downstream (15 vs 29; p=0.03, chi-squared goodness of fit test). (B) The distribution of absolute distance between each …
Figure 2 with 5 supplements
The HTLV-1 provirus makes chromatin contacts in cis with the infected chromosome.
(A) The HTLV-1 provirus is present in one copy per cell. The infected chromosome (green) can be distinguished from the uninfected homologous chromosome (dark blue) by heterozygous single-nucleotide …
Figure 2—figure supplement 1
Identification of infected chromosomes - clone 11.50
The infected chromosome was distinguished from the homologous uninfected chromosome using q4C data (top panel) and chromosome-specific PCR (bottom panel) (further example shown in Figure 2C). Top …
Figure 2—figure supplement 2
Identification of infected chromosomes - clone 11.65.
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Figure 2—figure supplement 3
Identification of infected chromosomes - clone 6.25.
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Figure 2—figure supplement 4
Identification of infected chromosomes - clone 8.13.
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Figure 2—figure supplement 5
Identification of infected chromosomes - clone TBX4B.
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Figure 3 with 1 supplement
Dependency of virus-host contacts on CTCF binding.
(A) Of 44 contacts identified by q4C in the clones examined, 22 contained one CTCF-BS (N = 17) or two CTCF-BS (N = 5); the remaining 22 contacts did not contain a CTCF-BS. The presence of one or …
Figure 3—figure supplement 1
CTCF-BS occupancy at 4C peaks is higher than random expectation.
For each observed peak, we selected random control sites within 2 Mb of the provirus and with a width equal to the observed peak and a position on the same chromosome, within a reasonable distance …
Figure 4 with 2 supplements
Integration site-specific upregulation of host transcription.
(A) In each column, the green arrow indicates the HTLV-1 proviral integration site in the clone indicated at the top of the column. Each row shows the the transcription density (normalized RNA-seq …
Figure 4—figure supplement 1
Upregulation of transcription within 100 kb of integration site.
Normalized ratio of transcription density in each clone (Figure 1, Figure 1—figure supplements 1–10) between 100 kb upstream and 100 kb downstream of the respective proviral integration site; …
Figure 4—figure supplement 2
Examples of clone-specific aberrant transcription and splicing.
(A) RNA-seq reads (upper panel) and splice junctions (boxed, lower panel) flanking the provirus in clone 3.60 and at the same genomic location in clone 3.83. Transcription in the same orientation as …
Figure 5
Clone-specific host transcription is derived from the infected chromosome.
(A) Allelic imbalance (AI) denotes the degree of monoallelic usage of identified SNPs: AI = 0 indicates biallelic transcription; AI = 0.5 indicates monoallelic transcription. In each clone, the AI …
Tables
Table 1
T cell clones used.
https://doi.org/10.7554/eLife.36245.014| Subject | Clone(s) |
|---|---|
| TBJ | 3.60, 3.83 |
| TCX | 8.13, 8.8 |
| TCT | 10.1 |
| TBW | 11.50, 11.63, 11.65, 13.50(U) |
| TBX | TBX4B |
| HAY | 6.25, 6.30(U) |
Additional files
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Supplementary file 1
T cell clones used.
Extended data on clones shown in Table 1. All subjects are HTLV-1 carriers with HAM/TSP, except for HAY who is an asymptomatic carrier of HTLV-1. tax expression of ‘high’ or ‘low’ denotes whether the frequency of plus-strand viral transcripts was higher or lower than the median, respectively.
- https://doi.org/10.7554/eLife.36245.027
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Supplementary file 2
Schematic diagram to compare conventional 4C (A) and q4C (B) protocol.
In the conventional protocol (A), after digesting the crosslinked chromatin with the first restriction enzyme (1 st RE) and ligating the free ends, the DNA was digested with a second restriction enzyme (second RE) followed by religation and inverse PCR to amplify viewpoint (VP)-linked genomic regions. In q4C, we modified the 4C protocol (Krijger and de Laat, 2016) by applying the approach used in our previously described linker-mediated (LM)-PCR protocol (Gillet et al., 2011) for identifying and quantifying proviral integration sites. In q4C, instead of the secondary restriction enzyme, sonication is used to process DNA circles. Linkers with a 6 bp specific tag was added to sonicated DNA. The end of the VP and a fragment of genomic DNA were amplified by LM-PCR. In this example, three ligation events occurred between the VP (red) and a genomic region (green) at the ligation site I and one event at the ligation site II (yellow). Because the DNA shear site is (approximately) random, the amplicon from each cell has a different shear site. The abundance of ligation events at each respective ligation site is quantified by counting the number of different shear sites.
- https://doi.org/10.7554/eLife.36245.028
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Supplementary file 3
q4C data analysis steps.
Summary of main steps in the analysis steps of q4C data. See Materials and methods for details.
- https://doi.org/10.7554/eLife.36245.029
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Transparent reporting form
- https://doi.org/10.7554/eLife.36245.030
