Cohesin residency determines chromatin loop patterns
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
Figures
Figure 1 with 1 supplement
Micro-C XL reveals positioned loops in mitotic chromosomes.
(A) Micro-C XL maps chromatin conformation by detecting nucleosomes that interact in vivo. Schematic illustrates how two interacting nucleosomes (e.g. 2 and 6) are visualized on the contact map. (B) …
Figure 1—figure supplement 1
Comparison of Micro-C XL and Hi-C mapping in budding yeast.
(A) Micro-C XL in mitotically arrested cells detects more positioned loops than Hi-C. Comparison of contact maps from mitotically arrested cells produced with Micro-C XL (top), Hi-C (center) (Schalbe…
Figure 2 with 2 supplements
Mitotic positioned loops are cohesin-dependent.
(A) Cohesin peaks colocalize with the loop anchors of positioned loops. Contact map showing the interactions in the 290–400 kb region of chromosome X overlays with Mcd1p ChIP-seq tracks on top and …
Figure 2—figure supplement 1
Mitotic loops are cohesin-dependent.
(A) Cohesin and condensin are efficiently depleted upon auxin addition. The depletion of Mcd1p and Brn1p tagged with AID upon auxin addition to the media is shown by western-blot analysis. Tubulin …
Figure 2—figure supplement 2
Comparison of chromosome contacts upon cohesin depletion of Micro-C XL versus Hi-C.
(A) Micro-C detects more cohesin-dependent chromosome contacts with a smaller size-range than Hi-C. Interactions-versus-distance decaying curve shows the normalized contact density (y-axis) against …
Figure 3
Ribosomal DNA (RDN) structure in mitosis is dependent on cohesin and condensin.
(A) Model for RDN structure in interphase and mitosis. RDN (purple) is visualized as a dispersed puff separated from the rest of the genome (black). In mitosis, the RDN structures in a thin line. (B)…
Figure 4 with 1 supplement
The organization of cohesin-dependent loops.
(A) Features of chromatin loops organization from the contact map. Contact map showing the interaction in the 40–160 kb region of chromosome I overlay with the tracks for Mcd1p ChIP-seq signal and …
Figure 4—figure supplement 1
Cohesin-dependent organization of loops.
(A) Genome-wide analysis confirms loop expansion in wild-type. Bar chart shows the percentage of the number of positioned loops per anchor in wild-type (WT) arrested in mitosis. (B) Around half of …
Figure 5 with 1 supplement
Chromatin loops are cell cycle dependent.
(A) Chromatin positioned loops emerge upon cohesin deposition during DNA replication. The figure shows Micro-C (top), Mcd1p ChIP-seq (middle), and Flow cytometry profile (bottom) data across a time …
Figure 5—figure supplement 1
Loop formation during the cell cycle.
(A) Positioned loops detected during the time course are less defined on the contact map. Snapshots for cells for each time point after G1 release at 30°C and then cells arrested in mitosis (right). …
Figure 6 with 1 supplement
Wpl1p- and Pds5p-depletion perturb the looping pattern.
(A) Wpl1p-depletion causes excessive loop expansion on the contact map. Contact maps for WT (top) and WPL1-AID (bottom) show the chromatin interactions over the 200–450 kb region of chromosome X. …
Figure 6—figure supplement 1
Wpl1p- and Pds5p-depletion alters the pattern of loops genome-wide.
(A) Wpl1p and Pds5p are efficiently depleted upon auxin addition. The depletion of Wpl1p and Pds5p tagged with AID upon auxin addition to the media is shown by western-blot analysis. Tubulin is used …
Figure 7 with 1 supplement
Cohesin depletion alters the domain landscape.
(A) Contact map of mitotic chromatin in wild-type cells reveals the presence of CAR domains and their boundaries. Contact map showing the interaction in the 100–550 kb region of chromosome V …
Figure 7—figure supplement 1
Cohesin depletion alters the chromatin domain landscape.
(A) Chromosome domains are reorganized after cohesin removal. Wild-type (WT) (top), cohesin-depleted cells (MCD1-AID) (middle), and asynchronous cells (bottom) Micro-C XL contact maps are plotted at …
Figure 8
Cohesin residency model for loop formation.
Loop-extrusion with a heterogenous cohesin residency gives rise to a heterogeneous pattern of chromatin looping and domains. The intensity of a cohesin ChIP-seq peak reflects the probability of the …
Tables
Table 1
Strains.
| Strain name in the paper | Genotype | Request code | Reference |
|---|---|---|---|
| WT | MATa trp1∆::pGPD1-TIR1-CaTRP1 lys4::LacO(DK)-NAT leu2-3,112 pHIS3-GFPLacI-HIS3:his3-11,15 ura3-52 bar1 | VG3620 | Çamdere et al., 2015 |
| MCD1-AID | MATa MCD1-AID-KANMX6 ADH1-OsTIR1- URA3::ura3-52 lys4::LacO(DK)-NAT trp1-1 GFPLacI-HIS3:his3-11,15 bar1 leu2-3,112 | DK5542 | Eng et al., 2014 |
| BRN1-AID | MATa BRN1-D375-3V5-AID2-HPHMX trp1∆::pGPD1-TIR1-CaTRP1 lys4::LacO(DK)-NAT leu2-3,112 pHIS3-GFPLacI-HIS3:his3-11,15 ura3-52 bar1 | RL401 | Lamothe et al., 2020 |
| BRN1-AID MCD1-AID | MATa MCD1-AID-KANMX6 BRN1-D375-3V5-AID2-HPHMX ADH1-OsTIR1- URA3::ura3-52 lys4::LacO(DK)-NAT trp1-1 GFPLacI-HIS3:his3-11,15 bar1 leu2-3,112 | RL406 | Lamothe et al., 2020 |
| PDS5-AID | MATa PDS5-3V5-AID2-KANMX6 lys4::LacO(DK)-NAT pHIS3-GFP-LacIHIS3::his3-11,15 trp1-1 ura3-52 bar1 | TE228 | Eng et al., 2014 |
| WPL1-AID | WPL1-3V5-AID-G418 TIR1-CaTRP1 bar1 LacO-NAT::lys4 leu2-3,112 GAL+ pHIS3-GFPLacI-HIS3:his3-11,15 ura3-52 | VG3629-3B | this work |
Additional files
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Supplementary file 1
Summary of Micro-C and Hi-C data used in this study.
- https://cdn.elifesciences.org/articles/59889/elife-59889-supp1-v1.xlsx
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Supplementary file 2
Summary of loop calling.
- https://cdn.elifesciences.org/articles/59889/elife-59889-supp2-v1.xlsx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/59889/elife-59889-transrepform-v1.docx
