Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, United States
- Department of Genome Sciences, University of Washington, United States
- Department of Chemistry, New York University, United States
- Institute of Cellular and Organismic Biology, Academia Sinica, Taiwan
- Courant Institute of Mathematical Sciences, New York University, United States
- New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, China
- Paul G. Allen School of Computer Science and Engineering, University of Washington, United States
Figures
Figure 1 with 3 supplements
Local inter-nucleosome interactions are distinct in quiescent cells.
(A) Left, contact probability map of nucleosome (n) interactions from exponentially growing (Log) and quiescent (Q) Micro-C XL data (3). Contacts between ligated di-nucleosomes in the ‘same’ …
Figure 1—figure supplement 1
HiCRep scores of Micro-C data.
(A) Stratum-adjusted correlation coefficients (SCCs) calculated by HiCRep of Micro-C XL data from two biological replicates of each of the indicated conditions. HHF2 was completed in only one …
Figure 1—figure supplement 2
Long-distance and gene-specific contacts in Log and Q.
(A) Cumulative contact probability of contacts between distances of 10 kb and 1000 kb. (A, B) Left, contacts separated into clusters based on RNA Polymerase II (Pol II) occupancy in Log (A) and Q (B)…
Figure 1—figure supplement 3
Omitting DSG from the Micro-C XL protocol diminishes contacts in log cells.
(A) Genome-wide Micro-C XL data in Q with and without DSG. (B) Micro-C XL data at 1 kb resolution. (C) Genome-wide Micro-C XL data in Log with and without DSG. (D) Micro-C XL data at 1 kb …
Figure 2 with 3 supplements
Local chromatin fiber compaction increases in quiescent cells.
(A) HAADF-STEM images of uranyl acetate and lead citrate stained G1-arrested, Q cell, and magnesium-treated chicken erythrocyte nuclei slices. Chromatin fibers appear as white. NE is nuclear …
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Figure 2—source data 1
Tail-core contact counts.
- https://cdn.elifesciences.org/articles/72062/elife-72062-fig2-data1-v2.xlsx
Figure 2—figure supplement 1
Morphological erosion analysis of chromatin fiber diameters.
(A) The residual volume of the chromatin fiber is plotted against the filter radius. A liner function is used to fit the first five data points to estimate the diameter of chromatin fibers based on …
Figure 2—figure supplement 2
Input parameters for mesoscale modeling.
(A) Starting configurations for Q and Log cell chromatin fibers. Genes are shown in light blue and blue for Log and Q, respectively. For both systems, intergenic regions are shown in dark red, …
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Figure 2—figure supplement 2—source data 1
Input parameters for modeling.
- https://cdn.elifesciences.org/articles/72062/elife-72062-fig2-figsupp2-data1-v2.xlsx
Figure 2—figure supplement 3
Mesoscale modeling of Log and Q chromatin fibers.
(A, B) Simulation convergence assessed through global and local properties. Shown are the average dimer distance, total energy, and sedimentation coefficient along 80 million MC steps. We show the …
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Figure 2—figure supplement 3—source data 1
Compaction parameters.
- https://cdn.elifesciences.org/articles/72062/elife-72062-fig2-figsupp3-data1-v2.xlsx
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Figure 2—figure supplement 3—source data 2
Tail-tail contact counts.
- https://cdn.elifesciences.org/articles/72062/elife-72062-fig2-figsupp3-data2-v2.xlsx
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Figure 2—figure supplement 3—source data 3
Tail-DNA contact counts.
- https://cdn.elifesciences.org/articles/72062/elife-72062-fig2-figsupp3-data3-v2.xlsx
Figure 3 with 1 supplement
Histone deacetylation is necessary for quiescence-specific chromatin folding.
(A) H4 tail penta-acetylation ChIP-seq heatmaps ±1 kb of all transcription start sites (TSS). Rows are linked across all heatmaps. (B) Chromatin volume measurements following DAPI staining of at …
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Figure 3—source data 1
Chromatin volume measurements.
- https://cdn.elifesciences.org/articles/72062/elife-72062-fig3-data1-v2.xlsx
Figure 3—figure supplement 1
TSA treatment increases H4 tail acetylation and decompacts chromatin in Q cells.
(A) Representative Western blots of H4 penta-acetylation (H4Ac) and H2B in Log, Q, and TSA-treated Q cells. Band volumes were quantified using Fiji and H4Ac volumes were normalized to H2B volumes. …
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Figure 3—figure supplement 1—source data 1
H4Ac and H2B Western blots.
- https://cdn.elifesciences.org/articles/72062/elife-72062-fig3-figsupp1-data1-v2.pdf
Figure 4 with 2 supplements
The H4 tail basic patch regulates quiescence-specific chromatin folding.
(A) Chromatin volume measurements following DAPI staining of at least 100 cells of two biological replicates of quiescent H4 mutant cells. HHF2 is the single-copy HHT2-HHF2 WT control strain. Bars …
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Figure 4—source data 1
Chromatin volume measurements.
- https://cdn.elifesciences.org/articles/72062/elife-72062-fig4-data1-v2.xlsx
Figure 4—figure supplement 1
Phenotypes of H4 basic patch and H2A acidic patch substitutions in quiescence.
(A) Representative images of DAPI-stained cells. Chromatin volumes were calculated as described in Figure 3 and in the Materials and methods. Mean volumes are shown below. HHF2 is a WT control. Raw …
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Figure 4—figure supplement 1—source data 1
Q cell counts.
- https://cdn.elifesciences.org/articles/72062/elife-72062-fig4-figsupp1-data1-v2.xlsx
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Figure 4—figure supplement 1—source data 2
Q cell longevity.
- https://cdn.elifesciences.org/articles/72062/elife-72062-fig4-figsupp1-data2-v2.xlsx
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Figure 4—figure supplement 1—source data 3
Chromatin volume measurements.
- https://cdn.elifesciences.org/articles/72062/elife-72062-fig4-figsupp1-data3-v2.xlsx
Figure 4—figure supplement 2
H4 basic patch substitutions decompact chromatin in Q.
(A) Cumulative contact probability of contacts between distances of 10 kb to 1000 kb. (B, C) Genome-wide Micro-C XL data. (D, E) Micro-C XL data at 1 kb resolution.
Figure 5 with 1 supplement
Quiescence-specific local chromatin folding represses transcription.
(A) Genome browser view of Pol II subunit Rpb3 ChIP-seq data in quiescent mutant strains across a portion of Chromosome II. (B) Heatmaps of Rpb3 across all TSSs in Log and (C) Q cells. Rows are the …
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Figure 5—source data 1
Chromatin volume measurements.
- https://cdn.elifesciences.org/articles/72062/elife-72062-fig5-data1-v2.xlsx
Figure 5—figure supplement 1
Pol II and H3 ChIP-seq in Log and Q.
(A) Genome browser view of Pol II subunit Rpb3 ChIP-seq data in log and quiescent mutant strains across the entirety of Chromosome V. (B) Pearson correlation scores calculated and hierarchically …
Figure 6 with 1 supplement
H4-tail mediated chromatin folding inhibits condensin loop extrusion.
(A) Condensin subunit Brn1 ChIP-seq data overlayed beneath representative Micro-C XL data at 200 bp resolution. (B) Schematic showing one-sided loop extrusion by condensin between two boundaries. (C)…
Figure 6—figure supplement 1
H4-mediated chromatin fiber folding represses condensin loop extrusion.
(A–C) Condensin subunit Brn1 ChIP-seq in R17R19A (top) and HHF2 (bottom) data overlayed across Micro-C XL data at 200 bp resolution. (D) Metaplots of Micro-C XL data showing aggregate peak analysis …
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Figure 6—figure supplement 1—source data 1
Brn1-FLAG and H2B Western blots.
- https://cdn.elifesciences.org/articles/72062/elife-72062-fig6-figsupp1-data1-v2.pdf
Figure 7
Chromatin fiber folding and condensin looping are complementary mechanisms of transcriptional repression.
(A) MACS differential peak calls for SMC4-off and 5toA Brn1 ChIP-seq in Q. SMC4-off cells contain a doxycycline-inducible Tet repressor system to shut off the expression of the condensin subunit …
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Saccharomyces cerevisiae) | WT | McKnight et al., 2015 | yTT5781 | MATa RAD5+ prototroph: |
| Strain, strain background (S. cerevisiae) | WT | McKnight et al., 2015 | yTT5783 | MATa RAD5+ prototroph |
| Strain, strain background (S. cerevisiae) | Hho1-FLAG | This Paper | yTT6336 | MATa RAD5+ prototroph HHO1- 2L-3FLAG::KanMX |
| Strain, strain background (S. cerevisiae) | Hho1-FLAG | This Paper | yTT6337 | MATa RAD5+ prototroph HHO1- 2L-3FLAG::KanMX |
| Strain, strain background (S. cerevisiae) | HHF2 | This Paper | yTT7177 | MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2- hhf2::Hyg trp1-1::pRS 404-HHT2-HHF2 |
| Strain, strain background (S. cerevisiae) | HHF2 | This Paper | yTT7206 | MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2- hhf2::Hyg trp1-1::pRS 404-HHT2-HHF2 |
| Strain, strain background (S. cerevisiae) | hhf2-5toA | This Paper | yTT7175 | MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2- hhf2::Hyg trp1-1::pRS 404-HHT2-hhf2-K16A, R17A,H18A,R19A,K20A |
| Strain, strain background (S. cerevisiae) | hhf2-5toA | This Paper | yTT7208 | MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2- hhf2::Hyg trp1-1::pRS 404-HHT2-hhf2-K16A, R17A,H18A,R19A,K20A |
| Strain, strain background (S. cerevisiae) | hhf2-R17A,R19A | This Paper | yTT7200 | MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2- hhf2::Hyg trp1-1::pRS 404-HHT2-hhf2- R17A,R19A |
| Strain, strain background (S. cerevisiae) | hhf2-R17A,R19A: | This Paper | yTT7207 | MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2- hhf2::Hyg trp1-1::pRS 404-HHT2-hhf2-R17A, R19A |
| Strain, strain background (S. cerevisiae) | hhf2-K16A | This Paper | yTT7202 | MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2- hhf2::Hy g trp1-1::pRS404- HHT2-hhf2-K16A |
| Strain, strain background (S. cerevisiae) | hhf2-K16A | This Paper | yTT7209 | MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2- hhf2::Hyg trp1-1::pRS404- HHT2-hhf2-K16A |
| Strain, strain background (S. cerevisiae) | hhf2-K16Q | This Paper | yTT7205 | MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2- hhf2::Hyg trp1-1::pRS 404-HHT2-hhf2-K16Q |
| Strain, strain background (S. cerevisiae) | hhf2-K16Q | This Paper | yTT7210 | MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2- hhf2::Hyg trp1-1::pRS404- HHT2-hhf2-K16Q |
| Strain, strain background (S. cerevisiae) | HHF2 Brn1-FLAG | This Paper | yTT7390 | MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2- hhf2::Hyg trp1-1::pRS 404-HHT2-HHF2 Brn1- 2L-3FLAG::KanMX |
| Strain, strain background (S. cerevisiae) | HHF2 Brn1-FLAG | This Paper | yTT7391 | MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2- hhf2::Hyg trp1-1::pRS 404-HHT2-HHF2 Brn1- 2L-3FLAG::KanMX |
| Strain, strain background (S. cerevisiae) | hhf2-5toA Brn1-FLAG | This Paper | yTT7388 | MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2- hhf2::Hyg trp1-1::pRS 404-HHT2-hhf2-K16A, R17A,H18A,R19A, K20A Brn1-2L- 3FLAG::KanMX |
| Strain, strain background (S. cerevisiae) | hhf2-5toA Brn1-FLAG | This Paper | yTT7389 | MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2- hhf2::Hyg trp1-1::pRS 404-HHT2-hhf2-K16A, R17A,H18A,R19A,K20A Brn1-2L-3FLAG::KanMX |
| Strain, strain background (S. cerevisiae) | hhf2-R17A,R19A Brn1-FLAG | This Paper | yTT7392 | MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2- hhf2::Hyg trp1-1::pRS 404-HHT2-hhf2-R17A, R19A Brn1-2L- 3FLAG::KanMX |
| Strain, strain background (S. cerevisiae) | hhf2-R17A,R19A Brn1-FLAG | This Paper | yTT7393 | MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2- hhf2::Hyg trp1-1::pRS 404-HHT2-hhf2-R17A, R19A Brn1-2L- 3FLAG::KanMX |
| Strain, strain background (S. cerevisiae) | hhf2-K16Q Brn1-FLAG | This Paper | yTT7394 | MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2- hhf2::Hyg trp1-1::pRS404- HHT2-hhf2-K16Q Brn1- 2L-3FLAG::KanMX |
| Strain, strain background (S. cerevisiae) | hhf2-K16Q Brn1-FLAG | This Paper | yTT7395 | MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2- hhf2::Hyg trp1-1::pRS 404-HHT2-hhf2-K16Q Brn1-2L-3FLAG::KanMX |
| Strain, strain background (S. cerevisiae) | HTA1 | This Paper | yTT6767 | MATa W303 Rad5+ ade2-1 can1-100 his3- 11,15 leu2-3,112 ura3-1 hta1-htb1::Hyg hta2- htb2::Nat trp1-1::pRS 404-HTA1-HTB1 |
| Strain, strain background (S. cerevisiae) | HTA1 | This Paper | yTT6773 | MATa W303 Rad5+ ade2-1 can1-100 his3- 11,15 leu2-3,112 ura3- 1 hta1-htb1::Hyg hta2- htb2::Nat trp1-1::pRS 404-HTA1-HTB1 |
| Strain, strain background (S. cerevisiae) | hta1-E57A | This Paper | yTT6768 | MATa W303 Rad5+ ade2-1 can1-100 his3- 11,15 leu2-3,112 ura3-1 hta1-htb1::Hyg hta2- htb2::Nat trp1-1::pRS404- hta1-E57A-HTB1 |
| Strain, strain background (S. cerevisiae) | hta1-E57A | This Paper | yTT6774 | MATa W303 Rad5+ ade2-1 can1-100 his3-11, 15 leu2-3,112 ura3-1 hta1- htb1::Hyg hta2-htb2::Nat trp1-1::pRS404-hta1- E57A-HTB1 |
| Strain, strain background (S. cerevisiae) | hta1-E65A | This Paper | yTT6769 | MATa W303 Rad5+ ade2-1 can1-100 his3- 11,15 leu2-3,112 ura3-1 hta1-htb1::Hyg hta2- htb2::Nat trp1-1::pRS404- hta1-E65A-HTB1 |
| Strain, strain background (S. cerevisiae) | hta1-E65A | This Paper | yTT6776 | MATa W303 Rad5+ ade2-1 can1-100 his3- 11,15 leu2-3,112 ura3-1 hta1-htb1::Hyg hta2- htb2::Nat trp1-1::pRS404- hta1-E65A-HTB1 |
| Strain, strain background (S. cerevisiae) | hta1-E93A | This Paper | yTT6772 | MATa W303 Rad5+ ade2-1 can1-100 his3- 11,15 leu2-3,112 ura3-1 hta1-htb1::Hyg hta2- htb2::Nat trp1-1::pRS404- hta1-E93A-HTB1 |
| Strain, strain background (S. cerevisiae) | hta1-E93A | This Paper | yTT6779 | MATa W303 Rad5+ ade2-1 can1-100 his3- 11,15 leu2-3,112 ura3-1 hta1-htb1::Hyg hta2- htb2::Nat trp1-1::pRS 404-hta1-E93A-HTB1 |
| Strain, strain background (S. cerevisiae) | hta1-E65A,D92A | This Paper | yTT6618 | MATa W303 Rad5+ ade2-1 can1-100 his3- 11,15 leu2-3,112 ura3- 1 hta1-htb1::Hyg hta2- htb2::Nat trp1-1::pRS 404-hta1-E65A, D92A-HTB1 |
| Strain, strain background (S. cerevisiae) | hta1-E65A,D92A | This Paper | yTT6765 | MATa W303 Rad5+ ade2-1 can1-100 his3-11, 15 leu2-3,112 ura3-1 hta1- htb1::Hyg hta2-htb2::Nat trp1-1::pRS404-hta1- E65A,D92A-HTB1 |
| Antibody | H2B (polyclonal, rabbit) | Active Motif | 39237 | WB (1:5000) |
| Antibody | H3 (rabbit polyclonal) | Abcam | 1791 | ChIP (1 μl) |
| Antibody | H4 penta-acetyl (rabbit polyclonal) | MilliporeSigma | 06-946 | WB (1:1000)ChIP (2 μl) |
| Antibody | Rpb3 (mouse monoclonal) | BioLegend | 665003 | ChIP (2 μl) |
| Antibody | FLAG M2 (mouse monoclonal) | Sigma-Aldrich | F1804 | WB (1:3000)ChIP (4 μl) |
| Chemical compound | Percoll | GE | 17-0891-01 | |
| Chemical compound, drug | Trichostatin A (TSA) | TCI | T247710MG | |
| Chemical compound, drug | Disuccinimidyl glutarate (DSG) | Thermo Fisher Scientific | PI20593 | |
| Commercial assay or kit | MinElute PCR Cleanup Kit | Qiagen | 28004 | |
| Other | Dynabeads M-280 sheep anti-mouse IgG beads | Invitrogen | 11201D | 20 μl |
| Other | Dynabeads Protein G beads | Invitrogen | 10004D | 20 μl |
| Commercial assay or kit | Ovation Ultralow v2 Kit | Tecan | 0344 | |
| Other | PTFE printed slides | Electron Microscopy Sciences | 63430-04 |
Additional files
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Supplementary file 1
Statistical values for all chromatin volume measurements, including n, mean, and standard deviation for all replicates as well as p values of comparisons between samples.
- https://cdn.elifesciences.org/articles/72062/elife-72062-supp1-v2.docx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/72062/elife-72062-transrepform1-v2.docx
