Haase J et al. (2022), The TFIIH complex is required to establish and ...

XB-ART-58933

Elife 2022 Mar 16;11. doi: 10.7554/eLife.75475.

Show Gene links Show Anatomy links

The TFIIH complex is required to establish and maintain mitotic chromosome structure.

Haase J , Chen R , Parker WM , Bonner MK , Jenkins LM , Kelly AE .

Abstract
Condensins compact chromosomes to promote their equal segregation during mitosis, but the mechanism of condensin engagement with and action on chromatin is incompletely understood. Here, we show that the general transcription factor TFIIH complex is continuously required to establish and maintain a compacted chromosome structure in transcriptionally silent Xenopus egg extracts. Inhibiting the DNA-dependent ATPase activity of the TFIIH complex subunit XPB rapidly and reversibly induces a complete loss of chromosome structure and prevents the enrichment of condensins I and II, but not topoisomerase II, on chromatin. In addition, inhibiting TFIIH prevents condensation of both mouse and Xenopus nuclei in Xenopus egg extracts, which suggests an evolutionarily conserved mechanism of TFIIH action. Reducing nucleosome density through partial histone depletion restores chromosome structure and condensin enrichment in the absence of TFIIH activity. We propose that the TFIIH complex promotes mitotic chromosome condensation by dynamically altering the chromatin environment to facilitate condensin loading and condensin-dependent loop extrusion.

PubMed ID: 35293859
Article link: Elife

Species referenced: Xenopus laevis
GO keywords: condensin complex [+]

Article Images: [+] show captions

	Figure 1. The TFIIH complex is required for chromosome condensation in Xenopus egg extracts. (A) Top: Schematic of chromatid assembly in M-phase high-speed supernatant (HSS) extract. Bottom: Representative fluorescence images of fixed samples from a chromatid assembly reaction taken at indicated timepoints after sperm addition. Chromatin was stained with Hoechst. (B) Representative fluorescence images of chromatid assembly at steady state (180 min after sperm addition) in the presence of indicated inhibitors. Each drug or DMSO control was added at 25 min to exclude effects on the protamine-histone exchange process. Final inhibitor concentrations: Triptolide (50 Î¼M), DRB (100 Î¼M), and a-amanitin (54 Î¼M). See Figure 1â€”figure supplement 1A for CAP-E depletion. Mean condensation parameters for each condition are indicated in lower left corner of each image. (C) Scatter plot of the percentage of pixels below a threshold of 35% of image maximum fluorescence intensity (the condensation parameter), which measures the progressive change in the fluorescence intensity distribution that occurs during condensation, for each condition. Error bars represent SD, and the mean values are indicated. n = 20 structures for each condition. Two biological replicates were performed, quantified structures are from a single experiment. (D) Schematic of the TFIIH complex. TFIIH core complex is green, CAK subcomplex in red. (E) Western blot for XPB, p62, and Tubulin in IgG or XPB-depleted extracts. (F) TFIIH complex members that interact with XPB in M-phase HSS extract, as identified by mass spectrometry. Purifications were performed in the absence of chromatin. PSMs = peptide spectrum matches. (G) Representative fluorescence images of chromatid assembly 90 min after sperm addition in IgG or XPB depleted extracts. Chromatin was stained with Hoechst. (H) Western blot for XPF, ERCC1, and Tubulin in IgG or ERCC1-depleted extracts. (I) Representative fluorescence images of chromatid assembly 180 min after sperm addition in IgG or ERCC1-depleted extracts. Chromatin was stained with Hoechst.
	Figure 2. Continuous TFIIH activity is required to maintain chromosome structure. (A) Representative fluorescence images of chromatid assembly reactions sampled at indicated timepoints. DMSO or triptolide (TPL) were added at indicated times, immediately after sample retrieval for imaging. Chromatin was stained with Hoechst. Red boxes indicate representative images of decondensed chromosomes after triptolide addition. Mean condensation parameters for each condition are indicated in lower left corner of each image, see Figure 2â€”figure supplement 1A for more details. (B) Representative fluorescence images of chromatid masses fixed and spun onto coverslips 215 min after sperm addition, subjected to the indicated manipulations. Nuclei were incubated in extracts for 180 min to allow for the formation of fully condensed chromatids, followed by addition of DMSO or triptolide. After 30 min of incubation with DMSO/triptolide, reactions were diluted 10-fold with extract containing DMSO or triptolide, and further incubated for 5 min before taking samples for imaging. See Figure 2â€”figure supplement 2 for additional controls. Chromatin was stained with Hoechst. (C) Scatter plots of the percentage of pixels below a threshold of 35% of image maximum fluorescence intensity (the condensation parameter), for each condition in (B). Error bars represent SD, and the mean values are indicated. n = 20 structures for each condition. Two biological replicates were performed, quantified structures are from a single experiment. (D) Schematic illustrating the effects of triptolide addition and dilution on chromosome structure maintenance and reformation.

	Figure 4. Triptolide perturbs condensation prior to its effects on condensin levels. (A) Schematic of assay to test the timing of triptolide-induced defects in condensation and condensin levels. After a twenty-five minute incubation, either DMSO or triptolide (TPL) was added, and samples were taken at indicated times and processed for immunofluorescence. (B) Representative immunofluorescence images of DMSO or triptolide treated extracts at indicated timepoints. Chromatids were labeled with Hoechst and anti-CAP-E (condensin I and II). Note that condensation is already lost in in the first timepoint after triptolide addition, as in Figure 2A. Mean condensation parameters for each condition are indicated in lower left corner of each image. (C) Quantification of fluorescence intensity of CAP-E from experiment in (B), normalized to the 180 min DMSO-treated sample. n = 50 structures for each condition. Error bars represent SD, and asterisks indicate a statistically significant difference (*, p < 0.001). A.U., arbitrary units. Two biological replicates were performed, quantified structures are from a single experiment.
	Figure 5. Partial histone H3/H4 depletion rescues chromosome condensation in the absence of TFIIH activity. (A) Representative fluorescence images of mouse sperm nuclei incubated with âˆ†IgG or âˆ†H4K12ac extracts and spun onto coverslips at indicated timepoints. DMSO or Triptolide were added at t = 25â€™, immediately after sample acquisition for imaging. Chromatin was stained with Hoechst. Mean condensation parameters for each condition are indicated in lower left corner of each image. (B) Representative immunofluorescence images of mouse sperm nuclei incubated with âˆ†IgG or âˆ†H4K12ac extracts for 180 min. DMSO or triptolide were added at t = 25â€™. Chromatids were labeled with anti-XPB, anti-CAP-E (condensin I and II), or anti-histone H3, and co-stained with Hoechst. (C) Quantification of fluorescent intensity of indicated proteins from (B), normalized to DMSO. n = 50 structures for each condition. Error bars represent SD, and asterisks indicate a statistically significant difference (*, p < 0.001). A.U., arbitrary units. Two biological replicates were performed, quantified structures are from a single experiment. (D) Model depicting the role of the TFIIH complex in regulating condensin dynamics. Our data are consistent with a model in which TFIIH alters the chromatin environment to allow condensins to load and extrude loops of DNA.
	Figure 1-Figure Supplement 1: Immunodepletions and the effects of RNases and various transcription inhibitors on chromosome condensation and cell cycle state. (A) Western blot for CAP-E, XPB, and Tubulin in Mock or CAP-E depleted extracts. Dilution series of Mock-depleted extracts was used to calculate the % depletion of CAP-E using quantitative fluorescence. (B) 1% agarose gel stained with SYBR safe stain showing RNase A dependent removal of total RNAs from high-speed supernatant egg extracts. (C) Representative fluorescence images of chromatid assembly at steady state (180 min after sperm addition) in the presence of indicated buffers and enzymes. See Materials and methods for details. Note that the high salt in the RNase H buffer causes morphological changes to chromatids regardless of activity. Mean condensation parameters for each condition are indicated in lower left corner of each image. (D) Western blot for XPB and Tubulin in IgG or XPB-depleted extracts. Dilution series of IgG-depleted extracts was used to calculate the % depletion of XPB using quantitative fluorescence. (E) Western blot for XPF, ERCC1, and Tubulin in IgG or ERCC1-depleted extracts. Dilution series of IgG-depleted extracts was used to calculate the % depletion of ERCC1 and XPF using quantitative fluorescence. (F) Representative fluorescence images of chromatid assembly at steady state (180 min after sperm addition) in the presence of DMSO, 30 Î¼M CDK7 inhibitor THZ1, or 30 Î¼M THZ1 and 50 Î¼M triptolide (TPL). (G) Triptolide does not affect CDK1 activation or maintenance of M phase. Western blot for CDK1 T161ph, histone H3T3ph, and Tubulin in M phase HSS extracts in the presence of DMSO or 50 Î¼M triptolide. Both CDK1T161ph (a CDK7 substrate) and H3T3ph are only highly phosphorylated in M phase, and their appearance is not affected by triptolide treatment.
	Figure 1-Figure Supplement 2: Effects of various transcription inhibitors on RNA Polymerase II C-terminal phosphorylation at centromeres. (A) Representative immunofluorescence images of Xenopus sperm nuclei incubated in HSS extracts for 180 min. DMSO was added at 25 min as a control. Chromatids were labeled with Hoechst, either anti-Pol II S5ph (paused) or anti-Pol II S2ph (elongating), and co-stained with anti-CENP-A antibodies. (B) Representative immunofluorescence images of Xenopus sperm nuclei incubated in DMSO, triptolide (TPL), THZ1, DRB, or alpha-amanitin treated HSS extracts for 180 min. All inhibitors were added 25 min after sperm addition. Chromatids were labeled with Hoechst, anti-Pol II S5ph, or anti-Pol II S2ph antibodies.
	Figure 1-Figure Supplement 3: Condensation parameters. (AâD) Scatter plots of the percentage of pixels below a threshold of 35% of image maximum fluorescence intensity (the condensation parameter), for indicated conditions in Figure 1 and Figure 1âfigure supplement 1. Error bars represent SD, and the mean values are indicated. n = 20 structures for each condition. Two biological replicates were performed, quantified structures are from a single experiment.
	Figure 2—figure supplement 1 Condensation parameters of condensation kinetics after DMSO or Triptolide treatment. (A) Scatter plots of the percentage of pixels below a threshold of 35% of image maximum fluorescence intensity (the condensation parameter), for each drug condition and indicated time point. Error bars represent SD, and the mean values are indicated. n = 20 structures for each condition. Two biological replicates were performed, quantified structures are from a single experiment.

	Figure 3—figure supplement 1 The TFIIH complex is required for the enrichment of condensins on chromosomes. (A) Left: Representative immunofluorescence images of Xenopus sperm nuclei incubated with Mock or CAP-E depleted extracts for 180 min. Chromatids were labeled with Hoechst and anti-XPB antibodies. Right: Quantification of fluorescence intensity of XPB on chromatin, normalized to Mock depleted condition. n = 24 structures for each condition. Error bars represent SD, and ‘NS’ indicates no statistically significant difference (p > 0.001). A.U., arbitrary units. Two biological replicates were performed, quantified structures are from a single experiment. (B) Western blot for indicated proteins that copurify with anti-XPB or IgG beads isolated from HSS extracts. IP, immunoprecipitate. (C) Western blot for indicated proteins that copurify with anti-CAP-E or Mock-treated beads isolated from HSS extracts. For condensin subunit detection, the blot was probed simultaneously with the indicated antibodies. Beads were coupled to either anti-CAP-E or pre-immune serum (“Mock”) and processed as indicated in the methods. IP, immunoprecipitate. (D) Representative immunofluorescence images of Xenopus sperm nuclei incubated with HSS extracts for 180 min. Chromatids were labeled with Hoechst and co-stained with anti-XPB and anti-CAP-E antibodies. Images of three representative individual chromatids are shown.
	Figure 4—figure supplement 1 Condensation parameters of condensation kinetics after DMSO or Triptolide treatment. (A) Scatter plots of the percentage of pixels below a threshold of 35% of image maximum fluorescence intensity (the condensation parameter), for each drug condition and indicated time point. Error bars represent SD, and the mean values are indicated. n = 20 structures for each condition. Two biological replicates were performed, quantified structures are from a single experiment.

	Figure 5—figure supplement 1 Effects of triptolide and histone depletion on condensation using mouse sperm. (A) Representative fluorescence images of chromatid assembly at steady state with mouse sperm nuclei in egg extracts (180 min after sperm nuclei addition) in the presence of indicated inhibitors. Triptolide or DMSO control was added at 25 min after nuclei addition. Triptolide was added at 50 μM. (B) Western blot for histone H3, CAP-E, and XPB in histone H4K12ac or IgG-depleted extracts in the presence of triptolide (TPL) or DMSO. Relative percentage of protein remaining after indicated treatments is shown.
	Figure 5—figure supplement 2 Condensation parameters of condensation kinetics after DMSO or Triptolide treatment. (A) Scatter plots of the percentage of pixels below a threshold of 35% of image maximum fluorescence intensity (the condensation parameter), for each drug condition and indicated time point, see Figure 5A for images. Error bars represent SD, and the mean values are indicated. n = 20 structures for each condition. Two biological replicates were performed, quantified structures are from a single experiment.

References [+] :

Aibara, Structures of mammalian RNA polymerase II pre-initiation complexes. 2021, Pubmed