A compartmentalized signaling network mediates crossover control in meiosis
- University of California, Berkeley, United States
- Howard Hughes Medical Institute, United States
- Lawrence Berkeley National Laboratory, United States
- California Institute for Quantitative Biosciences, United States
Figures
Figure 1 with 3 supplements
ZHP proteins exhibit two distinct patterns of dynamic localization.
(A–D) Projection images showing immunofluorescent localization of 3xFLAG tagged ZHP-1 (A), ZHP-2 (B), ZHP-3 (C) and ZHP-4 (D) relative to SCs (marked by SYP-1) and CO sites (marked by GFP-COSA-1) …
Figure 1—figure supplement 1
Sequence alignment of C. elegans ZHPs, and the evolution of ZHPs in nematodes.
(A) Sequence alignment of C. elegans F55A12.10 (ZHP-1), D1081.9 (ZHP-2), K02B12.8 (ZHP-3) and Y39B6A.16 (ZHP-4) generated with T-Coffee (Notredame et al., 2000). Dark and gray shading indicate …
Figure 1—figure supplement 2
Absence of nonspecific staining with anti-FLAG antibodies in the C. elegans germline.
Projection images showing C. elegans germline immunostained with anti-3xFLAG epitope antibody (red) and anti-SYP-1 antibody (indicating synaptonemal complex (SC), blue). Insets in each panel show …
Figure 1—figure supplement 3
Localization of the ZHPs along meiotic chromosomes depends on SCs.
(A,B) Projection images of mid- and late pachytene nuclei, showing the localization of ZHP-2-HA (A) and ZHP-4-HA (B) in syp-1 mutant hermaphrodites and heterozygous controls. Chromosome axes are …
Figure 2 with 2 supplements
ZHPs likely act as two heterodimeric protein complexes.
(A–H) Projection images of mid-pachytene and diplotene nuclei, showing the localization of ZHPs (green), with corresponding Western blots to assess protein levels in the presence and absence of …
Figure 2—figure supplement 1
Depletion of ZHP proteins using the AID system.
(A) Western blots showing robust, rapid degradation of AID-tagged ZHP proteins in animals exposed to 1 mM auxin. Blots were done with anti-FLAG and anti-tubulin antibodies, respectively. Tubulin was …
Figure 2—figure supplement 2
Additional antibody validation, ZHP-4 in zhp-3 mutants, and yeast 2-hybrid analysis of ZHP protein interactions.
(A,B) Projection images showing dissected C. elegans gonads stained with anti-HA antibodies (green) (A) or anti-V5 antibodies (green) (B), and anti-SYP-1 antibodies (red). Anti-epitope antibodies do …
Figure 3 with 3 supplements
ZHP proteins play a central role in chiasma formation and meiotic chromosome segregation.
(A–D) Upper: DAPI-stained oocyte nuclei at late diakinesis. Each panel shows a representative nucleus. Lower: Graphs indicating the distribution of DAPI-staining bodies observed at diakinesis. ZHPs …
Figure 3—figure supplement 1
Chiasma formation in zhp-1 or zhp-3 null mutants.
(A–C) Null mutations in zhp-1 and zhp-3 quantitatively recapitulate the effects of AID-mediated depletion. Upper: Representative examples of DAPI-stained oocyte nuclei at diakinesis. Lower: Graphs …
Figure 3—figure supplement 2
ZHP are dispensable for homolog pairing and synapsis.
(A) Projection images of representative pachytene nuclei stained for SYP-1 (green) and HTP-3 (red), revealing normal synapsis in ZHP-depleted worms. Animals expressing the indicated transgene, along …
Figure 3—figure supplement 3
ZHPs are dispensable for DSB induction and the crossover assurance checkpoint.
(A) Projection images of mid-pachytene nuclei stained for RAD-51 (yellow) and DNA (blue), showing accumulation of DSB repair intermediates in the absence of ZHP-1 or ZHP-4. Scale bars, 5 µm. (B) …
Figure 4 with 2 supplements
ZHP-3/4 are required to stabilize recombination intermediates, while ZHP-1/2 promote accumulation of pro-CO factors at a subset of intermediates during late prophase.
(A–F) Low-magnification images of mid- and late pachytene nuclei stained for GFP-COSA-1 (green) and SYP-1 (red). Insets on the right showing corresponding nuclei at late pachynema. (A) …
Figure 4—figure supplement 1
ZHP-3/4 are required for the appearance of MSH-5 foci, while ZHP-1/2 limit the number of foci during late prophase.
(A–D) Recombination intermediates visualized by immunolocalization of MSH-5. Low-magnification images of pachytene nuclei stained for MSH-5 (green) and SYP-1 (red). Larger magnification insets on …
Figure 4—figure supplement 2
Robust protein co-depletion by the AID system and persistence of ZHP-3 throughout SCs following ZHP-1/2 depletion.
(A) Images of representative pachytene nuclei stained for ZHP-1-AID-3xFLAG (green), RAD-51 (cyan) and SYP-1 (red). ZHP-1 and recombination intermediates were undetectable following treatment with …
Figure 5 with 2 supplements
CO designation in the absence of ZHP-1/2.
(A) Projection images of representative late pachytene nuclei stained for GFP-COSA-1 (green) and SYP-1 (red). In the absence of DSB-2 at 24 hr post-L4, an average of 3 bright GFP-COSA-1 foci are …
Figure 5—figure supplement 1
Validation of protein depletion, and further characterization of ZHP-1/2.
(A) Western blot showing efficient auxin-mediated depletion of DSB-2 alone, or co-depletion of ZHP-2 and DSB-2. Blots were probed with anti-FLAG and anti-tubulin antibodies, respectively. Tubulin …
Figure 5—figure supplement 2
Partial depletion fails to separate the roles of ZHP-1/2 in limiting late recombination intermediates and promoting crossover maturation.
(A) Western blots showing partial depletion of AID-tagged ZHP-2 in animals exposed to low concentrations of auxin. Blots were probed with anti-FLAG and anti-tubulin antibodies, respectively. Tubulin …
Figure 6 with 2 supplements
ZHP-1/2 act at the top of a hierarchy of chromosome remodeling factors.
(A) Late pachytene nuclei in a dsb-2 mutant at 48 hr post-L4, stained for ZHP-3-V5 (green) and SYP-2 (red). ZHP-3 is depleted and SYP-2 is enriched specifically along SCs with bright ZHP-3 foci. …
Figure 6—figure supplement 1
ZHP-1/2 are required for chromosome remodeling.
(A–C) Images of late pachytene nuclei stained for SYP-1 (green) and HTP-1 (red). (A) In zhp-1 heterozygotes, SYP-1 and HTP-1 show normal, reciprocal localization in late prophase. (B) In dsb-2 null …
Figure 6—figure supplement 2
ZHP-1/2 are required for chromosome remodeling.
(A,B) ZHP-2 is required for asymmetric localization of PLK-2 following crossover designation. (A) In wild-type nuclei, and in animals expressing ZHP-AID in the absence of auxin, PLK-2 (red) …
Figure 7
Compartmentalization of CO signaling within polycomplexes.
Polycomplexes assemble from SC proteins in meiotic nuclei of htp-3 mutants. During late meiotic prophase, a single focus containing COSA-1 and ZHP-3 appears on each polycomplex (Rog et al., 2017and …
Figure 8
Schemata for crossover control and chromosome remodeling.
(A) Spatial regulation of CO designation by ZHP proteins. In early prophase, all 4 ZHPs concentrate within SCs at the interface between homologous chromosomes. DSBs are induced and homologous …
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Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Caenorhabditis elegans) | zhp-1 | WormBase/This paper | WormBase ID: F55A12.10; WBGene00018867 | |
| Gene (Caenorhabditis elegans) | zhp-2 | WormBase/This paper | WormBase ID: D1081.9; WBGene00008387 | |
| Gene (Caenorhabditis elegans) | zhp-3 | WormBase/(Jantsch et al., 2004) PMID: 15340062 | WormBase ID: K02B12.8b; WBGene00006976 | |
| Gene (Caenorhabditis elegans) | zhp-4 | WormBase/This paper | WormBase ID: Y39B6A.16; WBGene00012678 | |
| Strain, strain background (Saccharomyces cerevisiae) | S. cerevisiae: MaV203 | Invitrogen, Thermo Fisher Scientific, Waltham, MA | Cat#11445012 | |
| Strain, strain background (Caenorhabditis elegans) | For C. elegans allele and strain information, see Supplementary file 1, Tables S2 and S4. | This paper | N/A | |
| Genetic reagent | For CRISPR/Cas9 reagents, see sequence-based reagent and peptide, recombinant protein. | This paper | N/A | |
| Antibody | Rabbit polyclonal anti-SYP-1 | (MacQueen et al., 2002) PMID: 12231631 | N/A | (1:500 IF) |
| Antibody | Rabbit polyclonal anti-SYP-2 | (Colaiácovo et al., 2003) PMID: 12967565 | N/A | (1:500 IF) |
| Antibody | Rabbit polyclonal anti-HTP-1 | (Martinez-Perez et al., 2008) PMID: 18923085 | N/A | (1:500 IF) |
| Antibody | Rabbit polyclonal anti-RAD-51 | Millipore Sigma, St. Louis, MO | Cat#29480002 | (1:5,000 IF) |
| Antibody | Rabbit polyclonal anti-pHIM-8/ZIMs | (Kim et al., 2015) PMID: 26506311 | N/A | (1:500 IF) |
| Antibody | Rabbit polyclonal anti-ZHP-3 | ModENCODE/SDIX; (Rog et al., 2017) PMID: 28045371 | Cat#SDQ3956 | (1:5,000 IF) |
| Antibody | Rabbit polyclonal anti-MSH-5 | ModENCODE/SDIX | Cat#SDQ2376 | (1:5,000 IF) |
| Antibody | Rabbit polyclonal anti-REC-8 | ModENCODE/SDIX | Cat#SDQ0802 | (1:5,000 IF) |
| Antibody | Rabbit polyclonal anti-COH-3 | ModENCODE/SDIX | Cat#SDQ3972 | (1:5,000 IF) |
| Antibody | Rat polyclonal anti-HIM-8 | (Phillips et al., 2005) PMID: 16360035 | N/A | (1:500 IF) |
| Antibody | Goat polyclonal anti-SYP-1 | (Harper et al., 2011) PMID: 22018922 | N/A | (1:300 IF) |
| Antibody | Chicken polyclonal anti-HTP-3 | (MacQueen et al., 2005) PMID: 16360034 | N/A | (1:500 IF) |
| Antibody | Guinea pig polyclonal anti-HTP-3 | (MacQueen et al., 2005) PMID: 16360034 | N/A | (1:500 IF) (1:1,500 WB) |
| Antibody | Guinea pig polyclonal anti-PLK-2 | (Harper et al., 2011) PMID: 22018922 | N/A | (1:100 IF) |
| Antibody | Rabbit polyclonal anti-V5 | Millipore Sigma | Cat#V8137; RRID:AB_261889 | (1:250 IF) |
| Antibody | Mouse monoclonal anti-V5 | Thermo Fisher Scientific | Cat#R960-25; RRID:AB_2556564 | (1:500 IF) (1:1,000 WB) |
| Antibody | Mouse monoclonal anti-FLAG M2 | Millipore Sigma | Cat#F1804; RRID:AB_262044 | (1:500 IF) (1:1,000 WB) |
| Antibody | Mouse monoclonal anti-HA, clone 2–2.2.14 | Thermo Fisher Scientific | Cat#26183; RRID:AB_10978021 | (1:400 IF) (1:1,000 WB) |
| Antibody | Mouse monoclonal anti-GFP | Millipore Sigma | Cat#11814460001; RRID:AB_390913 | (1:500 IF) (1:1,000 WB) |
| Antibody | Mouse monoclonal anti-α-tubulin, clone DM1A | Millipore Sigma | Cat#05–829; RRID:AB_310035 | (1:5,000 WB) |
Recombinant DNA reagent | Peft-3::AID::GFP::unc-54 3’UTR | (Zhang et al., 2015) PMID: 26552885; Addgene | pLZ29; Addgene plasmid #71719 | |
| Recombinant DNA reagent | cDNA zhp-1 | WormBase | WormBase ID: F55A12.10; WBGene00018867 | |
| Recombinant DNA reagent | cDNA zhp-2 | WormBase | WormBase ID: D1081.9; WBGene00008387 | |
| Recombinant DNA reagent | cDNA zhp-3 | WormBase | WormBase ID: K02B12.8b; WBGene00006976 | |
| Recombinant DNA reagent | cDNA zhp-4 | WormBase (codon-optimized byIntegrated DNA Technologies to facilitate gBlock synthesis) | WormBase ID: Y39B6A.16; WBGene00012678 | |
| Recombinant DNA reagent | Plasmid: pDEST32-zhp-1-V5 | This paper | N/A | |
| Recombinant DNA reagent | Plasmid: pDEST32-zhp-2-3xFLAG | This paper | N/A | |
| Recombinant DNA reagent | Plasmid: pDEST32-zhp-3-3xFLAG | This paper | N/A | |
| Recombinant DNA reagent | Plasmid: pDEST32-zhp-4-HA | This paper | N/A | |
| Recombinant DNA reagent | Plasmid: pDEST22-zhp-1-V5 | This paper | N/A | |
| Recombinant DNA reagent | Plasmid: pDEST22-zhp-2-3xFLAG | This paper | N/A | |
| Recombinant DNA reagent | Plasmid: pDEST22-zhp-3-3xFLAG | This paper | N/A | |
| Recombinant DNA reagent | Plasmid: pDEST22-zhp-4-HA | This paper | N/A | |
| Sequence-based reagent | FISH probe to the right arm of Chromosome V (5S rDNA) | (Dernburg et al., 1998) PMID: 9708740 | N/A | |
| Sequence-based reagent | FISH Probe to the right arm of X Chromosome | (Phillips et al., 2005) PMID: 16360035 | N/A | |
| Sequence-based reagent | CRISPR tracrRNA | Integrated DNA Technologies, Skokie, IL | Cat#1072534 | |
| Sequence-based reagent | For crRNAs, repair templates and genotyping primers, see Supplementary file 1,Table S3 | This paper | N/A | |
| Peptide, recombinant protein | S. pyogenes Cas9-NLS purified protein | QB3 MacroLab at UC Berkeley | N/A | |
| Chemical compound, drug | Auxin: 1H-Indole-3-acetic acid | Thermo Fisher Scientific, Waltham, MA | Cat#122160250; CAS:87-51-4 | |
| Chemical compound, drug | NuSieve 3:1 agarose | Lonza, Walkersville, MD | Cat#50090 | |
| Chemical compound, drug | Nuclease-Free Duplex Buffer | Integrated DNA Technologies | Cat#11-01-03-01 | |
| Commercial assay or kit | SuperSignal West Femto Maximum Sensitivity Substrate kit | Thermo Fisher Scientific | Cat #34095 | |
| Software, algorithm | SoftWorx package | Applied Precision; GE Healthcare Bio- Sciences, Pittsburgh, PA | http://www.gelifesciences.com/webapp/wcs/stores/servlet/productById/en/GELifeSciences-us/29065728 | |
| Software, algorithm | ImageJ | NIH | https://imagej.nih.gov/ij/ | |
| Software, algorithm | Adobe Photoshop CC 2014 | Adobe Systems, San Jose, CA | http://www.adobe.com/products/photoshop.html | |
| Software, algorithm | T-COFFEE | Swiss Institute of Bioinformatics; (Notredame et al., 2000) PMID:10964570 | http://tcoffee.vital-it.ch/apps/tcoffee/index.html | |
| Software, algorithm | IBS_1.0.1 | (Liu et al., 2015) PMID: 26069263 | http://ibs.biocuckoo.org/download.php | |
| Software, algorithm | Clustal Omega | EMBL-EBI | http://www.clustal.org/omega/ | |
| Software, algorithm | Graphpad Prism | Graphpad Software, Inc., La Jolla, CA | http://www.graphpad.com/ | |
| Software, algorithm | MSG software package | (Andolfatto et al., 2011) PMID: 21233398 | https://github.com/JaneliaSciComp/msg |
Additional files
-
Supplementary file 1
This file includes four tables (Table S1-S4).
Table S1 reports analysis of the progeny produced by animals expressing epitope-tagged proteins described in this work. In all cases, animals homozygous for these epitope-tagged alleles show no reduction in embryonic viability or increase in male production, indicating that the epitope tags used to detect various proteins do not impair their meiotic functions. Table S2 provides a list of all new alleles generated in this work, with details about the genome editing methods used to introduce epitope tags or mutations. Table S3 includes the sequences of RNA and DNA sequences used for genome editing, including synthetic CRISPR RNAs (crRNAs), repair templates, and DNA primers used for detecting or genotyping these mutations. In cases where restriction digests were used for genotyping, fragment sizes for wild-type and mutant alleles are also provided. Table S4 lists new worm strains constructed in the course of this work, as well as previously referenced strains.
- https://doi.org/10.7554/eLife.30789.025
