Volume 21, Issue 6, Pages 1092-1103 (December 2011) The Chromodomain Protein MRG-1 Facilitates SC-Independent Homologous Pairing during Meiosis in Caenorhabditis elegans  Carolyn R. Dombecki, Ason C.Y. Chiang, Hyun-Joo Kang, Ceyda Bilgir, Nicholas A. Stefanski, Bryan J. Neva, Elke P.F. Klerkx, Kentaro Nabeshima  Developmental Cell  Volume 21, Issue 6, Pages 1092-1103 (December 2011) DOI: 10.1016/j.devcel.2011.09.019 Copyright © 2011 Elsevier Inc. Terms and Conditions

Developmental Cell 2011 21, 1092-1103DOI: (10.1016/j.devcel.2011.09.019) Copyright © 2011 Elsevier Inc. Terms and Conditions

Figure 1 mrg-1 Mutant Displays a Non-PC and Autosome-Specific Pairing Defect (A) Pachytene nuclei were hybridized with FISH probes targeted to the PC end (green) and the non-PC end (red) of chromosome IV in a whole-mount gonad. In mrg-1 nuclei, the non-PC ends are frequently unpaired (arrows). Bar: 5 μm. (B) Schematic diagram of subzones of the gonad. The distal end is shown toward the left. (C and D) The pairing efficiency at the indicated locus is presented as the percentage of nuclei with paired FISH signals in each subzone. Asterisks indicate a statistically significant difference between wild-type and mrg-1 in the corresponding stage (∗0.01 ≤ p < 0.05, ∗∗0.001 ≤ p < 0.01, ∗∗∗p < 0.001). The total number of nuclei scored is given in parentheses. (E) A nucleus in the transition zone (top) or pachytene (middle) in the wild-type, or in the transition zone in mrg-1 mutant (bottom) whole-mount gonad stained with DAPI (light blue), MRG-1 (green), and HIM-8 (orange). The DNA staining associated with HIM-8 staining (arrows) represents the X chromosome. Bar: 2 μm. See also Figure S1. Developmental Cell 2011 21, 1092-1103DOI: (10.1016/j.devcel.2011.09.019) Copyright © 2011 Elsevier Inc. Terms and Conditions

Figure 2 mrg-1 Displays Delayed SC Assembly Dependent on HTP-1 (A) mrg-1 whole-mount gonad stained with DAPI, HIM-3, and SYP-1. A clustered chromosome distribution is observed in a large region of the gonad reaching the late pachytene stage (toward the right end) in mrg-1 mutants (underline). Bar: 10 μm. (B) Early pachytene nuclei stained with HIM-3 and SYP-1. In mrg-1 germlines, many HIM-3 axes lack SYP-1 staining (arrows). Bar: 5 μm. (C) Late pachytene nuclei stained with HIM-3 and SYP-1. Bar: 5 μm. (D) Quantification of SC assembly. Nuclei were examined for full or partial colocalization of HIM-3 and SYP-1 staining (Full SC or Partial SC). Discrete staining of HIM-3 only was scored as partial SC (arrows). The percentage of nuclei with partial synapsis in each subzone is shown in the histograms. Zoning follows the scheme in Figure 1B. The total number of nuclei is given in parentheses. Bar: 2 μm. (E) Early pachytene nuclei stained with HIM-3 and SYP-1 in a whole-mount gonad of htp-1 and htp-1; mrg-1 mutants. Most of the HIM-3 axes overlap with SYP-1 and associate with two DAPI-staining stretches (paired arrows). In both mutants, a small number of HIM-3 axes do not load SYP-1. These axes are not flanked by the two stretches of DNA (light blue in the inset, arrow). Bar: 5 μm (1 μm in the inset). Developmental Cell 2011 21, 1092-1103DOI: (10.1016/j.devcel.2011.09.019) Copyright © 2011 Elsevier Inc. Terms and Conditions

Figure 3 Proper Initiation but Delayed Completion of Meiotic Homologous Recombination in mrg-1 (A) DAPI and RAD-51 staining of meiotic nuclei. Zoning follows the scheme in Figure 1B. Bar: 5 μm. (B) Histograms showing the mean number of RAD-51 foci ± SEM in each subzone. The total number of nuclei scored is given in parentheses. Asterisks indicate an extremely significant difference between wild-type and mrg-1 (p < 0.0001). (C) Successful bivalent formation in diakinesis nuclei from wild-type (left) and mrg-1 (right) stained with DAPI and HIM-3. Six DAPI-stained bodies associating with cruciform-shaped HIM-3 axes staining are shown. (D) Histograms showing the mean number of DAPI-stained bodies in diakinesis nuclei ± SEM. The total number of nuclei scored is given in parentheses. See also Figure S3. Developmental Cell 2011 21, 1092-1103DOI: (10.1016/j.devcel.2011.09.019) Copyright © 2011 Elsevier Inc. Terms and Conditions

Figure 4 mrg-1 Displays Reduced Presynaptic Non-PC Alignment (A) Nuclei in the middle meiotic prophase (zone 3 in B) were hybridized with FISH probes targeted to the PC end (green) and the non-PC end (red) of chromosome IV in a whole-mount gonad. Bar: 5 μm. (B) Schematic of five subzones of a gonad for scoring. (C) Quantification of the pairing efficiency. Asterisks indicate a statistically significant difference (∗0.01 ≤ p < 0.05, ∗∗∗p < 0.001) between syp-1 and syp-1; mrg-1. The total number of nuclei is given in parentheses. (D) 3D volume renderings of meiotic nuclei in whole-mount syp-1 mutant germlines hybridized with a paint probe for chromosome IV. Four typical bivalents in zone 3 are shown. The schematic of a four-color chromosome paint FISH probe is shown at the bottom. The gray sections in the schematic represent regions not covered by the paint probe. PC-V: only the green segments containing the PC end associate homologously; PC-Y1: the green segments and neighboring yellow segments align and closely associate; PC-Y2: alignment and close association from the green segment to the red segment next to the yellow segment; Full alignment: alignment and close association along the entire chromosome length. (E) Histogram showing the percentage of each alignment type. Asterisks indicate a statistically significant difference (∗0.01 ≤ p < 0.05, ∗∗0.001 ≤ p < 0.01) between syp-1 and syp-1; mrg-1. The total number of nuclei is given in parentheses. Developmental Cell 2011 21, 1092-1103DOI: (10.1016/j.devcel.2011.09.019) Copyright © 2011 Elsevier Inc. Terms and Conditions

Figure 5 The mrg-1 Mutant Displays Incomplete and Aberrant SC Formation (A) 3D volume renderings of pachytene nuclei stained with DAPI (blue) and SYP-1 (white) in conjunction with hybridization of FISH probes for both the PC (green) and the non-PC (red) ends of chromosome IV in whole-mount mrg-1 mutant gonads. Three typical examples (Aa–Ac) are shown. (Aa–Aa″) Both unpaired non-PC ends are associated with SYP-1 (arrowheads). (Ab–Ab″) One unpaired locus is associated with SYP-1 (arrowhead), while the other is not (arrow). (Ac–Ac″) Both unpaired ends are not associated with SYP-1 (arrows). Scale is indicated by the square grid in the background, in which the length of each side of the unit squares is 0.5 μm. (B) Cumulative histogram showing quantification of nuclei in each subzone with a specific SYP-1 association pattern. Only nuclei that have paired PC ends and unpaired non-PC ends of chromosome IV were scored. The inset schematically shows the five subzones for scoring. Zones 3–5 roughly correspond to the early, middle, and late pachytene stages, respectively. The six association patterns are color-coded as indicated. PC(S), the PC end associated with SYP-1. PC(n), the PC end not associated with SYP-1. Association of SYP-1 with unpaired non-PC ends is shown by the following three types: NPC(S, S), association at both ends; NPC(n, S), association at only one end; and NPC(n, n), association at neither end. (C) Mildly squashed mrg-1 mutant nuclei stained with DAPI, SYP-1 IF, and FISH for the 5SrDNA locus. The positions of two unpaired 5S rDNA loci are marked with arrowheads. Both of these loci associate with SYP-1. In high magnification (right), two DAPI stretches (red) shown by paired arrows flank a SYP-1 stretch (green) that is associated with unpaired 5S rDNA FISH signals (blue). Developmental Cell 2011 21, 1092-1103DOI: (10.1016/j.devcel.2011.09.019) Copyright © 2011 Elsevier Inc. Terms and Conditions

Figure 6 Direct Visualization of Nonhomologous SC Assembly in mrg-1 Squashed nuclei with SYP-1 IF staining (light blue) and chromosome paint for non-PC regions of chromosomes I (yellow), III (green), and V (pink) in mrg-1 (A–D) and wild-type (E and F). Type 1 Nonhomologous Synapsis (NHS): paint signals of two different chromosomes (A, III and V; B, I and III) are overlapped and run alongside the same SYP-1 stretch (arrows, and white dotted lines in schematic). Type 2 NHS: Branched paint signals (double arrows) associating with SYP-1 stretches in a fork shape (C, Ch. V) or a bubble shape (E, Ch. I). Homologous Synapsis (HS): paint signals associated with individual SYP-1 stretches for each chromosome (D and F). The arrowhead shows overlap between two paint signals that is not counted as nonhomologous synapsis because they do not associate with the same SYP-1 stretch. In the schematic, dotted lines in colors corresponding to the paints fill the gaps in paint signals. mrg-1 showed both Type 1 NHS (3% among 147 nuclei scored) and Type 2 NHS (8%), whereas wild-type showed only Type 2 NHS in a small population (1% among 140 nuclei scored). Bar: 2 μm. Developmental Cell 2011 21, 1092-1103DOI: (10.1016/j.devcel.2011.09.019) Copyright © 2011 Elsevier Inc. Terms and Conditions