Homologous centromere pairing is disrupted upon loss of Kdm5/Lid.

<p>(A) Centromere clustering in pre-meiotic nuclei of 16-cell cysts (16 cc) in wild-type and <i>Kdm5/lid</i> mutant ovaries. Parts of the germarium containing 16-cell cyst (circled) are shown in the left panels (Scale bar = 5 μm), and magnified images of one cell, in each case, are shown in the right panels (Scale bar = 3 μm). The anterior end of the germarium is oriented towards the top. The stage of each cyst was determined using the morphology of fusome visualised by Hts. (B) Increased number of centromere clusters in <i>Kdm5</i>/<i>lid</i> mutant oocytes in comparison to wild type in region 3. The SC component C(3)G was used to identify oocytes. Scale bars = 3 μm. (C) The number of centromere clusters in pre-meiotic and meiotic nuclei in various oogenesis stages of wild type and the <i>Kdm5/lid</i> mutant. cc; cell cyst, reg; region, st; stage. ** and *** (p<0.01 and 0.001) indicate significant differences from wild type in terms of the frequency of nuclei with one or two centromere clusters. ≥32 nuclei and meiotic nuclei were quantified for each pre-meiotic stage and region 2a, while ≥16 germaria were quantified for each later meiotic stage. (D) A schematic diagram showing three levels of centromere association in oocytes, cohesion of sister-centromeres, pairing of homologous centromeres and clustering of non-homologous centromeres. (E) Closely paired signals of the pericentromeric dodeca satellite specific to chromosome 3 (periCen3) that co-localise with CenpA/Cid foci in the wild-type oocyte at stage 6, and which are clearly separated into two foci in the <i>Kdm5/lid</i> RNAi oocyte at stage 6. Arrows indicate Cid and periCen3 foci. Scale bars = 5 μm. (F) Schematic representation of the behaviour of the pericentromere 3 signals (periCen3) in control and <i>Kdm5/lid</i> RNAi oocytes. (G) The proportion of paired or separate pericentromeric signals (periCen3) in control and <i>Kdm5/lid</i> RNAi oocytes. Two signals separated by ≥1 μm were defined as "separate" in this quantification. ** indicates significant difference from the control (p<0.01). n≥17.</p

Loss of Kdm5/Lid leads to instability of chromosome cores along arms but does not affect persistence at centromeres.

<p>(A) SMC1 signals in meiotic nuclei in region 2a and 2b of control and <i>Kdm5/lid</i> RNAi ovaries, showing filamentous patterns in control, and fragmented filaments in region 2a and mainly diffuse pattern in region 2b of <i>Kdm5/lid</i> RNAi ovaries. (B) Quantification of SMC1 staining pattern in control and <i>Kdm5/lid</i> RNAi meiotic nuclei. *** indicates a significant difference in the pattern distribution from the control (p<0.001). n≥7. Chromosome cores visualised by filamentous SMC staining fails to be maintained in <i>Kdm5/lid</i> RNAi. (C) Centromeric SMC1/3 localisation in control and <i>Kdm5/lid</i> oocytes at stage 4. Colocalisation between Cid and SMC1/3 foci was observed in all oocytes examined (n = 13 for stage 4–6). Arrows indicate Cid and SMC1/3 foci. Scale bars = 5 μm.</p

Loss of Kdm5/Lid leads to partial formation and instability of the SC along chromosome arms but does not affect persistence of a transverse protein at centromeres.

<p>(A) Schematic representation of early meiotic events. In region 2a, the SC starts to assemble to promote synapsis which results in crossover and chiasmata formation. The filamentous structure of the SC mostly disassembles by stage 6 of oogenesis except at centromeres. (B) A control region-3 oocyte with filamentous C(3)G staining, and a <i>Kdm5/lid</i> RNAi oocyte with spots of C(3)G staining. (C) Quantification of C(3)G staining pattern in control and <i>Kdm5/lid</i> RNAi oocytes. For region 2a, we classified each germarium based on the majority of the SC morphology in multiple nuclei which accumulate C(3)G. For region 2b where the two nuclei accumulate C(3)G, each germarium was scored for the morphology of the better formed SC. ** and *** indicate significant differences in the pattern distribution from control (p<0.01 and p<0.001, respectively). n≥14. (D) Centromeric C(3)G localisation in control and <i>Kdm5/lid</i> RNAi oocytes at stage 5. Cid, the <i>Drosophila</i> CenpA, highlights all centromeres. The arrows indicate colocalisation of the Cid signals with centromeric C(3)G. Colocalisation was observed in all oocytes examined (n = 27 for stage 4–6). Scale bars = 5 μm.</p

Kdm5/Lid demethylase activity is dispensable for meiotic chromatin reorganisation.

<p>(A) Distribution and intensity of H3K4me3 on meiotic chromosomes in a <i>Kdm5/lid</i> mutant (<i>lid</i>^{<i>10424/k06801</i>}) without a transgene (–), the <i>Kdm5/lid</i> mutant carrying a wild-type transgene (<i>lid[WT])</i> and <i>the Kdm5/lid</i> mutant carrying a catalytically inactive transgene (<i>lid[JmjC*]</i>). Images of the karyosome in stage-5 oocytes were taken and the contrast has been enhanced using identical conditions. The total signal intensity of H3K4me3 on the karyosome was measured as described in Materials and Methods. Error bars indicate standard errors. n≥6. The signal intensity in the <i>Kdm5/lid</i> mutant carrying no transgenes (–) or the <i>lid[JmjC*]</i> transgene is significantly different from the one carrying the <i>lid[WT]</i> transgene at all stages (p<0.001). (B) Rescue of karyosome defects of the <i>Kdm5/lid</i> mutant by both the wild-type transgene (<i>lid[WT]</i>) and demethylase-inactive transgene (<i>lid[JmjC*]</i>). Karyosome morphology was observed in the <i>Kdm5/lid</i> mutant oocytes carrying no transgenes (–), the <i>lid[WT]</i> transgene or the <i>lid[JmjC*]</i> transgene, and was classified as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006241#pgen.1006241.g001" target="_blank">Fig 1C</a>. *** indicates a significant difference in the pattern of distribution from the control (p<0.001). n≥18. (C) Centromere pairing and clustering do not require the demethylase activity of Kdm5/Lid. Centromeres highlighted by the Cid antibody are indicated by arrows, and foci of pericentromeric dodeca satellite specific to chromosome 3 (periCen3) are indicated by arrowheads. The numbers of centromere (Cid) clusters were counted for each group of stages (n≥12). Oocyte nuclei with tightly paired (<1 μm) or separate (≥1 μm) periCen3 foci were counted for each group of stages (n≥11). ***, ** and * indicate significant differences (p<0.001, p<0.01 and p<0.05, respectively). (D) SC morphology is not affected by loss of the Kdm5/Lid demethylase activity. Filamentous structures of C(3)G observed in region 3 oocytes from the <i>Kdm5/lid</i> mutant carrying the <i>lid[WT]</i> or <i>lid[JmjC*]</i> transgene, and a spotty appearance observed in the <i>Kdm5/lid</i> mutant alone. The SC component C(3)G and H3K4me3 were co-stained, imaged and contrast-enhanced using identical conditions. The morphology of the C(3)G-containing structure was categorised and counted for each group of stages (n≥10). ***, ** and * indicate significant differences (p<0.001, p<0.01 and p<0.05, respectively). Scale bars = 5 μm in all images.</p

Loss of Kdm5/Lid results in high H3K4me3 and abnormal karyosomes independently from the meiotic recombination checkpoint.

<p>(A) Schematic representation of <i>Drosophila</i> oogenesis. A germline stem cell produces a cystoblast which undergoes four rounds of pre-meiotic mitosis to form a cyst consisting of 16 cells. In region 2a, up to four cells in a cyst initiate meiosis and form the SC. In region 2b, two cells (pro-oocytes) maintain the meiotic state. By region 3, one of these cells is finally selected as the oocyte, and all other cells have become nurse cells. Karyosome forms at stage 2–3 of oogenesis. At stage 3 and later, the SC gradually disassembles from chromosome arms, except in centromeric regions. At stage 14, the oocyte completes maturation and arrests in meiotic metaphase I. (B) The spatial distribution and quantified level of H3K4me3 in control and <i>Kdm5/lid</i> RNAi oocytes. The total H3K4me3 signal intensity was significantly higher in <i>Kdm5/lid</i> RNAi oocytes at all stages (p<0.001). n≥7. Error bars represent the standard errors of the mean. reg; region, st; stage. (C) Karyosome defects caused by two different shRNAs (<i>lid</i> RNA1 and <i>lid</i> RNAi2) and a <i>Kdm5/lid</i> mutant (<i>lid</i>^{<i>10424/k06801</i>}). The karyosome morphologies at stages 3–9 were classified into three categories: "spherical" when the karyosome shows a spherical shape, "mildly distorted" when spherical shape was distorted but largely maintained, and "distorted" when spherical shape was largely disrupted. *** indicates a significant difference from the control (p<0.001). n≥18. (D) γH2Av foci which mark DSBs in meiotic nuclei in region 2a, 2b and region 3 of control and <i>Kdm5/lid</i> RNAi ovaries. DSBs are repaired by region 3 in both. Meiotic nuclei were identified by C(3)G staining. n≥12. (E) Karyosome morphology at stage 4/5 in control RNAi, <i>Rad51/spnA</i>, <i>Kdm5/lid RNAi</i>, <i>Chk2/mnk</i>^<i>p</i>6/+ <i>spnA</i> double mutant, <i>Chk2/mnk</i>^p6/+ mutant with <i>Kdm5/lid</i> RNAi, and <i>Kdm5/lid p53</i> double RNAi. The frequency of abnormal karyosomes at stage 3–9 was quantified for each genotype. n≥16. Suppression of meiotic checkpoint does not rescue the karyosome defect of <i>Kdm5/lid</i> RNAi (p = 1.00). Scale bars = 5 μm.</p

Additional file 2 of Accurate chromosome segregation by probabilistic self-organisation

Mathematica codes. The Mathematica codes used in this study. To read the file, Wolfram CDF player (available free from https://www.wolfram.com/cdf-player/ ) or Mathematica (Wolfram Research) is required. (ZIP 62 kb

Abnormal chromosome positioning and orientation in prometa/metaphase I and a potential reduction in crossovers in oocytes lacking Kdm5/Lid.

<p>(A) Mis-positioned chromosomes with normal spindle morphology in <i>Kdm5/lid</i> RNAi oocytes in prometa/metaphase I in comparison to control RNAi. Chromosome orientation was assessed by <i>in situ</i> hybridisation using dodeca satellite as a pericentromere 3 probe (arrows). Scale bar = 5 μm. (B) Quantification of chromosome configuration in control and <i>Kdm5/lid</i> RNAi oocytes. The “other” category includes a meiotic figure with more than two foci of the pericentromere 3 signal. The frequency of mis-oriented pericentromere 3 in <i>Kdm5/lid</i> RNAi is significantly different from the control RNAi (p<0.05). n≥45. (C) Localisation and signal intensity of Vilya-3xHA foci in meiotic nuclei in region 2a and 2b of control and <i>Kdm5/lid</i> ovaries expressing HA-tagged Vilya. Scale bar = 5 μm. (D) The signal intensity of Vilya^3xHA foci in region 2a and 2b meiotic nuclei of control and <i>Kdm5/lid</i> RNAi ovaries expressing HA-tagged Vilya. The graphs show the numbers of foci per meiotic nucleus with the maximum signal intensity in indicated ranges. Foci with a signal intensity lower than 30 are significantly more frequent in <i>Kdm5/lid</i> RNAi than in control (p<0.001). Intensities of ≥66 Vilya^3XHA foci have been measured for each region of each genotype.</p

Kank localises to muscle-tendon attachment sites in late stage <i>Drosophila</i> embryos.

<p>(A) The ∼160 kDa Kank band was detected in embryos from 3–6 hours after egg laying (AEL). The amount of Kank detected by immunoblotting was observed to increase during embryonic development. The ∼140 kDa band becomes apparent 15–18 hours AEL. (B) An antibody against Kank(489–900) stained a distinct pattern in stage 16/17 embryos. This staining was not observed in <i>kank</i> deletion mutants. The 22c10 antibody, which highlights neurons, was used to orient embryos. (C) β3-tubulin staining reveals the structure of microtubules in somatic muscle cells. Co-staining with the Kank antibody showed that Kank localises at sites of muscle attachment to the epidermis. (D) A schematic of <i>Drosophila</i> embryonic somatic musculature with sites of Kank staining indicated. Scale bars = 25 µm.</p

Kank can localise transiently to the nucleus of S2 cells.

<p>(A) Kank(1–500) and Kank(889–1224) exhibit nuclear localisation, while truncations of Kank which contain the middle region do not. S2 cells were transfected with GFP-fused Kank truncations. Cells were then co-stained for GFP, α-tubulin and DNA. (B) Kank shuttles between the nucleus and the cytoplasm in some cells. S2 cells transfected with GFP-Kank were incubated with media containing leptomycin B for 3–3.5 hours, to inhibit nuclear export. Control cells were incubated with media containing methanol, the solvent for leptomycin B. Nuclear localisation was observed more frequently in leptomycin B treated cells than control cells. Significance was determined by Fishers exact chi squared test. Error bars show the 95% confidence interval. (C) A summary of Kank truncations and their nuclear localisation. + and – indicate the presence and absence of the nulcear localisation with (+LB) or without (–LB) Leptomycin B. ND (Not done). Scale bars = 5 µm.</p

Kank is expressed throughout development but is dispensable for viability and fertility.

<p>(A) <i>kank</i> (<i>CG10249</i>) is a ∼27 kb gene found at 51D2 on chromosome arm 2R. Putative isoforms are shown. Those in black are likely to be expressed while those in grey are less likely to be expressed based on ModEncode data. The cDNA clone GH03482 that we used in our analysis represents isoform A of <i>kank</i> (highlighted in blue). This isoform lacks the KN motif found in other Kank proteins (shown in purple). (B) Kank was deleted using transposons containing <i>FRT</i> sites. Firstly, the appropriate two transposons flanking the Kank coding sequence were introduced in trans positions on homologous chromosomes (i). A flippase was induced to promote recombination between the <i>FRT</i> sites (ii) and generated a deletion of the intervening sequence (iii) (C) The fragment of Kank(489–900) used for generating an antibody against the Kank protein. (D–G) The Kank antibody detected the endogenous protein in all lifecycle stages examined by immunoblotting in wild type but not in <i>Kank</i> deletion mutants. Kank was detected in embryos 21–24 hrs after egg laying (D), in 3rd instar larvae (E), in male and female late pupae [ = L] and early pupae of undetermined gender [ = E] (F), and in both male and female adult flies (G).</p