Molecular structure of a functional Drosophila centromere

Abstract

Centromeres play a critical role in chromosome inheritance but are among the most difficult genomic components to analyze in multicellular eukaryotes. Here, we present a highly detailed molecular structure of a functional centromere in a multicellular organism. The centromere of the Drosophila minichromosome Dp1187 is contained within a 420 kb region of centric heterochromatin. We have used a new approach to characterize the detailed structure of this centromere and found that it is primarily composed of satellites and single, complete transposable elements. In the rest of the Drosophila genome, these satellites and transposable elements are neither unique to the centromeres nor present at all centromeres. We discuss the impact of these results on our understanding of heterochromatin structure and on the determinants of centromere identity and function.

Figure 1. Strategy for Molecular Analysis of the Minichromosome Centromere

(A) Gross structure of γ1230, the smallest stable derivative available (only 620 kb, compared to the 1.3 Mb in the parental Dp8-23 minichromosome). (B) Purification and Southern hybridization analysis of γ1230. Minichromosomal DNA is separated from the rest of the genome by PFGE. An agarose block containing the DNA is then excised and digested with a restriction enzyme (SpeI), and restriction fragments are resolved by a second round of PFGE. The gel is blotted and probed with a Drosophila repetitive DNA sequence (F transposable element) that works as a single copy probe on the purified minichromosome DNA. Pulse conditions were 20–80 s pulses, 2 s ramp, 20 hr for resolving undigested γ1230; 1–21 s pulses, 1 s ramp, and 15 hr for resolving the SpeI fragments.

Figure 2. Detailed Structure of the 420 kb of Centric Heterochromatin that Contains a Fully Functional Centromere

(A) Organization of the centric heterochromatin in γ1230. Transposable elements are shown as black boxes and satellites as blank and striped boxes (numbers above the boxes show size of satellite arrays in kilobases). Orientation of transposable elements is indicated by arrows, which point to 3′ ends. Only a subset of characterized restriction sites are shown (see Experimental Procedures for a complete list of restriction enzymes used. A complete map cannot be displayed effectively here but is available upon request). Complex DNA sequence at the fifth restriction cluster (at the junction of the AATAT and AA-GAG satellites) remains to be identified (see Discussion). The region corresponding to the previously identified complex DNA island Bora Bora is indicated, as is the newly identified island Maupiti. (B) Southern hybridization of SpeI partially digested γ1230 with two probes located close to either end of this region, which localized the four SpeI fragments in the order of (from left to right) 70, 135, 235, and 35 kb (the 70 kb fragment contains the euchromatin/heterochromatin junction because it also hybridizes to the 6.1XR2.5 probe in complete digests). (C) Restriction fragments can be visualized by ethidium bromide staining and by hybridization with satellite probes. AAGAG and AATAT satellites are localized to either side of the fifth restriction site cluster by hybridizing to specific restriction fragments. For example, the AATAT satellite probe detected the 70, 135, and 235 kb SpeI fragments, but not the 150 kb SpeI/NsiI fragment (from the fifth cluster to Maupiti); the latter is the only SpeI/NsiI fragment detected by the AAGAG satellite probe. (D) Southern hybridization demonstrates high sequence homogeneity of the two satellites (see text). The blot was successively probed with the AATAT and AAGAG satellite probes. When this blot was probed with the centromeric transposons, each probe detected specific fragments that corresponded to the AATAT arrays (data not shown). For example, the 412 probe detected the 50 and 20 kb HaeIII fragments, and the BEL probe hybridized to the 50 and 18 kb fragments. Thus, the 20 kb AATAT fragment is positioned to the left of the 412 element, the 18 kb fragment is to the right of BEL, and the 50 kb fragment is in between the two elements (A). (E) Southern hybridization of F element probe to digested γ1230. This result indicates that the centromeric F is a single intact element located at the second restriction site cluster (compare the hybridization pattern with the known F map shown in [A]). (F) Southern hybridization with the A+T-rich sequence on purified γ1230. The probe detected two SalI and two SmaI fragments, indicating that homologous sequences are present at both sides of the Doc element in Maupiti (see the enlarged Maupiti structure in [A]). The same hybridization pattern was observed with the A+T-rich probe on total genomic DNA of a strain (y; ry⁵⁰⁶) that lacks the minichromosome (data not shown). Size of restriction fragments is indicated in kilobases. Abbreviations are: EtBr, ethidium bromide; Ba, BamHI; Hd, HindIII; Mb, MboII; No, NotI; Ns, NsiI; Sa, SalI; Sm, SmaI; Sp, SpeI; Ss, SspI; Xh, XhoI. Pulse conditions were 10–50 s pulses, 1 s ramp, 17 hr for (B); 1–21 s pulses, 1 s ramp, 12 hr for (C) and (E), and 20 hr for (D); 0.5–10.5 s pulses, 0.5 s ramp, 18 hr for (F).

Figure 3. Analysis of the Maupiti A+T-Rich Sequence

(A) Nucleotide sequence of the A+T-rich sequence. This sequence is followed by the 3′ end of a Doc element in the D8 clone (not shown). (B) DotPlot of the A+T-rich sequence showing multiple short stretches of internal repeats. DNAStar program, percentage: 70; Window: 30; Min Quality: 1.

Figure 4. Fluorescence In Situ Hybridization (FISH) to Mitotic Metaphase Chromosomes with AATAT (A) and AAGAG (B) Satellites, and transposable elements 412 (C) and F (D)

DAPI stained (blue) neuroblast squashes are superimposed with the hybridization signals (pseudocolored FITC fluorescence in red). The normal chromosomes are indicated, as is the γ1230 minichromosome that serves as an internal quantitation control. Note that only one copy of γ1230 is present in (A) and (B) (outcrossed stocks), while five copies are seen in (C) and two in (D) (inbred stocks). None of these probes hybridizes to all centromeric regions (arrows); for example, the centromeric regions of the second chromosomes in (A) lack AATAT satellite signal, the centromeric regions of the third chromosomes in (B) are not labeled by the AAGAG probe, and the fourth chromosomes contain no 412 signal. None of these sequences are confined only to the centromeric regions.

Figure 5. The Structure of Dp8-23 and Its Derivatives

(A) A single 420 kb region of centric heterochromatin is necessary and sufficient for fully stable chromosome transmission. The ruler defines the position along Dp8-23 relative to the euchromatin/heterochromatin junction (Le et al., 1995). Structure is shown along with the percent monosome transmission in females (Murphy and Karpen, 1995b). Regions corresponding to previously identified islands of complex DNA (Tahiti, Moorea, and Bora Bora) are indicated; Maupiti is the newly identified island (see Figure 2). Note that our new, more precise alignment of γ1230 with Dp8-23 has moved Bora Bora 200 kb leftward compared to the previous location (Le et al., 1995; Murphy and Karpen, 1995b). γ1230 and 10B, the two smallest derivatives that display normal monosome transmission (50%), share almost the exact same 420 kb region of centric heterochromatin. (B) Hybridization of AATAT and AAGAG satellite probes to XhoI fragments of Dp8-23, γ238, and γ1230, demonstrating that γ1230 was produced by an internal and a terminal deletion. γ1230 lacks the 220 kb XhoI fragment (from +80 to +300) detected by the AATAT satellite probe in Dp8-23 and γ238, and contains a 30 kb fragment instead of a 100 kb fragment (from +300 to +400). In addition, the 200 kb fragment (from +800 to +1000) detected by the AAGAG satellite probe in Dp8-23 is missing in γ1230. Note that the signal intensity of the 220 kb XhoI fragment (from +80 to +300) detected by the AATAT probe is approximately equal to that of the 50 kb XhoI fragment (left), indicating that AATAT satellite comprises about 50 kb of the 220 kb XhoI fragment. This maps, as shown in (A), the transition point between the 1.688 and the AATAT satellite to approximately +250 (300–50 = 250). γ238 displays a 280 kb Xho fragment instead of the 200 kb fragment in Dp8-23 (right), consistent with the inversion in γ238 that placed the 200 kb of AAGAG satellite to the left of the y⁺ gene. (C) Hybridization of the 2156 probe to SpeI digested Dp8-23, γ238, and γ1230. The fragment corresponding to the 12 kb SpeI fragment in Dp8-23 is either larger (in γ238) or smaller (in γ1230), indicating that the right breakpoints of γ238 and γ1230 fall into this SpeI fragment in Dp8-23. This made the size of Maupiti in γ1230, and γ238 is smaller than in Dp8-23. (D) Hybridization with the AATAT probe on SpeI digested γ1230, 10B, 1B, and J21A. Comparison of the patterns confirms that these derivatives contain progressively larger deletions of the centromere and precisely maps the positions of the terminal breakpoints. (E) Hybridization of the 1.688 satellite probe to SmaI digested Dp8-23, γ238, and γ240. The hybridization pattern indicates that the first 250 kb of centric heterochromatin is largely composed of the 1.688 satellite. Extensive mapping suggested that stretches of complex DNA are present around +100 kb and +300 kb, including a Doc at +300 kb (data not shown; see also Le et al., 1995). Only the restriction sites relevant to the hybridization results shown in (B)–(E) are shown in (A). The following pulse conditions were used for all blots shown in this figure: 1–21 s pulses, 1 s ramp, and 20 hr. Size of restriction fragments is indicated in kilobases, and abbreviations are the same as in Figure 2.