: : Schematic representation of the prophase differentiation of the Y chromosome. Solid segments are brightly fluorescing or, in the case of N banding, darkly staining; crosshatched regions are moderately fluorescing; hatched regions are dully fluorescing; and empty regions are non staining or non fluorescing. The upper diagram represents the fluorescence of Hoechst-33258-stained chromosomes; the second row depicts the quinacrine staining pattern; the third row indicates chromomy- cin staining; and the fourth row shows the N-banding pattern (provided by Gatti and Pimpinelli). NORMAL CHROMOSOME COMPLEMENT ____________________________________________________________________ This section contains brief descriptions of the normal chro- mosome cytology, both in mitotic and polytene cells. Polytene maps are included as foldouts at the end of the book, and com- bine material from C. B. Bridges (1935, J. Hered. 26: 60-64; 1938, J. Hered. 29: 11-13), C. B. Bridges and P. N. Bridges (1939, J. Hered. 30: 475-76) and P. N. Bridges (1941, J. Hered. 32: 64-65; 299-300; 1942, J. Hered. 33: 403-408), and Lefevre [1976, The Genetics and Biology of Drosophila (Ash- burner and Novitski, eds.). Academic Press, London, New York, San Francisco, Vol. 1a, pp. 31-66]. In addition detailed polytene maps based on electron-microscopic examination of thin sections of polytene-chromosome squashes were presented, one numbered section at a time, by Sorsa (1988, Chromosome Maps of Drosophila, CRC Press, Inc., Boca Raton, Florida, Vol II). Each of the major chromosome arms is divided into twenty numbered sections, each of which is divided into six subsec- tions, lettered A-F, and within which the bands are numbered sequentially. Mitotic prophase cytology has been perfected by Gatti and Pimpinelli; using several fluorescent dyes, principally, Hoechst 33258, and N-banding techniques they are able to detect considerable linear differentiation of the pericentric heterochromatin, which is not amplified and thus not amenable to analysis in polytene chromosomes. The main publications dealing with prophase cytology are Gatti and Pimpinelli (1983, Chromosoma 88: 349-73) and Dimitri (1991, Genetics 127: 553-64). # X chromosome Also known as chromosome 1. Present in one dose in male and two doses in female. In mitotic figures, the X is a rod-shaped element with a nearly terminal centromere and a minute second arm designated as the right arm, XR. The left arm, XL, is divided into a distal isopycnotic euchromatic region, Xe, in which the chromatids are usually separated, and a proximal heterochromatic or heteropycnotic region, Xh, in which the chromatids are not separated. The heterochromatic region comprises one-third to one-half the DNA content of the X chromosome. Tritiated thymidine incorporation studies (Bari- gozzi, Dolfini, Fraccaro, Raimondi, and Tiepolo, 1966, Exp. Cell Res. 43: 231-34) demonstrate that the heterochromatic region is late replicating. In second meiotic prophase of spermatogenesis, on the other hand, both euchromatin and heterochromatin are visibly double. In mitotic prophase cells, the heterochromatic region can be subdivided into nine seg- ments by means of a variety of staining procedures (Gatti and Pimpinelli); these are designated, from left to right, h26 through h34; h26 is juxtaposed to the euchromatin; the ribo- somal cistrons are thought to occupy h29 and the centromere has been placed between h32 and h33. Cooper (1959, Chromosoma 10: 535-88) characterized the heterochromatin of aceto- orcein-stained prophase X chromosomes as comprising four major orcein-staining segments designated from right to left hA, hB, hC, and hD and separated by three secondary constrictions, the central one of which corresponds to the nucleolus organizer, i.e., the site of the bb locus, which comprises a tandem array of repeats encoding the 5.8 S, 18 S, and 28 S ribosomal RNA's; other than the nucleolus organizer, correspondences between Cooper's map on one hand and that of Gatti and Pimpinelli on the other have not been determined. Schematic representation of the prophase differentiation of the pericentric heterochromatin of the X chromosome. Solid segments are brightly fluorescing or, in the case of N banding, darkly staining, crosshatched regions moderately fluorescing, hatched regions dully fluorescing, and empty regions are non staining or nonfluorescing. The upper diagram represents the fluorescence of Hoechst-33258 stained chromosomes; the second row depicts the quinacrine staining pattern; the third row indicates chromomycin staining; and the fourth row shows the N-banding pattern (pro- vided by Gatti and Pimpinelli). The polytene X chromosome (see foldout at end of book) extends from region 1 at the tip through region 20 at the cen- tromere; Xe comprises approximately 1000 bands (1008 according to Bridges and 979 according to Sorsa), and is thought to extend at least through 20D, with 20E and F perhaps corresponding to the distalmost portion of Xh and residing in the chromocenter; all known genes except bb and possibly su(f) are located distal to 20E [Schalet and Lefevre, 1973, Chromo- soma 44: 181-202; Lefevre, 1976, The Genetics and Biology of Drosophila (Ashburner and Novitski, eds.). Academic Press, London, New York, San Francisco, Vol. 1a, pp. 31-66]. Several polytene landmarks given mnemonic designations by Bridges (1935, J. Hered. 26: 60-64) are as follows: the puff at 2B, the four brothers in 9A, the two sisters in 10A and B, the weak spot in 11A, the chains in 15B and D, the turnip in 16A- B, and the offset in 19E. # Y chromosome In mitotic figures, the Y chromosome appears as an entirely heterochromatic element; tritiated thymidine incorporation studies (Barigozzi, Dolfini, Fraccaro, Raimondi, and Tiepolo, 1966, Exp. Cell Res. 43: 231-34) show it to be late replicat- ing. The Y is a two-armed chromosome, the short arm, YS, being about two-thirds the length of the long arm, YL. At metaphase the Y is somewhat shorter than the X chromosome. Sister chromatids are not in evidence in prophase or metaphase Y chromosomes during mitosis, but in second meiotic prophase of spermatogenesis sister chromatids are well separated. In mitotic prophase preparations the Y chromosome can, by a com- bination of staining procedures, be subdivided into 25 dis- tinct segments (Gatti and Pimpinelli, 1983, Chromosoma 88: 349-73); they are designated h1 at the terminus of YL through h25 at the end of YS (see diagram on the preceding page). Gatti and Pimpinelli have placed the Y male-fertility genes as follows: kl-5 in h2-h3, kl-3 in h4-h9, kl-2 in h10, kl-1 in h13-h15, ks-1 in h21-h23, and ks-2 in h24-h25; in addition, Su(Ste) resides in h11 (Hardy, Lindsley, Livak, Lewis, Sivertsen, Joslyn, Edwards, and Bonaccorsi, 1984, Genetics 107: 591-610), and the ribosomal cistrons of the Y are in h20 (Gatti and Pimpinelli). Mapping of eight different satellite DNA sequences with respect to the 25 segments of the Y is described by Bonaccorsi and Lohe (1991, Genetics 129: 177-89). In aceto-orcein-stained prophase chromosomes Cooper (1959, Chromosoma 10: 535-88) reported that YS is sub- divided by the nucleolus constriction into a distal segment, SB, comprising two-thirds of YS, and a proximal segment, SA, comprising the other one-third; YL is divided into three seg- ments of approximately equal length by two constrictions, the more distal of which is the more constant landmark. From the centromere, the segments are designated LA, LB, and LC. Gatti and Pimpinelli have equated the constriction between LB and LC with their brightly fluorescing segments h8-h9 and in general find a correspondence between secondary constrictions seen in aceto-orcein- or Giemsa-stained chromosomes with brightly fluorescing blocks and not with nonfluorescing gaps in Hoechst-stained material. The Y chromosome does not undergo polytenization. In salivary-gland preparations, Prokofyeva-Belgovskaya (1937, Genetics 22: 94-103) observed a small collection of bands that she attributed to the Y. However, Nicoletti and Lindsley (1960, Genetics 45: 1705-22) found no evidence of bands attributable to the Y chromosome in a study of T(1;Y)'s; their observations were confirmed in the polytene analysis of a large collection to T(Y;A)'s (Lindsley, Sandler, Baker, Car- penter, Denell, Hall, Jacobs, Miklos, Davis, Gethmann, Hardy, Hessler, Miller, Nozawa, Parry, and Gould-Somero, 1972, Genet- ics 71: 157-84). Several complex structural elements in the primary spermato- cyte nucleus depend on the presence of the Y chromosome; two, designated tubuli and reticular material in electron micro- graphs (Meyer, Hess, and Beerman, 1961, Chromosoma 12: 676- 716), are associated with the male-fertility genes, kl-5 and kl-3, respectively (Hardy, Tokuyasu, and Lindsley, 1981, Chro- mosoma 83: 593-617). These and another associated with ks-1 can be recognized in the light microscope (Bonaccorsi, Pisano, Puoti, and Gatti, 1988, Genetics 120: 1015-34). Their func- tion is unknown. Addition of Y chromosomes to a normal chromosome complement suppresses variegated position effects, and removal of the Y from the male enhances variegation (1933, Gowan and Gay, Proc. Nat. Acad. Sci. USA 19: 122-26). Two or more Y's added to the normal complement cause variegation of otherwise self-colored eyes (Cooper, 1956, Genetics 41: 242-64). # Chromosome 2 In mitotic figures, chromosome 2 is less than twice the length of the X and slightly smaller than chromosome 3. It contains two euchromatic arms separated by the centromere and the pericentric heterochromatin. In acetic-orcein-stained preparations of mitotic prophase chromosomes, the pericentric heterochromatin comprises two segments separated by the cen- tric constriction; Gatti and Pimpinelli, utilizing Hoechst 33258 and N banding, recognize linear differentiation of the pericentric heterochromatin into twelve segments, designated from left to right h35 to h46; h42 is subdivided into 42A and 42B in some strains; the centromere is placed in h38. Dmitri (1991, Genetics 127: 553-64) has produced a cytogenetic map of the chromosome-2 heterochromatin; the l(2)40F loci, includ- ing lt, as well as cta and E(SD) are confined to segment h35 at the euchromatic-heterochromatic junction; the responder sequences, Rsp, comprise segment 39 in 2R, which varies in size according to the sensitivity of the chromosome to distor- tion by SD (Pimpinelli and Dimitri, 1989, Genetics 121: 765- 72); in addition, l(2)41Ab is located at the h39-h40 junction, l(2)41Aa and rl are in h40, and l(2)41Ad is in h43-h44; l(2)41Ae and l(2)41Ah are located in h46 at the heterochromatic-euchromatic junction. Dimitri has also located a number of heterochromatic breakpoints in chromosome 2. Schematic representation of the prophase differentiation of the pericentric heterochromatin of chromosome 2. Solid segments are brightly fluorescing or, in the case of N banding, darkly stain- ing; crosshatched regions moderately fluorescing; hatched regions dully fluorescing; and empty regions are non staining or non fluorescing. The upper diagram represents the fluorescence of Hoechst-33258 stained chromosomes; the second row depicts the N- banding pattern (provided by Gatti and Pimpinelli). In polytene preparations the left arm contains 804 bands according to Bridges and 869 as estimated by Sorsa, with an upper limit of 927; its 20 sections are numbered 21-40 from tip to centromere. Land mark regions named by Bridges (1935, J. Hered. 26: 60-64) for mnemonic purposes include the dog collar at 21C-D, the shoe buckle at 25A, the shield at 30A, the gooseneck at 31B-F; in addition, regions of the proximal half of 2L tend to fold back on themselves, frequently impart- ing a convoluted conformation to this part of the chromosome; these regions are termed the spiral loop in 31B-F, the turn back in 36, and the basal loop in region 37-39. The right arm of chromosome 2 is subdivided into 20 sections labeled 41 at the centromere to 60 at the tip; it contains 1136 bands on the Bridges maps and 1009 to 1152 according to Sorsa, depending on whether doublets are considered single or double; its land- marks are the onion base at 42A, the barrel in section 47 [Lefevre, 1976, The Genetics and Biology of Drosophila (Ash- burner and Novitski, eds.). Academic Press, London, New York, San Francisco, Vol. 1a, pp. 31-66], goggles at 50A and B (Lefevre), the miniskirt at 50C-D (Strathern), and the huckle- berry tip at 60E. # Chromosome 3 In mitotic figures, chromosome 3 is less than twice the length of the X and slightly larger than chromosome 2. It con- tains two euchromatic arms separated by the centromere and the pericentric heterochromatin. In acetic-orcein-stained preparations of mitotic prophase chromosomes, the pericentric heterochromatin comprises two segments separated by the cen- tric constriction. Gatti and Pimpinelli subdivide the third- chromosome heterochromatin into twelve sections, numbered from left to right h47 through h58; the centromere is placed in h53, but other than that no further characterization has been undertaken. Schematic representation of the prophase differentiation of the pericentric heterochromatin of chromosome 3. Solid segments are brightly fluorescing or, in the case of N banding, darkly stain- ing; crosshatched regions moderately fluorescing; hatched regions dully fluorescing; and empty regions are non staining or non fluorescing. The upper diagram represents the fluorescence of Hoechst-33258 stained chromosomes; the second row depicts the N- banding pattern (provided by Gatti and Pimpinelli). In polytene preparations, the left arm of chromosome 3, 3L, comprises twenty divisions numbered from tip to centromere 61 through 80 and containing 884 bands according to P. N. Bridges. Sorsa's estimates are considerably higher; consider- ing doublets to be single bands he recognizes 1032 bands and considering them as two bands he enumerates 1073. The mnemon- ics suggested by Bridges for designating cytological landmarks on 3L are the barrel at 61C-F, the ballet skirt at 68B-C, the Chinese lanterns, two large puffs, at 74-75, and the graded capsules in 79D-E. The twenty divisions of 3R, numbered 81F (81A-E do not appear on polytene maps) at the centromere through 100 at the tip contain 1178 bands according to P. N. Bridges. Sorsa estimates that there are 1147 bands if doublets are treated as single bands and 1233 if they are treated as two. Bridges' landmarks for 3R are the cucumber base in 81 to 83D, the road apple at 85F (Strathern), the duck's head at 89E-91A, and the goblet tip at 100. # Chromosome 4 Schematic representation of the prophase differentiation of the heterochromatin of chromosome 4. Solid segments are brightly fluorescing or, in the case of N banding, darkly staining; crosshatched regions moderately fluorescing; hatched regions dully fluorescing; and empty regions are non staining or non fluorescing. The upper diagram represents the fluorescence of Hoechst-33258 stained chromosomes; the second row depicts the N- banding pattern (provided by Gatti and Pimpinelli). In mitotic figures, chromosome 4 is a dot-like element that is separated into two segments (4L and 4R) of grossly unequal size by a sometimes-visible centric constriction. The bulk of chromosome 4 is heterochromatic and in prophase has been dif- ferentiated into three segments designated h59, h60, and h61 by Gatti and Pimpinelli. The presence of a short left arm is indicated by its involvement in chromosome rearrangements [e.g., T(1;4)wm11 (Panshin and Khvostova, 1938, Biol. Zh. 7: 359-80) and T(1;4)wmA (Griffen and Stone, 1940, Texas Univ. Publ. 4032: 201-07)]. In polytene configurations, chromosome 4 is a short element emerging from the chromocenter. It is divided into two sec- tions, 101 proximally and 102 distally; no reliable bands can be identified proximal to 101D, nor does any of the material in 4L polytenize (Lefevre). Hochman [1976, The Genetics and Biology of Drosophila (Ashburner and Novitski, eds.). Academic Press, London, New York, San Francisco, Vol. 1b, pp. 903-28], Lefevre, and Sorsa agree that the 137 bands on the detailed map of chromosome 4 produced by Slizinsky (1944, J. Hered. 35: 322-25), and included in the previous edition of this work, cannot be confirmed. They estimate 40-50 bands. Note that the centromere positions of the two subtelocentric ele- ments of the genome differ. It is on the right in the case of the X and on the left in chromosome 4. # 4-sim: chromosome 4 from Drosophila simulans (H. A. Orr) A single fourth chromosome from D. simulans was introduced into an otherwise D. melanogaster genome by Muller and Pon- tecorvo (1940, Nature 146: 199-200; 1940, Science 92: 418). Phenotypic effects of 4-sim were described by Muller and Pon- tecorvo (1942, Genetics 27: 157) and Pontecorvo (1943, Proc. Roy. Soc. Edinburgh B 61: 385-97; J. Genet. 45: 51-66). Although 4-sim/4 is apparently normal, 4-sim/4-sim homozygotes suffer decreased viability and show subtle peculiarities: flattened body, heavy trident, and reduced eyes. 4-sim/4-sim male genitalia also slightly resemble those of D. simulans (Muller and Pontecorvo, 1942; Coyne, 1983, Evolution 37: 1101-18). Some genes on 4-sim show unusual dominance relations: spaCat is not seen in 4-sim/spaCat heterozygotes. Conversely, 4-sim/ci shows occasional wing-vein interruptions; 4-sim/ciW shows more extreme cubitus-interruptus phenotype than 4/ciW (Uphoff, 1949, Genetics 34: 315-27). Appearance of ci is not due to the presence of a mutation at ci+ on the sin- gle 4-sim chromosome introduced into D. melanogaster as Stur- tevant (1946, Genetics 31: 259-68) suggested: D. melanogaster ci-D. simulans ci+ species hybrids also occasionally show ci [several D. simulans stocks tested (Uphoff, 1949; Orr, unpub- lished)]. Segregation of 4-sim and 4 is fairly regular (Muller and Pontecorvo, 1942). 4-sim/4-sim are completely sterile, whereas 4-sim/4 males are fully fertile. All female genotypes are fertile. Testes of sterile males appear normal. Meiosis occurs, but very few motile sperm are produced; about 75% of 4-sim/4-sim males pro- duce no motile sperm at all (Orr, 1992, Genet Res.). Pon- tecorvo (1943) claimed that sterility results from a breakdown in the last stages of spermiogenesis. The factor(s) causing sterility map to the proximal end of chromosome 4 within a large Minute deletion (Muller and Pontecorvo, 1942). Subse- quent deletion and translocation mapping shows that sterility maps to 101F, 102A2-B5, or both, representing less than 15% of the cytological length of the dot chromosome. Df(4)M101-3/4- sim and Df(4)M101-62f/4-sim are male sterile; Df(4)M101- 63a/4-sim and Df(4)G/4-sim are fertile (Orr, 1992). Male sterility is therefore apparently due to a single gene, dubbed hms (hybrid male sterile). hms complements all known genes in the Df(4)M101 region and shows no interaction with testis- specific |-tubulin. 4-sim male sterility depends only on zygotic genotype at hms. Comparisons of D. melanogaster and D. simulans polytene chromosomes were made by Kerkis (1936, Am. Nat. 70: 81-86), Horton (1939, Genetics 24: 234-43) and Patau (1935, Naturwissenschaften 23: 537-43). Chromosome 4 of D. simulans differs from that of D. melanogaster by a fairly long inver- sion, including at least 102B1-2 through 102E1-2 and probably 102E3, 4, and 5 (Horton, 1939). A darkly staining terminal ring is sometimes seen at the tip of the D. simulans chromo- some. The proximal third of chromosome 4 from D. simulans tends to be narrower than the distal two-thirds. Slizynski (1941, Proc. Roy. Soc. Edinburgh B 61: 95-106) claimed to identify the short left arm of 4-sim and compares it with that of D. melanogaster; however, recent workers dispute the claim that 4L can be seen in polytene preparations. Horton (1939) never observed synapsis of chromosome 4 in salivary-gland cells of D. melanogaster-D. simulans species hybrids. Although 4-sim and 4 in the "4-sim" stock of D. melanogaster also do not usually pair, Slizynski (1941) found one nucleus in which the inverted segments paired. In triplo-4 larvae, the D. melanogaster 4's pair and the 4-sim chromosome remains unpaired. As expected, the 4-sim chromosome from the 4-sim stock pairs normally with wild-type D. simulans fourth chromo- somes in species hybrids (Orr, 1992). In both species hybrids and on a D. melanogaster genetic background, the tip of the D. melanogaster 4R tends to stick into the chromocenter; the tip of the D. simulans 4, however, is always free of the chromo- center (Horton, 1939; Slizynski, 1941).