Chromosomal localization of a highly repeatedEcoRI DNA fragment inMegoura viciae (Homoptera,Aphididae) by nick translation and fluorescencein situ hybridization

To investigate the genome of the aphidMegoura viciae at molecular level, we have studied total DNA by agarose gel electrophoresis after cleavage with different restriction endonucleases.EcoRI digestion produced a highly repeated DNA fragment, about 600 bp long. The contribution of thisEcoRI element to the total genome ofM. viciae was estimated at about 6% by means of densitometric scanning of agarose gel photographs. The chromosomal localization of this fragment, investigated by fluorescentin situ hybridization (FISH), constantly showed one large and two narrower fluorescent bands located on the X chromosome, all corresponding to C-positive heterochromatic areas. These results are in full accordance with the data obtained byin situ nick translation experiments carried out afterEcoRI digestion, and clearly demonstrate that a substantial amount ofM. viciae heterochromatin consists ofEcoRI fragments which are mainly located on the X chromosome. Using theEcoRI restriction fragment as a molecular probe may prove to be a practical tool for the investigation of taxonomic and evolutionary relationships in this group of insects.accepted for publication by J. S. (Pat) Heslop-Harrison     

Application of synthetic DNA probes of human alpha satellite consensus monomer for detection of centromereinvolved chromosome abnormalities

We have synthesized the alphoid monomer of 171 bp based on the consensus sequence of human alpha satellite DNA and constructed a clone of dimeric or tetrameric sequence unit. Southern blot analysis using the clone as a probe showed restriction site periodicities in human DNA digested byEcoRI orBamHI. The synthetic consensus unit could detect the alpha repeated centromeric regions of all human chromosomes by fluorescencein situ hybridization. Using the cells having a dicentric X chromosome, we showed that the two centromeric regions were stained with fluorescent alpha satellite DNA probes. Thus the probe would be useful to detect chromosomal abnormalities such as dicentrics.     

Chromosomal location and evolution of a satellite DNA family in seven sturgeon species

The Hind III satellite DNA family, isolated from the Acipenser naccarii genome, was used as a probe for fluorescent in-situ hybridization (FISH) on the karyotype of seven sturgeon species, six belonging to the genus Acipenser and one to Huso. All species except one (A. sturio) exhibit from 8 to 80 chromosome hybridization signals, mainly localized at the pericentromeric regions. Eight chromosomes with weak hybridization signals are present in H. huso and A. ruthenus, which are characterized by a karyotype with about 120 chromosomes. The species with 240–260 chromosomes, A. transmontanus, A naccarii, A. gueldenstaedtii, and A. baerii, show from 50 to 80 signals, prevalently localized around centromeres. Moreover, A. transmontanus and A. gueldenstaedtii show from 4 to 8 chromosomes with a double signal. The phylogenetic and evolutionary relationships among sturgeon species are discussed on the basis of number and morphology of signal-bearing chromosomes and on the localization of signals.     

Characterization of DNA sequences constituting the terminal heterochromatin of the chicken Z chromosome

Two clones, pCZTH5-8 and pCZTH12-8, were isolated from a female chicken genomic library by screening with sequences obtained from genomic libraries which had been constructed from a terminal region of a single Z chromosome of chicken utilizing laser microbeam irradiation and PCR amplification. Fluorescencein situ hybridization to the mitotic Z chromosome and the lampbrush ZW bivalent of chicken demonstrated that both the cloned sequences are located in the heterochromatic region of the Z chromosome at the end opposite to the pairing region with the W chromosome. The sequences pCZTH5-8 and pCZTH12-8 are distributed widely on both the telomeric bow-like loops (TBL) and the region I (short loops region) of the Z lampbrush chromosome. These clones, pCZTH12-8 particularly notably, hybridized also to the TBLs of lampbrush bivalents 1–4 of chicken. Both sequence are transcribed in the lampbrush stage oocytes on the Z chromosome and on other macrobivalents. The subfragment of pCZTH5-8 which hybridizes to the TBLs and the insert of pCZTH12-8 contain regions that are closely similar in sequence. The pCZTH5-8 sequence has no internal repeats and may be part of the 24-kb macrosatellite repeating unit that is evident afterNhel digestion of the genomic DNA. A cloned 24-kb unit, pFN-1, does not show significant DNA curvature, but cytosines of its CpG dinucleotides may be highly methylatedin vivo. This contrasts with the repeat sequences of the W heterochromatin which not only have highly methylated CpG but are also strongly curved. The 24-kb unit is repeated about 830 times in the diploid genome of a female chicken, suggesting that nearly the entire terminal heterochromatin on the Z chromosome consists of this macrosatellite family. Sequences of the greater part of the pCZTH5-8 are restricted to the genusGallus but the sequence of one subregion which hybridizes to TBLs is present in the genomes of the order Galliformes.accepted for publication by M. Schmid     

Chromosomal location of endogenous geminivirus-related DNA sequences inNicotiana tabacum L.

TheN. tabacum (tobacco) nuclear genome carries approximately 25 multiple direct repeats of a geminivirus-related DNA (GRD) sequence that probably arose by illegitimate recombination, following geminivrus infection, duringNicotiana evolution. Each GRD repeat carries sequences similar to the geminiviralAL1 gene of the tomato golden mosaic virus (TGMV), encoding a protein required for viral DNA replication, plus thecis-essential replication origin. Using a cloned 14-kb GRD repeat sequence as a probe for fluorescencein situ hybridization (FISH), we identified a unique tobacco chromosome carrying GRD. Translocations between chromosomes of the tobacco S and T genomes were used as physical markers by sequentially hybridizing chromosomes with labelled GRD and total genomic DNA fromN. sylvestris (equivalent to the S genome). The 25S, 18S and 5.8S ribosomal gene clusters were detected in double-labelling experiments for use as additional markers to identify the chromosomal location of GRD. GRD occupies one site on a homologous pair of small submetacentrics from the T genome characterized by a lack of either translocated segments from the S genome or ribosomal genes. GRD provides an additional marker for the small chromosomes of the T genome and a useful phylogenetic tool.     

Barley telomeres are associated with two different types of satellite DNA sequences

The genomic organization of two different types of satellite DNA sequences was analysed by means of fluorescencein situ hybridization (FISH) and pulsedfield gel electrophoresis (PFGE) in barley. Satellite HvT01 was detected at all chromosome ends except the long arms of chromosomes 2 and 7. The unrelated satellite pAS1 was found at all chromosome ends except the long arm of chromosome 7 and at two interstitial sites, both located on the long arm of chromosome 4 on the standard karyotype. Southern andin situ hybridizations further indicate that pAS1 also occurs interspersed in the barley genome. For most chromosome ends, the linear order of HvT01 and pAS1 could not be determined byin situ hybridization except at the short arms of chromosomes 2 and 6, where HvT01 is more distal than pAS1. This is confirmed by PFGE analysis, HvT01 being frequently associated with the telomeric repeat but not pAS1. Furthermore, we found that HvT01 occurred in clusters up to 1000 kb in size, whereas the pAS1 cluster had a maximum size of 500 kb. Sequence comparison revealed that both satellites are completely unrelated and differ considerably in their G + C contents.     

Direction of DNA sequences within chromatids determined using strand-specific FISH

The 5 to 3 direction of DNA strands within chromatids of metaphase chromosomes can be determined by using simultaneous hybridization of a single strand of the telomere probe and a single strand of a repetitive sequence to slides pretreated for strand-specific hybridization. The telomere probe identifies the direction of the DNA helical strand remaining in each chromatid of the metaphase chromosomes. The direction of the repetitive sequence is then determined from the direction of the strand to which it hybridizes. This method was used to determine the 5 to 3 direction of three repetitive DNA sequences, each for a different human repeat family.     

Physical relationship between satellite I and II DNA in centromeric regions of sheep chromosomes

Fluorescence in situ hybridization (FISH) with probes representing sheep satellite I and satellite II DNAs shows a different distribution of the two repetitive DNA families in the centromeric region of most chromosomes. The single signal per chromosome produced by the satellite I probe suggests close proximity of this DNA family to the primary constriction. Satellite II produces two separate signals on the sister chromatids, and large blocks of satellite II DNA constitute most of the short arm of all acrocentric chromosomes. We have isolated and sequenced a phage clone containing a junction between discrete blocks of satellite I and satellite II sequences. The junction is characterized by an abrupt juxtaposition of arrays of the two satellites. The possibility that the peculiar structural features of this junction could have a functional significance is discussed.This revised version was published online in November 2005 with corrections to the Cover Date.     

Tenebrio obscurus satellite DNA is resistant to cleavage by restriction endonucleasesin situ

Satellite DNA from the mealworm beetle,Tenebrio obscurus, is composed of 344 bp long monomers of high AT content (68%), and represents 15% of the total DNA.In situ hybridization reveals the positions of the satellite on the pericentromeric heterochromatin of allT. obscurus chromosomes. To compare restriction enzyme (RE) effects with those on naked DNA, fixed chromosomes were digested with REs having recognition sites in most of the satellite monomers, and also with enzymes having target sites present only partially, or very rarely in the satellite units. All enzymes produce similar C-like banding patterns showing heterochromatin resistance to digestion regardless of the enzyme used.In situ nick translation suggests the inability of REs to cleave satellite DNA rather than the inefficient extraction of DNA fragments. DNA in heterochromatin was only extensively digested when the chromosomes were preincubated with proteinase K, indicating that accessibility of REs to DNA is increased by the removal of chromosomal proteins. This is in contrast to recently obtained results inTenebrio molitor, where cleavage of satellite DNA is equally efficient in both fixed chromosomes and in naked DNA. The satellite DNAs of the two congeneric species differ in their AT content, and their primary and higher order structure, which could influence both heterochromatin structure and the accessibility of REs to satellite DNA.     

Multi-chromosomal location of ribosomal RNA genes and heterochromatin association in brown trout

The ribosomal rRNA genes have been mapped by fluorescentin situ hybridization (FISH) to brown trout chromosomes. One major NOR chromosome pair and 8 novel minor NOR chromosome pairs have been found. Both major and minor NORs were closely related to polymorphic heterochromatin, as revealed by FISH and C-banding. These results are discussed with respect to NOR expression, the relationship between rDNA and heterochromatin, and evolutionary aspects.     

Distribution and linkage of repetitive clusters from the heterochromatic region of human chromosome 22

The pericentric regions of eukaryotic chromosomes consist of several types of repetitive DNA families. In human chromosome 22, the organization of such families was studied in more detail. In addition to the known families of alpha and beta repeats, an additional repeat with a 48-bp motif was previously assigned to 22pter-q11. Here, we report in more detail the distribution of these repeat families, applying pulsed-field gel electrophoresis, fluorescencein situ hybridization and physical linkage on cosmid recombinants. At least two clusters of 48-bp repeats are localized on chromosome 22, one on the distal p-arm and one in the region 22cen-q11. Cosmids from a chromosome 22 library, containing both 48-bp and -repeats, link both arrays on 22p and define their maximum distances to less than 44 kb. Loss of 48-bp repeat sequences in a Di-George cell line carrying a deletion in 22q11 suggests the presence of a second cluster in 22q11, a distribution supported by (fluorescenein situ hybridization)-FISH signal analysis. As additional members of the 48-bp repeat family can be found on all acrocentric chromosomes it remains to be determined whether the distribution seen on chromosome 22 is also common in other human acrocentric chromosomes.accepted for publication by M. Schmid     

Population variation in the A chromosome distribution of satellite DNA and ribosomal DNA in the grasshopper Eyprepocnemis plorans

The double FISH analysis of two repetitive DNAs (a satellite DNA and ribosomal DNA) in 12 natural populations of the grasshopper Eyprepocnemis plorans collected at the south (Granada and Málaga provinces) and south-east (Albacete and Murcia provinces) of the Iberian Peninsula has shown their widespread presence throughout the whole genome as well as extensive variation among populations. Both DNAs are found in most A chromosomes. Regularly, both DNAs occurred in the S₁₁ and X chromosomes, rDNA in the S₁₀ and satDNA in the L₂ and M₃. No correlation was found between the number of satDNA and rDNA clusters in the A genomes of the 12 populations analysed, and both figures were independent of the presence of B chromosomes. The genomic distribution of both DNAs showed no association with the geographical localization of the populations analysed. Finally, we provide evidence that the supernumerary chromosome segment proximally located on the S₁₁ chromosome is, in most cases, the result of satDNA amplification but, in some cases, it might also derive from amplification of both satDNA and rDNA.     

Organization and chromosomal location of repetitive DNA sequences in three species of squamate reptiles

Repetitive DNA sequences were isolated from the genomes of species representing three major clades of squamate reptiles. A repetitive sequence (Cn4C7) was isolated from the New Mexican whiptail lizard,Cnemidophorus neomexicanus. This sequence is distributed throughout the chromosomes, but is more concentrated in the telomeric region. Cn4C7 also hybridizes to the chromosomes of otherCnemidophorus. Some evidence was found for concerted evolution of this repeat in hybrid unisexual lineages. In the lesser earless lizard,Holbrookia maculata, the predominant repeat in the genome is represented by a sequence (Hm1E11) which is restricted to the area flanking the centromere in all species ofHolbrookia. Two families of repetitive sequences (one dispersed, and the other telomeric) were isolated from the western diamondback rattlesnake,Crotalus atrox. The type and distribution of repetitive sequences in squamates is often taxon-specific, and may be useful as characters for elucidating taxonomic relationships.     

Identification of highly conserved loci by genome painting

Fluorescencein situ hybridization was used to identify patterns of DNA similarity among the genomes of several rodent taxa. Total genomic or Cot-1 DNAs were used as hybridization probes against metaphase preparations across different taxonomic levels, including three species ofMicrotus (suborder Sciurognathi),Mus musculus (suborder Sciurognathi) andCtenomys steinbachi (suborder Hystricognathi). The hybridization patterns ofMus orPeromyscus (sciurognath) DNA toMus metaphases, which were consistent with what is known of the satellite sequences in these species, demonstrated the efficacy of this approach for molecular cytogenetics and evolutionary biology. Additional hybridizations to chromosomes ofCtenomys orMicrotus identified loci consisting of highly conserved DNA sequences. This approach has proved useful in investigating genome homologies across divergent rodent lineages. Chromosome microdissection can be used to characterize these regions further.     

Cytogenetic and molecular analysis of the satellite DNA of the genusCtenomys (Rodentia Octodontidae) from Uruguay

The genus of subterranean rodentsCtenomys presents the widest range of variability in diploid number among mammals (from2n=10 to2n=70). In Uruguay, this variability is observed in karyotypes with2n=44, 50 or 58 and two geographically isolated populations with 70 chromosomes but different karyotypic structure. The last three populations were analyzed in the present study. They present a satellite DNA, which was isolated from genomic DNA afterAlul digestion.In situ hybridization showed that this satellite DNA is located in the centromeric region of a few chromosomes, coincident with Hoechst 33258 staining and C-banding patterns. A similar satellite DNA was detected in Argentinian species of this genus. We established that, in spite of differences in number of positive heterochromatic blocks per karyotype, the C value is the same in the three populations studied. The nature and possible evolutionary path of this repeated DNA is discussed.Accepted for publication by M. Schmid     

Comparative genomic in situ hybridization (cGISH) analysis on plant chromosomes revealed by labelled Arabidopsis DNA

A new approach for comparative cytogenetic banding analysis of plant chromosomes has been established. The comparative GISH (cGISH) technique is universally applicable to various complex genomes of Monocotyledonae (Triticumaestivum, Agropyronelongatum, Secalecereale, Hordeumvulgare, Alliumcepa, Muscariarmenaticum and Liliumlongiflorum) and Dicotyledonae (Viciafaba, Betavulgaris, Arabidopsisthaliana). Labelled total genomic DNA of A. thaliana generates signals at conserved chromosome regions. The nucleolus organizing regions (NORs) containing the majority of tandemly repeated rDNA sequences, N-band regions containing satellite DNA, conserved homologous sequences at telomeres and additional chromosome-characteristic markers were detected in heterologous FISH experiments. Multicolour FISH analysis with repetitive DNA probes simultaneously revealed the chromosome assignment of 56 cGISH signals in rye and 61 cGISH signals in barley. Further advantages of this technique are: (1) the fast and straightforward preparation of the probe; (2) the generation of signals with high intensity and reproducibility even without signal amplification; and (3) no requirement of species-specific sequences suitable for molecular karyotype analysis. Hybridization can be performed without competitive DNA. Signal detection without significant background is possible under low stringency conditions. The universal application of this fast and simple one-step fluorescence banding technique for plant cytogenetic and plant genome evolution is discussed.     

Analysis using dual-colour fluorescencein situ hybridization of meiotic chromosome segregation in male mice heterozygous for a reciprocal translocation

Meiotic chromosome behaviour was investigated in male mice heterozygous for the translocation T(7;16)67H. At metaphase I, chain-of-four quadrivalents were present in approximately 80% of the spermatocytes; the bulk of remaining cells contained a ring quadrivalent, with only a few having either a trivalent plus univalent configuration or two bivalents. A low rate of non-disjunction, approximately 5%, was found through analysis of C-banded metaphase II spermatocytes. Using fluorescencein situ hybridization with differentially labelled whole chromosome paints, a wide array of segregation products were observed at metaphase II, depending on whether they arose from alternate, adjacent I, adjacent II orientation at metaphase I or were uninformative for alternative/adjacent I because of the presence of a chiasma in an interstitial pairing segment. Some 62% of the cells fell into this latter category, with only small proportions clearly arising through alternate (1.8%) or adjacent I (0.7%) orientations. Approximately 30% of the cells contained the products of adjacent II orientation. Consideration of the data suggested that most of these cells arose from metaphase I cells that contained a chain quadrivalent. Ring quadrivalents appeared predominantly to orientate in an alternate/adjacent I manner.for publication by J. S. (Pat) Heslop-Harrison